[ Started: 2025-04-23 22:38:28 CEST ] [ OmnipathR v3.15.99 for BioC-3.21 from https://github.com/saezlab/OmnipathR@devel (7e5f894 2025-04-08 17:45:46) ] * using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck’ * using R Under development (unstable) (2025-02-12 r87715) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.15.99’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘OmnipathR’ can be installed ... OK * checking installed package size ... INFO installed size is 6.8Mb sub-directories of 1Mb or more: doc 5.4Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... NOTE [2025-04-23 22:38:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:38:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:38:56] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:38:56] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-23 20:37:22 UTC; omnipath [2025-04-23 22:38:56] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-04-23 22:38:56] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-23 20:38:30 UTC; unix [2025-04-23 22:38:56] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.99 [2025-04-23 22:38:56] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-04-23 22:38:56] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-04-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-04-23 22:38:56] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-04-23 22:38:56] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.99(2025-04-23); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-04-23 22:38:56] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-04-23 22:38:56] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-23 22:38:56] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:38:57] [TRACE] [OmnipathR] Contains 1 files. [2025-04-23 22:38:57] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-23 22:38:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:38:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:38:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:38:57] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-04-23 22:38:57] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-23 22:38:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:38:57] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-23 22:38:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:38:57] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-23 22:38:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:38:57] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-23 22:38:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:38:57] [TRACE] [OmnipathR] Cache locked: FALSE It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE [2025-04-23 22:39:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:39:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:39:06] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:39:06] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-23 20:37:22 UTC; omnipath [2025-04-23 22:39:06] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-04-23 22:39:06] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-23 20:38:30 UTC; unix [2025-04-23 22:39:06] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.99 [2025-04-23 22:39:06] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-04-23 22:39:07] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-04-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-04-23 22:39:07] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-04-23 22:39:07] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.99(2025-04-23); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-04-23 22:39:07] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-04-23 22:39:07] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-23 22:39:07] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:39:07] [TRACE] [OmnipathR] Contains 1 files. [2025-04-23 22:39:07] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-23 22:39:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:39:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:39:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:39:07] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-04-23 22:39:07] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-23 22:39:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:39:07] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-23 22:39:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:39:07] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-23 22:39:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:39:07] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-23 22:39:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:39:07] [TRACE] [OmnipathR] Cache locked: FALSE * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘bioc_workshop.Rmd’ using rmarkdown Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' [2025-04-23 22:47:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:18] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:47:18] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-23 20:37:22 UTC; omnipath [2025-04-23 22:47:18] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-04-23 22:47:18] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-23 20:38:30 UTC; unix [2025-04-23 22:47:18] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.99 [2025-04-23 22:47:18] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-04-23 22:47:18] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-04-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-04-23 22:47:18] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-04-23 22:47:18] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.25(2024-08-28); BiocStyle 2.36.0(2025-04-15); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.43(2025-04-15); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.99(2025-04-23); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-04-23 22:47:18] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-04-23 22:47:18] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-23 22:47:18] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:47:18] [TRACE] [OmnipathR] Contains 14 files. [2025-04-23 22:47:18] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-23 22:47:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:47:18] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-04-23 22:47:18] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-23 22:47:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:18] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-23 22:47:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:18] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-23 22:47:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:18] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-23 22:47:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:18] [TRACE] [OmnipathR] Cache locked: FALSE [2025-04-23 22:47:18] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:47:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions] [2025-04-23 22:47:18] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-04-23 22:47:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:18] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-04-23 22:47:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:18] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-04-23 22:47:18] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-04-23 22:47:18] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-04-23 22:47:18] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-04-23 22:47:18] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-04-23 22:47:18] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-04-23 22:47:18] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-23 22:47:18] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:47:18] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:47:18] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-23 22:47:18] [TRACE] [OmnipathR] Sending HTTP request. [2025-04-23 22:47:19] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-04-23 22:47:19] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:47:19] [TRACE] [OmnipathR] Downloaded 30.9 Kb in 0.215272s from www.ensembl.org (143.7 Kb/s); Redirect: 0s, DNS look up: 0.001369s, Connection: 0.019405s, Pretransfer: 0.072695s, First byte at: 0.198631s [2025-04-23 22:47:19] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Wed, 23 Apr 2025 20:47:19 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31676; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:47:18 GMT; Set-cookie: ENSEMBL_HINX_SESSION=3797ea4d3718a8b10b38432668586bd7097efa914b272603d3603de9; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:47:18 GMT; Set-cookie: ENSEMBL_HINX_SESSION=3797ea4d3718a8b10b38432668586bd7097efa914b272603d3603de9; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-35.ebi.ac.uk [2025-04-23 22:47:19] [TRACE] [OmnipathR] Response headers: [Date=Wed, 23 Apr 2025 20:47:19 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31676,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:47:18 GMT,Set-cookie=ENSEMBL_HINX_SESSION=3797ea4d3718a8b10b38432668586bd7097efa914b272603d3603de9; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:47:18 GMT,Set-cookie=ENSEMBL_HINX_SESSION=3797ea4d3718a8b10b38432668586bd7097efa914b272603d3603de9; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-35.ebi.ac.uk] [2025-04-23 22:47:19] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-04-23 22:47:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:19] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-04-23 22:47:19] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-04-23 22:47:19] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-04-23 22:47:19] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:47:19] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-04-23 22:47:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:19] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-04-23 22:47:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-04-23 22:47:19] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:47:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:47:19] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:47:19] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:47:19] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:47:19] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-04-23 22:47:19] [TRACE] [OmnipathR] Downloaded 1.3 Kb in 0.06902s from omabrowser.org (18.3 Kb/s); Redirect: 0s, DNS look up: 0.010247s, Connection: 0.021338s, Pretransfer: 0.054883s, First byte at: 0.068964s [2025-04-23 22:47:19] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 23 Apr 2025 20:47:19 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip [2025-04-23 22:47:19] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-04-23 22:47:19] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-04-23 22:47:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:19] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-04-23 22:47:19] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-04-23 22:47:19] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:47:19] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:47:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-04-23 22:47:19] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-04-23 22:47:19] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-04-23 22:47:19] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-04-23 22:47:19] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-04-23 22:47:19] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-04-23 22:47:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-04-23 22:47:19] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:47:19] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:47:19] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:47:19] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:47:19] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.090356s from omnipathdb.org (173.4 Kb/s); Redirect: 0s, DNS look up: 0.000952s, Connection: 0.019386s, Pretransfer: 0.052711s, First byte at: 0.089979s [2025-04-23 22:47:19] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:47:19 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:47:19 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:47:20] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-04-23 22:47:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:20] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`. [2025-04-23 22:47:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2025-04-23 22:47:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2025-04-23 22:47:20] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1] [2025-04-23 22:47:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:20] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`. [2025-04-23 22:47:24] [SUCCESS] [OmnipathR] Downloaded 128218 interactions. [2025-04-23 22:47:27] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:47:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2025-04-23 22:47:27] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:47:27] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:47:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:47:27] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:47:27] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:47:27] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:47:27] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:47:27] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:47:27] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:47:27] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:47:27] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:47:27] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:47:27] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:47:27] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.094569s from omnipathdb.org (165.7 Kb/s); Redirect: 0s, DNS look up: 0.000974s, Connection: 0.021152s, Pretransfer: 0.05354s, First byte at: 0.094199s [2025-04-23 22:47:27] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:47:27 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:47:27 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:47:27] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:47:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:27] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2025-04-23 22:47:27] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2025-04-23 22:47:28] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2025-04-23 22:47:28] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2025-04-23 22:47:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:28] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2025-04-23 22:47:29] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships. [2025-04-23 22:47:29] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:47:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions] [2025-04-23 22:47:29] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:47:29] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:47:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:47:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:47:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:47:29] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:47:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:47:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:47:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:47:29] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:47:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:47:29] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:47:29] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:47:29] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.096297s from omnipathdb.org (162.7 Kb/s); Redirect: 0s, DNS look up: 0.000993s, Connection: 0.021489s, Pretransfer: 0.055167s, First byte at: 0.095925s [2025-04-23 22:47:29] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:47:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:47:29 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:47:30] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:47:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:30] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2025-04-23 22:47:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-04-23 22:47:30] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-04-23 22:47:30] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2025-04-23 22:47:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:30] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2025-04-23 22:47:33] [SUCCESS] [OmnipathR] Downloaded 81529 interactions. [2025-04-23 22:47:33] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:47:33] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=complexes] [2025-04-23 22:47:33] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:47:33] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:47:33] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic` [2025-04-23 22:47:33] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic` [2025-04-23 22:47:33] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic` [2025-04-23 22:47:33] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic` [2025-04-23 22:47:33] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic` [2025-04-23 22:47:33] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic` [2025-04-23 22:47:33] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic` [2025-04-23 22:47:33] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:47:33] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:47:33] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:47:33] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:47:33] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.115961s from omnipathdb.org (135.1 Kb/s); Redirect: 0s, DNS look up: 0.001006s, Connection: 0.022248s, Pretransfer: 0.07239s, First byte at: 0.115264s [2025-04-23 22:47:33] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:47:33 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:47:33 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:47:33] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic` [2025-04-23 22:47:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:33] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`. [2025-04-23 22:47:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2025-04-23 22:47:34] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2025-04-23 22:47:34] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1] [2025-04-23 22:47:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:34] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`. [2025-04-23 22:47:34] [SUCCESS] [OmnipathR] Downloaded 35459 protein complexes. [2025-04-23 22:47:34] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:47:34] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2025-04-23 22:47:34] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:47:34] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:47:34] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-23 22:47:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:34] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-23 22:47:34] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-23 22:47:34] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-23 22:47:34] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-23 22:47:34] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-23 22:47:34] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-23 22:47:34] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-23 22:47:34] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:47:34] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:47:34] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:47:34] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:47:34] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.103822s from omnipathdb.org (150.9 Kb/s); Redirect: 0s, DNS look up: 0.000792s, Connection: 0.023831s, Pretransfer: 0.057386s, First byte at: 0.103465s [2025-04-23 22:47:34] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:47:34 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:47:34 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:47:34] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-23 22:47:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:34] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2025-04-23 22:47:34] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-04-23 22:47:35] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-04-23 22:47:35] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2025-04-23 22:47:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:35] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2025-04-23 22:47:35] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records. [2025-04-23 22:47:35] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:47:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations] [2025-04-23 22:47:35] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:47:35] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:47:35] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-23 22:47:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:35] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-04-23 22:47:35] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-04-23 22:47:35] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-04-23 22:47:35] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-04-23 22:47:35] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-04-23 22:47:35] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-04-23 22:47:35] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-04-23 22:47:35] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:47:35] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:47:35] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:47:35] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:47:35] [TRACE] [OmnipathR] Downloaded 60 bytes in 0.081103s from omnipathdb.org (739 bytes/s); Redirect: 0s, DNS look up: 0.000872s, Connection: 0.019404s, Pretransfer: 0.06237s, First byte at: 0.081086s [2025-04-23 22:47:35] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:47:35 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 60; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:47:35 GMT; Cache-Control: public; X-Frame-Options: DENY [2025-04-23 22:47:35] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-04-23 22:47:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:35] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`. [2025-04-23 22:47:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2025-04-23 22:47:35] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2025-04-23 22:47:35] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1] [2025-04-23 22:47:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:35] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`. [2025-04-23 22:47:35] [SUCCESS] [OmnipathR] Downloaded 0 annotation records. [2025-04-23 22:47:35] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:47:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations] [2025-04-23 22:47:35] [FATAL] [OmnipathR] Downloading the entire annotations database is not allowed by default because of its huge size (>1GB). If you really want to do that, you find static files at https://archive.omnipathdb.org/. However we recommend to query a set of proteins or a few resources, depending on your interest. [2025-04-23 22:47:35] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:47:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2025-04-23 22:47:36] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:47:36] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:47:36] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-23 22:47:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:36] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-23 22:47:36] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-04-23 22:47:36] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-23 22:47:36] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache. [2025-04-23 22:47:36] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:47:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations] [2025-04-23 22:47:36] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:47:36] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:47:36] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-23 22:47:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:36] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-04-23 22:47:36] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-04-23 22:47:36] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-04-23 22:47:36] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-04-23 22:47:36] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-04-23 22:47:36] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-04-23 22:47:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-04-23 22:47:36] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:47:36] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:47:36] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:47:36] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:47:36] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.106776s from omnipathdb.org (146.7 Kb/s); Redirect: 0s, DNS look up: 0.000803s, Connection: 0.024826s, Pretransfer: 0.057436s, First byte at: 0.106316s [2025-04-23 22:47:36] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:47:36 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:47:36 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:47:36] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-04-23 22:47:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:36] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`. [2025-04-23 22:47:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2025-04-23 22:47:37] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2025-04-23 22:47:37] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1] [2025-04-23 22:47:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:37] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`. [2025-04-23 22:47:37] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records. [2025-04-23 22:47:37] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:47:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2025-04-23 22:47:37] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:47:37] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:47:37] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-23 22:47:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:37] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-23 22:47:37] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-23 22:47:37] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-23 22:47:37] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-23 22:47:37] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-23 22:47:37] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-23 22:47:37] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-23 22:47:37] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:47:37] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:47:37] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:47:37] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:47:37] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.082308s from omnipathdb.org (190.3 Kb/s); Redirect: 0s, DNS look up: 0.000996s, Connection: 0.017085s, Pretransfer: 0.049651s, First byte at: 0.082006s [2025-04-23 22:47:37] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:47:37 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:47:37 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:47:37] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-23 22:47:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:37] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2025-04-23 22:47:37] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2025-04-23 22:47:37] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2025-04-23 22:47:37] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2025-04-23 22:47:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:37] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2025-04-23 22:47:37] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records. [2025-04-23 22:47:37] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:47:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2025-04-23 22:47:37] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:47:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2025-04-23 22:47:37] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:47:37] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:47:37] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:47:37] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-04-23 22:47:37] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:47:40] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache. [2025-04-23 22:47:40] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:47:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations] [2025-04-23 22:47:40] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:47:40] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:47:40] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-23 22:47:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:40] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-23 22:47:40] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2025-04-23 22:47:40] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-23 22:47:40] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache. [2025-04-23 22:47:40] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:47:40] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:47:40] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic` [2025-04-23 22:47:40] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic` [2025-04-23 22:47:40] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic` [2025-04-23 22:47:40] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic` [2025-04-23 22:47:40] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic` [2025-04-23 22:47:40] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic` [2025-04-23 22:47:40] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic` [2025-04-23 22:47:40] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:47:40] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:47:40] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:47:40] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:47:40] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.120369s from omnipathdb.org (130.2 Kb/s); Redirect: 0s, DNS look up: 0.000947s, Connection: 0.021412s, Pretransfer: 0.078213s, First byte at: 0.119137s [2025-04-23 22:47:40] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:47:40 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:47:40 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:47:42] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic` [2025-04-23 22:47:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:42] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`. [2025-04-23 22:47:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2025-04-23 22:47:43] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2025-04-23 22:47:43] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1] [2025-04-23 22:47:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:43] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`. [2025-04-23 22:47:43] [SUCCESS] [OmnipathR] Downloaded 332447 intercellular communication role records. [2025-04-23 22:47:44] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2025-04-23 22:47:44] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2025-04-23 22:47:44] [TRACE] [OmnipathR] Bypassing call: `intercell_network()`. [2025-04-23 22:47:44] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2025-04-23 22:47:44] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `. [2025-04-23 22:47:44] [TRACE] [OmnipathR] Bypassing call: ` loc_consensus_percentile = 50, simplify = TRUE)`. [2025-04-23 22:47:44] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2025-04-23 22:47:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-23 22:47:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:44] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:47:44] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:47:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2025-04-23 22:47:44] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2025-04-23 22:47:44] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2025-04-23 22:47:44] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2025-04-23 22:47:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2025-04-23 22:47:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2025-04-23 22:47:44] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2025-04-23 22:47:44] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:47:44] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:47:44] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:47:44] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:47:44] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.079738s from omnipathdb.org (109.3 Kb/s); Redirect: 0s, DNS look up: 0.001057s, Connection: 0.022251s, Pretransfer: 0.057354s, First byte at: 0.079573s [2025-04-23 22:47:44] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:47:44 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:47:44 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:47:44] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2025-04-23 22:47:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:44] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2025-04-23 22:47:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2025-04-23 22:47:44] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2025-04-23 22:47:44] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2025-04-23 22:47:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:45] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2025-04-23 22:47:45] [SUCCESS] [OmnipathR] Downloaded 1098 records. [2025-04-23 22:47:45] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`. [2025-04-23 22:47:45] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2025-04-23 22:47:45] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2025-04-23 22:47:45] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-04-23 22:47:45] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2025-04-23 22:47:45] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-04-23 22:47:45] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2025-04-23 22:47:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:47:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:47:45] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2025-04-23 22:47:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2025-04-23 22:47:45] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-04-23 22:47:45] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-04-23 22:47:45] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:47:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:47:45] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:47:45] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-04-23 22:47:45] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.744372s from rest.uniprot.org (57 bytes/s); Redirect: 0s, DNS look up: 0.001043s, Connection: 0.019949s, Pretransfer: 0.071816s, First byte at: 0.744299s [2025-04-23 22:47:45] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 23-April-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 23 Apr 2025 20:47:45 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_02; access-control-allow-origin: *; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 23-April-2025 [2025-04-23 22:48:08] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2025-04-23 22:48:08] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2025-04-23 22:48:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:08] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2025-04-23 22:48:08] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20421 records [2025-04-23 22:48:09] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data. [2025-04-23 22:48:09] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space. [2025-04-23 22:48:09] [TRACE] [OmnipathR] Translated 0 complexes to 0. [2025-04-23 22:48:09] [TRACE] [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`. [2025-04-23 22:48:09] [TRACE] [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`. [2025-04-23 22:48:09] [TRACE] [OmnipathR] Bypassing call: `go_ontology_download()`. [2025-04-23 22:48:09] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2025-04-23 22:48:09] [TRACE] [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`. [2025-04-23 22:48:09] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2025-04-23 22:48:09] [TRACE] [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`. [2025-04-23 22:48:09] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. --- finished re-building ‘bioc_workshop.Rmd’ --- re-building ‘cosmos.Rmd’ using rmarkdown Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' [2025-04-23 22:48:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:11] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:48:11] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-23 20:37:22 UTC; omnipath [2025-04-23 22:48:11] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-04-23 22:48:11] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-23 20:38:30 UTC; unix [2025-04-23 22:48:11] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.99 [2025-04-23 22:48:11] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-04-23 22:48:11] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-04-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-04-23 22:48:11] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-04-23 22:48:11] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.25(2024-08-28); BiocStyle 2.36.0(2025-04-15); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.43(2025-04-15); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.99(2025-04-23); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-04-23 22:48:11] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-04-23 22:48:11] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-23 22:48:11] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:48:11] [TRACE] [OmnipathR] Contains 14 files. [2025-04-23 22:48:11] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-23 22:48:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:48:11] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-04-23 22:48:11] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-23 22:48:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:11] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-23 22:48:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:11] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-23 22:48:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:11] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-23 22:48:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:11] [TRACE] [OmnipathR] Cache locked: FALSE [2025-04-23 22:48:11] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`. [2025-04-23 22:48:11] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2025-04-23 22:48:11] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`. [2025-04-23 22:48:11] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2025-04-23 22:48:12] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`. [2025-04-23 22:48:12] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2025-04-23 22:48:12] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-04-23 22:48:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:12] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-04-23 22:48:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:12] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-04-23 22:48:12] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-04-23 22:48:12] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-04-23 22:48:12] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-04-23 22:48:12] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-04-23 22:48:12] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-04-23 22:48:12] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-23 22:48:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:48:12] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:48:12] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-23 22:48:12] [TRACE] [OmnipathR] Sending HTTP request. [2025-04-23 22:48:12] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-04-23 22:48:12] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:48:12] [TRACE] [OmnipathR] Downloaded 31 Kb in 0.233575s from www.ensembl.org (132.9 Kb/s); Redirect: 0s, DNS look up: 0.001401s, Connection: 0.019584s, Pretransfer: 0.084143s, First byte at: 0.214123s [2025-04-23 22:48:12] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Wed, 23 Apr 2025 20:48:12 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31776; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:48:12 GMT; Set-cookie: ENSEMBL_HINX_SESSION=563e25226baab47709e0aaa068586c0c0ba66f86b075e2abe5d9d2ca; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:48:12 GMT; Set-cookie: ENSEMBL_HINX_SESSION=563e25226baab47709e0aaa068586c0c0ba66f86b075e2abe5d9d2ca; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-33.ebi.ac.uk [2025-04-23 22:48:12] [TRACE] [OmnipathR] Response headers: [Date=Wed, 23 Apr 2025 20:48:12 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31776,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:48:12 GMT,Set-cookie=ENSEMBL_HINX_SESSION=563e25226baab47709e0aaa068586c0c0ba66f86b075e2abe5d9d2ca; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:48:12 GMT,Set-cookie=ENSEMBL_HINX_SESSION=563e25226baab47709e0aaa068586c0c0ba66f86b075e2abe5d9d2ca; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-33.ebi.ac.uk] [2025-04-23 22:48:12] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-04-23 22:48:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:12] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-04-23 22:48:12] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-04-23 22:48:12] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-04-23 22:48:12] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:48:12] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-04-23 22:48:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:12] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-04-23 22:48:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-04-23 22:48:12] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:48:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:48:12] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:48:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:48:12] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:48:12] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-04-23 22:48:12] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.057829s from omabrowser.org (150.3 Kb/s); Redirect: 0s, DNS look up: 0.000915s, Connection: 0.011551s, Pretransfer: 0.044082s, First byte at: 0.057687s [2025-04-23 22:48:12] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 23 Apr 2025 20:48:12 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip [2025-04-23 22:48:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-04-23 22:48:13] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-04-23 22:48:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:13] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-04-23 22:48:13] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-04-23 22:48:13] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human. [2025-04-23 22:48:13] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:48:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions] [2025-04-23 22:48:13] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:48:13] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:48:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:48:13] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:48:13] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:48:13] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:48:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:48:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:48:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:48:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:48:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:48:13] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:48:13] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:48:13] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.103521s from omnipathdb.org (151.3 Kb/s); Redirect: 0s, DNS look up: 0.00102s, Connection: 0.020218s, Pretransfer: 0.064674s, First byte at: 0.10322s [2025-04-23 22:48:13] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:48:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:48:13 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:48:13] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:48:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:13] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2025-04-23 22:48:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-04-23 22:48:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-04-23 22:48:14] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2025-04-23 22:48:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:14] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2025-04-23 22:48:16] [SUCCESS] [OmnipathR] Downloaded 81529 interactions. [2025-04-23 22:48:16] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2025-04-23 22:48:16] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2025-04-23 22:48:16] [TRACE] [OmnipathR] BioMart query: [2025-04-23 22:48:16] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-04-23 22:48:16] [TRACE] [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2025-04-23 22:48:16] [INFO] [OmnipathR] Cache record does not exist: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2025-04-23 22:48:16] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2025-04-23 22:48:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:16] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`. [2025-04-23 22:48:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2025-04-23 22:48:16] [INFO] [OmnipathR] Retrieving URL: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2025-04-23 22:48:16] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-04-23 22:48:16] [TRACE] [OmnipathR] Attempt 1/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2025-04-23 22:48:16] [TRACE] [OmnipathR] Preparing httr2 request to URL `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2025-04-23 22:48:16] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-23 22:48:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:48:16] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:48:16] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-23 22:48:16] [TRACE] [OmnipathR] Sending HTTP request. [2025-04-23 22:48:24] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-04-23 22:48:24] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:48:24] [TRACE] [OmnipathR] Downloaded 1.2 Mb in 7.740523s from www.ensembl.org (152.3 Kb/s); Redirect: 0s, DNS look up: 0.001064s, Connection: 0.019502s, Pretransfer: 0.019552s, First byte at: 0.093603s [2025-04-23 22:48:24] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Wed, 23 Apr 2025 20:48:16 GMT; Server: Apache; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; Transfer-Encoding: chunked; Content-Type: text/plain; charset=utf-8 [2025-04-23 22:48:24] [TRACE] [OmnipathR] Response headers: [Date=Wed, 23 Apr 2025 20:48:16 GMT,Server=Apache,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',Transfer-Encoding=chunked,Content-Type=text/plain; charset=utf-8] [2025-04-23 22:48:24] [TRACE] [OmnipathR] Calling reader callback on response. [2025-04-23 22:48:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2025-04-23 22:48:24] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1] [2025-04-23 22:48:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:24] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`. [2025-04-23 22:48:24] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 122413 records [2025-04-23 22:48:24] [TRACE] [OmnipathR] Translating complexes: 592 complexes in data. [2025-04-23 22:48:24] [TRACE] [OmnipathR] 433 complexes after removing the ones mapping to more than 1 items in target identifier space. [2025-04-23 22:48:25] [TRACE] [OmnipathR] Translated 433 complexes to 433. [2025-04-23 22:48:25] [TRACE] [OmnipathR] 67526 rows before translation, 4551 uniprot IDs in column `source`. [2025-04-23 22:48:25] [TRACE] [OmnipathR] 67599 rows after translation; translated 4551 `uniprot` IDs in column `source` to 4392 `genesymbol` IDs in column `genesymbol_source`. [2025-04-23 22:48:25] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2025-04-23 22:48:25] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2025-04-23 22:48:25] [TRACE] [OmnipathR] BioMart query: [2025-04-23 22:48:25] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-04-23 22:48:26] [TRACE] [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2025-04-23 22:48:26] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2025-04-23 22:48:26] [SUCCESS] [OmnipathR] www.ensembl.org: loaded 122413 records from cache [2025-04-23 22:48:26] [TRACE] [OmnipathR] Translating complexes: 311 complexes in data. [2025-04-23 22:48:26] [TRACE] [OmnipathR] 220 complexes after removing the ones mapping to more than 1 items in target identifier space. [2025-04-23 22:48:26] [TRACE] [OmnipathR] Translated 220 complexes to 220. [2025-04-23 22:48:26] [TRACE] [OmnipathR] 67599 rows before translation, 4638 uniprot IDs in column `target`. [2025-04-23 22:48:26] [TRACE] [OmnipathR] 69184 rows after translation; translated 4638 `uniprot` IDs in column `target` to 4555 `genesymbol` IDs in column `genesymbol_target`. [2025-04-23 22:48:26] [INFO] [OmnipathR] OmniPath PPI for COSMOS PKN ready: 138490 interactions. --- finished re-building ‘cosmos.Rmd’ --- re-building ‘db_manager.Rmd’ using rmarkdown Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' [2025-04-23 22:48:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:28] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:48:28] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-23 20:37:22 UTC; omnipath [2025-04-23 22:48:28] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-04-23 22:48:28] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-23 20:38:30 UTC; unix [2025-04-23 22:48:28] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.99 [2025-04-23 22:48:28] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-04-23 22:48:28] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-04-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-04-23 22:48:28] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-04-23 22:48:29] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.25(2024-08-28); BiocStyle 2.36.0(2025-04-15); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.43(2025-04-15); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.99(2025-04-23); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-04-23 22:48:29] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-04-23 22:48:29] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-23 22:48:29] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:48:29] [TRACE] [OmnipathR] Contains 5 files. [2025-04-23 22:48:29] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-23 22:48:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:48:29] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-04-23 22:48:29] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-23 22:48:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:29] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-23 22:48:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:29] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-23 22:48:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:29] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-23 22:48:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:29] [TRACE] [OmnipathR] Cache locked: FALSE [2025-04-23 22:48:29] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2025-04-23 22:48:29] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2025-04-23 22:48:29] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-04-23 22:48:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:29] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-04-23 22:48:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:29] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-04-23 22:48:29] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-04-23 22:48:29] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-04-23 22:48:29] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-04-23 22:48:29] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-04-23 22:48:29] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-04-23 22:48:29] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-23 22:48:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:48:29] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:48:29] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-23 22:48:29] [TRACE] [OmnipathR] Sending HTTP request. [2025-04-23 22:48:29] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-04-23 22:48:29] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:48:29] [TRACE] [OmnipathR] Downloaded 30.9 Kb in 0.215435s from www.ensembl.org (143.2 Kb/s); Redirect: 0s, DNS look up: 0.001349s, Connection: 0.019887s, Pretransfer: 0.074552s, First byte at: 0.19256s [2025-04-23 22:48:29] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Wed, 23 Apr 2025 20:48:29 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31599; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:48:29 GMT; Set-cookie: ENSEMBL_HINX_SESSION=863c3fa19143476a09817e8d68586c1d0bc7b7fc1bc70899e13b973f; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:48:29 GMT; Set-cookie: ENSEMBL_HINX_SESSION=863c3fa19143476a09817e8d68586c1d0bc7b7fc1bc70899e13b973f; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-35.ebi.ac.uk [2025-04-23 22:48:29] [TRACE] [OmnipathR] Response headers: [Date=Wed, 23 Apr 2025 20:48:29 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31599,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:48:29 GMT,Set-cookie=ENSEMBL_HINX_SESSION=863c3fa19143476a09817e8d68586c1d0bc7b7fc1bc70899e13b973f; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:48:29 GMT,Set-cookie=ENSEMBL_HINX_SESSION=863c3fa19143476a09817e8d68586c1d0bc7b7fc1bc70899e13b973f; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-35.ebi.ac.uk] [2025-04-23 22:48:29] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-04-23 22:48:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:29] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-04-23 22:48:29] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-04-23 22:48:29] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-04-23 22:48:29] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:48:29] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-04-23 22:48:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:29] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-04-23 22:48:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-04-23 22:48:29] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:48:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:48:29] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:48:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:48:29] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:48:29] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-04-23 22:48:29] [TRACE] [OmnipathR] Downloaded 7.9 Kb in 0.060338s from omabrowser.org (131.6 Kb/s); Redirect: 0s, DNS look up: 0.001022s, Connection: 0.012536s, Pretransfer: 0.045625s, First byte at: 0.060203s [2025-04-23 22:48:29] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 23 Apr 2025 20:48:29 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip [2025-04-23 22:48:30] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-04-23 22:48:30] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-04-23 22:48:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:30] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-04-23 22:48:30] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-04-23 22:48:30] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2025-04-23 22:48:30] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-04-23 22:48:30] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2025-04-23 22:48:30] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-04-23 22:48:30] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2025-04-23 22:48:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:30] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2025-04-23 22:48:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2025-04-23 22:48:30] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-04-23 22:48:30] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-04-23 22:48:30] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:48:30] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:48:30] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:48:30] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-04-23 22:48:30] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.649497s from rest.uniprot.org (66 bytes/s); Redirect: 0s, DNS look up: 0.000943s, Connection: 0.019487s, Pretransfer: 0.081877s, First byte at: 0.649432s [2025-04-23 22:48:30] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 23-April-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 23 Apr 2025 20:48:30 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_02; access-control-allow-origin: *; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 23-April-2025 [2025-04-23 22:48:50] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2025-04-23 22:48:50] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2025-04-23 22:48:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:48:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:48:50] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2025-04-23 22:48:50] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20421 records [2025-04-23 22:48:50] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' [2025-04-23 22:49:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:03] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:49:03] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-23 20:37:22 UTC; omnipath [2025-04-23 22:49:03] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-04-23 22:49:03] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-23 20:38:30 UTC; unix [2025-04-23 22:49:03] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.99 [2025-04-23 22:49:03] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-04-23 22:49:03] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-04-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-04-23 22:49:03] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-04-23 22:49:03] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.25(2024-08-28); BiocStyle 2.36.0(2025-04-15); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.43(2025-04-15); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); colorspace 2.1-1(2024-07-26); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); ggplot2 3.5.2(2025-04-09); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); munsell 0.5.1(2024-04-01); OmnipathR 3.15.99(2025-04-23); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); scales 1.3.0(2023-11-28); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-04-23 22:49:03] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-04-23 22:49:03] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-23 22:49:03] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:49:03] [TRACE] [OmnipathR] Contains 4 files. [2025-04-23 22:49:03] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-23 22:49:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:49:03] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-04-23 22:49:03] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-23 22:49:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:03] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-23 22:49:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:03] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-23 22:49:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:03] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-23 22:49:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:03] [TRACE] [OmnipathR] Cache locked: FALSE [2025-04-23 22:49:03] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:49:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2025-04-23 22:49:03] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:49:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2025-04-23 22:49:03] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-04-23 22:49:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:03] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-04-23 22:49:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:03] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-04-23 22:49:03] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-04-23 22:49:03] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-04-23 22:49:03] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-04-23 22:49:03] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-04-23 22:49:03] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-04-23 22:49:03] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-23 22:49:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:49:03] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:49:03] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-23 22:49:03] [TRACE] [OmnipathR] Sending HTTP request. [2025-04-23 22:49:04] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-04-23 22:49:04] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:49:04] [TRACE] [OmnipathR] Downloaded 30.9 Kb in 0.205807s from www.ensembl.org (150.3 Kb/s); Redirect: 0s, DNS look up: 0.001362s, Connection: 0.019473s, Pretransfer: 0.089772s, First byte at: 0.183136s [2025-04-23 22:49:04] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Wed, 23 Apr 2025 20:49:04 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31671; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:49:04 GMT; Set-cookie: ENSEMBL_HINX_SESSION=13c8a3dafc497b590ee71a0868586c400ca1cb2aabecc1ec1d51e06d; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:49:04 GMT; Set-cookie: ENSEMBL_HINX_SESSION=13c8a3dafc497b590ee71a0868586c400ca1cb2aabecc1ec1d51e06d; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-32.ebi.ac.uk [2025-04-23 22:49:04] [TRACE] [OmnipathR] Response headers: [Date=Wed, 23 Apr 2025 20:49:04 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31671,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:49:04 GMT,Set-cookie=ENSEMBL_HINX_SESSION=13c8a3dafc497b590ee71a0868586c400ca1cb2aabecc1ec1d51e06d; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:49:04 GMT,Set-cookie=ENSEMBL_HINX_SESSION=13c8a3dafc497b590ee71a0868586c400ca1cb2aabecc1ec1d51e06d; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-32.ebi.ac.uk] [2025-04-23 22:49:04] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-04-23 22:49:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:04] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-04-23 22:49:04] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-04-23 22:49:04] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-04-23 22:49:04] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:49:04] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-04-23 22:49:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:04] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-04-23 22:49:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-04-23 22:49:04] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:49:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:49:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:49:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:49:04] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:49:04] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-04-23 22:49:04] [TRACE] [OmnipathR] Downloaded 7.9 Kb in 0.063425s from omabrowser.org (125.2 Kb/s); Redirect: 0s, DNS look up: 0.000979s, Connection: 0.011777s, Pretransfer: 0.049354s, First byte at: 0.063292s [2025-04-23 22:49:04] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 23 Apr 2025 20:49:04 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip [2025-04-23 22:49:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-04-23 22:49:04] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-04-23 22:49:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:04] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-04-23 22:49:04] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-04-23 22:49:04] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:49:04] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:49:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:49:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:49:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:49:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:49:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:49:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:49:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:49:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:49:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:49:04] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:49:05] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:49:05] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095143s from omnipathdb.org (164.7 Kb/s); Redirect: 0s, DNS look up: 0.000895s, Connection: 0.019306s, Pretransfer: 0.052879s, First byte at: 0.094364s [2025-04-23 22:49:05] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:49:05 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:49:05 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:49:05] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-23 22:49:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:05] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2025-04-23 22:49:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-04-23 22:49:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-04-23 22:49:05] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2025-04-23 22:49:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:05] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2025-04-23 22:49:08] [SUCCESS] [OmnipathR] Downloaded 81529 interactions. --- finished re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' [2025-04-23 22:49:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:11] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:49:11] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-23 20:37:22 UTC; omnipath [2025-04-23 22:49:11] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-04-23 22:49:11] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-23 20:38:30 UTC; unix [2025-04-23 22:49:11] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.99 [2025-04-23 22:49:11] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-04-23 22:49:11] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-04-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-04-23 22:49:11] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-04-23 22:49:11] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.25(2024-08-28); BiocStyle 2.36.0(2025-04-15); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.43(2025-04-15); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.99(2025-04-23); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-04-23 22:49:11] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-04-23 22:49:11] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-23 22:49:11] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:49:11] [TRACE] [OmnipathR] Contains 4 files. [2025-04-23 22:49:11] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-23 22:49:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:49:11] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-04-23 22:49:11] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-23 22:49:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:11] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-23 22:49:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:11] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-23 22:49:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:11] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-23 22:49:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:11] [TRACE] [OmnipathR] Cache locked: FALSE [2025-04-23 22:49:11] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:49:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions] [2025-04-23 22:49:11] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-04-23 22:49:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:11] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-04-23 22:49:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:11] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-04-23 22:49:11] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-04-23 22:49:11] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-04-23 22:49:11] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-04-23 22:49:11] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-04-23 22:49:11] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-04-23 22:49:11] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-23 22:49:11] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:49:11] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:49:11] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-23 22:49:11] [TRACE] [OmnipathR] Sending HTTP request. [2025-04-23 22:49:12] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-04-23 22:49:12] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:49:12] [TRACE] [OmnipathR] Downloaded 30.9 Kb in 0.199159s from www.ensembl.org (155.2 Kb/s); Redirect: 0s, DNS look up: 0.00127s, Connection: 0.020039s, Pretransfer: 0.077621s, First byte at: 0.175546s [2025-04-23 22:49:12] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Wed, 23 Apr 2025 20:49:12 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31648; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:49:11 GMT; Set-cookie: ENSEMBL_HINX_SESSION=7bc50fafd4f56e3c0c503ba668586c480e16e97e784dd47d17428940; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:49:11 GMT; Set-cookie: ENSEMBL_HINX_SESSION=7bc50fafd4f56e3c0c503ba668586c480e16e97e784dd47d17428940; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-32.ebi.ac.uk [2025-04-23 22:49:12] [TRACE] [OmnipathR] Response headers: [Date=Wed, 23 Apr 2025 20:49:12 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31648,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:49:11 GMT,Set-cookie=ENSEMBL_HINX_SESSION=7bc50fafd4f56e3c0c503ba668586c480e16e97e784dd47d17428940; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:49:11 GMT,Set-cookie=ENSEMBL_HINX_SESSION=7bc50fafd4f56e3c0c503ba668586c480e16e97e784dd47d17428940; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-32.ebi.ac.uk] [2025-04-23 22:49:12] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-04-23 22:49:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:12] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-04-23 22:49:12] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-04-23 22:49:12] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-04-23 22:49:12] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:49:12] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-04-23 22:49:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:12] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-04-23 22:49:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-04-23 22:49:12] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:49:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:49:12] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:49:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:49:12] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:49:12] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-04-23 22:49:12] [TRACE] [OmnipathR] Downloaded 7.9 Kb in 0.067497s from omabrowser.org (117.6 Kb/s); Redirect: 0s, DNS look up: 0.00102s, Connection: 0.012408s, Pretransfer: 0.053207s, First byte at: 0.067267s [2025-04-23 22:49:12] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 23 Apr 2025 20:49:12 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip [2025-04-23 22:49:12] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-04-23 22:49:12] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-04-23 22:49:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:12] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-04-23 22:49:12] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-04-23 22:49:12] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:49:12] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:49:12] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-23 22:49:12] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-23 22:49:12] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-23 22:49:12] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-23 22:49:12] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-23 22:49:12] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-23 22:49:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-23 22:49:12] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:49:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:49:12] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:49:12] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:49:12] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.088905s from omnipathdb.org (176.2 Kb/s); Redirect: 0s, DNS look up: 0.000933s, Connection: 0.018945s, Pretransfer: 0.052055s, First byte at: 0.088604s [2025-04-23 22:49:12] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:49:12 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:49:12 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:49:13] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-23 22:49:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:13] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`. [2025-04-23 22:49:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2025-04-23 22:49:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2025-04-23 22:49:14] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1] [2025-04-23 22:49:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:49:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:49:14] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`. [2025-04-23 22:49:14] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-04-23 22:49:22] [SUCCESS] [OmnipathR] Downloaded 134282 interactions. [2025-04-23 22:54:46] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:54:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations] [2025-04-23 22:54:46] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:54:46] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:54:47] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-23 22:54:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:54:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-04-23 22:54:47] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-04-23 22:54:47] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-04-23 22:54:47] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-04-23 22:54:47] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-04-23 22:54:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-04-23 22:54:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-04-23 22:54:47] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:54:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:54:47] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:54:47] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:54:47] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.105416s from omnipathdb.org (148.6 Kb/s); Redirect: 0s, DNS look up: 0.00091s, Connection: 0.019647s, Pretransfer: 0.06874s, First byte at: 0.105097s [2025-04-23 22:54:47] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:54:47 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:54:47 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:54:47] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-04-23 22:54:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:54:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:54:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:54:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:54:47] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`. [2025-04-23 22:54:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2025-04-23 22:54:48] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2025-04-23 22:54:48] [INFO] [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1] [2025-04-23 22:54:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:54:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:54:48] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`. [2025-04-23 22:54:48] [SUCCESS] [OmnipathR] Downloaded 205690 annotation records. [2025-04-23 22:54:48] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:54:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub] [2025-04-23 22:54:48] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:54:48] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:54:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-04-23 22:54:48] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-04-23 22:54:48] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-04-23 22:54:48] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-04-23 22:54:48] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-04-23 22:54:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-04-23 22:54:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-04-23 22:54:48] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:54:48] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:54:48] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:54:48] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:54:48] [TRACE] [OmnipathR] Downloaded 5.1 Kb in 0.091739s from omnipathdb.org (55.6 Kb/s); Redirect: 0s, DNS look up: 0.001069s, Connection: 0.02174s, Pretransfer: 0.07086s, First byte at: 0.091721s [2025-04-23 22:54:48] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:54:48 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 5219; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:54:48 GMT; Cache-Control: public; X-Frame-Options: DENY [2025-04-23 22:54:49] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-04-23 22:54:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:54:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:54:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:54:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:54:49] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`. [2025-04-23 22:54:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2025-04-23 22:54:49] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2025-04-23 22:54:49] [INFO] [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1] [2025-04-23 22:54:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:54:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:54:49] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`. [2025-04-23 22:54:49] [SUCCESS] [OmnipathR] Downloaded 70 enzyme-substrate relationships. --- finished re-building ‘extra_attrs.Rmd’ --- re-building ‘nichenet.Rmd’ using rmarkdown Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' --- finished re-building ‘nichenet.Rmd’ --- re-building ‘omnipath_intro.Rmd’ using rmarkdown Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' [2025-04-23 22:54:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:54:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:54:52] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:54:52] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-23 20:37:22 UTC; omnipath [2025-04-23 22:54:52] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-04-23 22:54:52] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-23 20:38:30 UTC; unix [2025-04-23 22:54:52] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.99 [2025-04-23 22:54:52] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-04-23 22:54:52] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-04-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-04-23 22:54:52] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-04-23 22:54:52] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.25(2024-08-28); BiocStyle 2.36.0(2025-04-15); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.43(2025-04-15); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.99(2025-04-23); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-04-23 22:54:52] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-04-23 22:54:52] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-23 22:54:52] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:54:52] [TRACE] [OmnipathR] Contains 6 files. [2025-04-23 22:54:52] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-23 22:54:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:54:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:54:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:54:52] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-04-23 22:54:52] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-23 22:54:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:54:52] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-23 22:54:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:54:52] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-23 22:54:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:54:52] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-23 22:54:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:54:52] [TRACE] [OmnipathR] Cache locked: FALSE [2025-04-23 22:54:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-23 22:54:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:54:53] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:54:53] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath] [2025-04-23 22:54:53] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:54:53] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions] [2025-04-23 22:54:53] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-04-23 22:54:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:54:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:54:53] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-04-23 22:54:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:54:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:54:53] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-04-23 22:54:53] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-04-23 22:54:53] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-04-23 22:54:53] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-04-23 22:54:53] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-04-23 22:54:53] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-04-23 22:54:53] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-23 22:54:53] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:54:53] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:54:53] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-23 22:54:53] [TRACE] [OmnipathR] Sending HTTP request. [2025-04-23 22:54:53] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-04-23 22:54:53] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:54:53] [TRACE] [OmnipathR] Downloaded 31 Kb in 0.199747s from www.ensembl.org (155.1 Kb/s); Redirect: 0s, DNS look up: 0.008281s, Connection: 0.026353s, Pretransfer: 0.083472s, First byte at: 0.177158s [2025-04-23 22:54:53] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Wed, 23 Apr 2025 20:54:53 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31727; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:54:53 GMT; Set-cookie: ENSEMBL_HINX_SESSION=3602232c085728b30c28780b68586d9d0e6f63304c68cbcc04095766; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:54:53 GMT; Set-cookie: ENSEMBL_HINX_SESSION=3602232c085728b30c28780b68586d9d0e6f63304c68cbcc04095766; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-32.ebi.ac.uk [2025-04-23 22:54:53] [TRACE] [OmnipathR] Response headers: [Date=Wed, 23 Apr 2025 20:54:53 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31727,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:54:53 GMT,Set-cookie=ENSEMBL_HINX_SESSION=3602232c085728b30c28780b68586d9d0e6f63304c68cbcc04095766; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:54:53 GMT,Set-cookie=ENSEMBL_HINX_SESSION=3602232c085728b30c28780b68586d9d0e6f63304c68cbcc04095766; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-32.ebi.ac.uk] [2025-04-23 22:54:53] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-04-23 22:54:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:54:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:54:53] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-04-23 22:54:53] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-04-23 22:54:53] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-04-23 22:54:53] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:54:53] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-04-23 22:54:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:54:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:54:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:54:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:54:54] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-04-23 22:54:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-04-23 22:54:54] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:54:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:54:54] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:54:54] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:54:54] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:54:54] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-04-23 22:54:54] [TRACE] [OmnipathR] Downloaded 1.3 Kb in 0.072336s from omabrowser.org (17.4 Kb/s); Redirect: 0s, DNS look up: 0.000872s, Connection: 0.011598s, Pretransfer: 0.058644s, First byte at: 0.072275s [2025-04-23 22:54:54] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 23 Apr 2025 20:54:54 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip [2025-04-23 22:54:54] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-04-23 22:54:54] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-04-23 22:54:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:54:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:54:54] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-04-23 22:54:54] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-04-23 22:54:54] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:54:54] [TRACE] [OmnipathR] Orthology targets: Quitting from omnipath_intro.Rmd:166-175 [interactions] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `file()`: ! cannot open the connection to 'https://omnipathdb.org/resources' --- Backtrace: ▆ 1. ├─OmnipathR::omnipath(...) 2. │ ├─rlang::exec(omnipath_interactions, !!!args) 3. │ └─OmnipathR (local) ``(resources = ``, datasets = "omnipath") 4. │ ├─rlang::exec(omnipath_query, !!!args) 5. │ └─OmnipathR (local) ``(datasets = "omnipath", resources = ``, query_type = "interactions") 6. │ └─environment() %>% as.list %>% c(list(...)) %>% ... 7. └─OmnipathR:::omnipath_check_param(.) 8. └─OmnipathR::resources(param$query_type) 9. └─OmnipathR:::safe_json(path = resources_url) 10. └─base::readLines(con = path, encoding = encoding) 11. └─base::file(con, "r") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics: cannot open the connection to 'https://omnipathdb.org/resources' --- failed re-building ‘omnipath_intro.Rmd’ --- re-building ‘paths.Rmd’ using rmarkdown Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' [2025-04-23 22:55:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:55:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:56] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:55:56] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-23 20:37:22 UTC; omnipath [2025-04-23 22:55:56] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-04-23 22:55:56] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-23 20:38:30 UTC; unix [2025-04-23 22:55:56] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.99 [2025-04-23 22:55:56] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-04-23 22:55:56] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-04-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-04-23 22:55:56] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-04-23 22:55:56] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.25(2024-08-28); BiocStyle 2.36.0(2025-04-15); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.43(2025-04-15); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.99(2025-04-23); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-04-23 22:55:56] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-04-23 22:55:56] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-23 22:55:56] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:55:56] [TRACE] [OmnipathR] Contains 3 files. [2025-04-23 22:55:56] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-23 22:55:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:55:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-04-23 22:55:56] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-04-23 22:55:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-23 22:55:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-23 22:55:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-23 22:55:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-23 22:55:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:56] [TRACE] [OmnipathR] Cache locked: FALSE [2025-04-23 22:55:56] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:55:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations] [2025-04-23 22:55:56] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-04-23 22:55:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:55:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:56] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-04-23 22:55:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:55:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:56] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-04-23 22:55:56] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-04-23 22:55:56] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-04-23 22:55:56] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-04-23 22:55:56] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-04-23 22:55:56] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-04-23 22:55:56] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-23 22:55:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:55:56] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:55:56] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-23 22:55:56] [TRACE] [OmnipathR] Sending HTTP request. [2025-04-23 22:55:56] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-04-23 22:55:56] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:55:56] [TRACE] [OmnipathR] Downloaded 30.9 Kb in 0.225169s from www.ensembl.org (137.4 Kb/s); Redirect: 0s, DNS look up: 0.001443s, Connection: 0.019978s, Pretransfer: 0.093113s, First byte at: 0.201854s [2025-04-23 22:55:56] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Wed, 23 Apr 2025 20:55:56 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31690; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:55:56 GMT; Set-cookie: ENSEMBL_HINX_SESSION=de725c78bf493f5f0cf0183f68586ddc0eb73fdd6f25792814c89054; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:55:56 GMT; Set-cookie: ENSEMBL_HINX_SESSION=de725c78bf493f5f0cf0183f68586ddc0eb73fdd6f25792814c89054; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-33.ebi.ac.uk [2025-04-23 22:55:56] [TRACE] [OmnipathR] Response headers: [Date=Wed, 23 Apr 2025 20:55:56 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31690,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:55:56 GMT,Set-cookie=ENSEMBL_HINX_SESSION=de725c78bf493f5f0cf0183f68586ddc0eb73fdd6f25792814c89054; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 20:55:56 GMT,Set-cookie=ENSEMBL_HINX_SESSION=de725c78bf493f5f0cf0183f68586ddc0eb73fdd6f25792814c89054; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-33.ebi.ac.uk] [2025-04-23 22:55:56] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-04-23 22:55:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:55:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:56] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-04-23 22:55:57] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-04-23 22:55:57] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-04-23 22:55:57] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:55:57] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-04-23 22:55:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:55:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:55:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:57] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-04-23 22:55:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-04-23 22:55:57] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:55:57] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-04-23 22:55:57] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:55:57] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:55:57] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:55:57] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-04-23 22:55:57] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.062798s from omabrowser.org (138.4 Kb/s); Redirect: 0s, DNS look up: 0.000908s, Connection: 0.011585s, Pretransfer: 0.049017s, First byte at: 0.062655s [2025-04-23 22:55:57] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 23 Apr 2025 20:55:57 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip [2025-04-23 22:55:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-04-23 22:55:57] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-04-23 22:55:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:55:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:57] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-04-23 22:55:57] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-04-23 22:55:57] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:55:57] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:55:57] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-23 22:55:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-04-23 22:55:57] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-04-23 22:55:57] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-04-23 22:55:57] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-04-23 22:55:57] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-04-23 22:55:57] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-04-23 22:55:57] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-04-23 22:55:57] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:55:57] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:55:57] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:55:57] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:55:57] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.125016s from omnipathdb.org (125.3 Kb/s); Redirect: 0s, DNS look up: 0.000855s, Connection: 0.02321s, Pretransfer: 0.079769s, First byte at: 0.124642s [2025-04-23 22:55:57] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:55:57 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:55:57 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:55:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-04-23 22:55:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:55:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:55:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:57] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`. [2025-04-23 22:55:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2025-04-23 22:55:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2025-04-23 22:55:57] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1] [2025-04-23 22:55:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:55:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:57] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`. [2025-04-23 22:55:57] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records. [2025-04-23 22:55:57] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-04-23 22:55:57] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2025-04-23 22:55:57] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2025-04-23 22:55:57] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2025-04-23 22:55:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:55:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:55:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:58] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`. [2025-04-23 22:55:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2025-04-23 22:55:58] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2025-04-23 22:55:58] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2025-04-23 22:55:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:55:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:55:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:55:58] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-04-23 22:55:58] [TRACE] [OmnipathR] Downloaded 10.8 Kb in 0.088927s from static-content.springer.com (121 Kb/s); Redirect: 0s, DNS look up: 0.008481s, Connection: 0.01545s, Pretransfer: 0.047255s, First byte at: 0.088398s [2025-04-23 22:55:58] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; cache-control: private, max-age=86400; last-modified: Thu, 16 Nov 2023 16:51:13 GMT; etag: "daa03c1eafd00cad9456b660ca85b849"; x-goog-generation: 1700153472991609; x-goog-metageneration: 1; x-goog-stored-content-encoding: identity; x-goog-stored-content-length: 160972; content-type: application/octet-stream; x-goog-hash: crc32c=v/3p0Q==; x-goog-hash: md5=2qA8Hq/QDK2UVrZgyoW4SQ==; x-goog-storage-class: MULTI_REGIONAL; x-guploader-uploadid: AFiumC7ZpYKgxNZtW8bqZY8u8z2x9V62Ud4hs7Wz5zewS1xt8QPnURGT01ram66yNo-OgPW_uOsydnKUF6Xmdbs; server: UploadServer; x-cdn-origin: GCS, SNPaaS; accept-ranges: bytes; age: 0; date: Wed, 23 Apr 2025 20:55:58 GMT; via: 1.1 varnish; x-served-by: cache-fra-eddf8230112-FRA; x-cache: HIT; x-cache-hits: 0; x-timer: S1745441758.079705,VS0,VE33; vary: Origin; alt-svc: h3=":443";ma=86400,h3-29=":443";ma=86400,h3-27=":443";ma=86400; content-length: 160972 [2025-04-23 22:55:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2025-04-23 22:55:58] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1] [2025-04-23 22:55:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:55:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:58] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`. [2025-04-23 22:55:58] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records [2025-04-23 22:55:58] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:55:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions] [2025-04-23 22:55:58] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:55:58] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:55:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-04-23 22:55:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-04-23 22:55:58] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-04-23 22:55:58] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-04-23 22:55:58] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-04-23 22:55:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-04-23 22:55:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-04-23 22:55:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:55:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:55:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:55:58] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:55:58] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.113376s from omnipathdb.org (138.2 Kb/s); Redirect: 0s, DNS look up: 0.000969s, Connection: 0.02187s, Pretransfer: 0.070759s, First byte at: 0.112682s [2025-04-23 22:55:58] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:55:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:55:58 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:55:58] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-04-23 22:55:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:55:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:55:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:58] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`. [2025-04-23 22:55:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2025-04-23 22:55:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2025-04-23 22:55:59] [INFO] [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1] [2025-04-23 22:55:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:55:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:55:59] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`. [2025-04-23 22:56:02] [SUCCESS] [OmnipathR] Downloaded 121170 interactions. [2025-04-23 22:56:02] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:56:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations] [2025-04-23 22:56:02] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:56:02] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:56:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-23 22:56:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-04-23 22:56:02] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-04-23 22:56:02] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-04-23 22:56:02] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-04-23 22:56:02] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-04-23 22:56:02] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-04-23 22:56:02] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-04-23 22:56:02] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:56:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:56:02] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:56:03] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:56:03] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.116475s from omnipathdb.org (134.5 Kb/s); Redirect: 0s, DNS look up: 0.000814s, Connection: 0.020538s, Pretransfer: 0.075968s, First byte at: 0.115999s [2025-04-23 22:56:03] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:56:03 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:56:03 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:56:03] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-04-23 22:56:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:03] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`. [2025-04-23 22:56:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2025-04-23 22:56:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2025-04-23 22:56:04] [INFO] [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1] [2025-04-23 22:56:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:04] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`. [2025-04-23 22:56:04] [SUCCESS] [OmnipathR] Downloaded 353573 annotation records. [2025-04-23 22:56:04] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:56:04] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:56:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-04-23 22:56:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-04-23 22:56:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-04-23 22:56:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-04-23 22:56:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-04-23 22:56:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-04-23 22:56:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-04-23 22:56:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:56:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:56:04] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:56:05] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:56:05] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.09687s from omnipathdb.org (161.7 Kb/s); Redirect: 0s, DNS look up: 0.000995s, Connection: 0.021599s, Pretransfer: 0.054327s, First byte at: 0.095925s [2025-04-23 22:56:05] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:56:05 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:56:05 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:56:05] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-04-23 22:56:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:05] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`. [2025-04-23 22:56:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2025-04-23 22:56:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2025-04-23 22:56:05] [INFO] [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1] [2025-04-23 22:56:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:05] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`. [2025-04-23 22:56:05] [SUCCESS] [OmnipathR] Downloaded 10040 intercellular communication role records. [2025-04-23 22:56:05] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:56:05] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:56:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-23 22:56:05] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-23 22:56:05] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-23 22:56:05] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-23 22:56:05] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-23 22:56:05] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-23 22:56:05] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-23 22:56:05] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:56:05] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:56:05] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:56:05] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:56:05] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.092031s from omnipathdb.org (170.2 Kb/s); Redirect: 0s, DNS look up: 0.000967s, Connection: 0.019724s, Pretransfer: 0.052431s, First byte at: 0.091655s [2025-04-23 22:56:05] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:56:05 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:56:05 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:56:05] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-23 22:56:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:05] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`. [2025-04-23 22:56:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-04-23 22:56:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-04-23 22:56:05] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1] [2025-04-23 22:56:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:05] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`. [2025-04-23 22:56:05] [SUCCESS] [OmnipathR] Downloaded 21862 intercellular communication role records. [2025-04-23 22:56:05] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:56:05] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:56:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-04-23 22:56:05] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-04-23 22:56:05] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-04-23 22:56:05] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-04-23 22:56:05] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-04-23 22:56:05] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-04-23 22:56:05] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-04-23 22:56:05] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:56:05] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:56:05] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:56:06] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:56:06] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.101478s from omnipathdb.org (154.4 Kb/s); Redirect: 0s, DNS look up: 0.000976s, Connection: 0.022316s, Pretransfer: 0.055002s, First byte at: 0.10054s [2025-04-23 22:56:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:56:05 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:56:05 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:56:06] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-04-23 22:56:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:06] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`. [2025-04-23 22:56:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2025-04-23 22:56:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2025-04-23 22:56:06] [INFO] [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1] [2025-04-23 22:56:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:06] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`. [2025-04-23 22:56:06] [SUCCESS] [OmnipathR] Downloaded 21455 intercellular communication role records. [2025-04-23 22:56:06] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:56:06] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:56:06] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-23 22:56:06] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-04-23 22:56:06] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-23 22:56:06] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache. [2025-04-23 22:56:06] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:56:06] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:56:06] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-04-23 22:56:06] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-04-23 22:56:06] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-04-23 22:56:06] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-04-23 22:56:06] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-04-23 22:56:06] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-04-23 22:56:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-04-23 22:56:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:56:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:56:06] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:56:06] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:56:06] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.096227s from omnipathdb.org (162.8 Kb/s); Redirect: 0s, DNS look up: 0.000833s, Connection: 0.021394s, Pretransfer: 0.054207s, First byte at: 0.095805s [2025-04-23 22:56:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:56:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:56:06 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:56:06] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-04-23 22:56:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:06] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`. [2025-04-23 22:56:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2025-04-23 22:56:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2025-04-23 22:56:06] [INFO] [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1] [2025-04-23 22:56:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:06] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`. [2025-04-23 22:56:07] [SUCCESS] [OmnipathR] Downloaded 14602 intercellular communication role records. [2025-04-23 22:56:07] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:56:07] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:56:07] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-23 22:56:07] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-04-23 22:56:07] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-23 22:56:07] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache. [2025-04-23 22:56:07] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:56:07] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:56:07] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-04-23 22:56:07] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-04-23 22:56:07] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-04-23 22:56:07] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-04-23 22:56:07] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-04-23 22:56:07] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-04-23 22:56:07] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-04-23 22:56:07] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:56:07] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:56:07] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:56:07] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:56:07] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.091672s from omnipathdb.org (170.9 Kb/s); Redirect: 0s, DNS look up: 0.001014s, Connection: 0.019964s, Pretransfer: 0.052807s, First byte at: 0.091343s [2025-04-23 22:56:07] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:56:07 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:56:07 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:56:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-04-23 22:56:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:07] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`. [2025-04-23 22:56:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2025-04-23 22:56:07] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2025-04-23 22:56:07] [INFO] [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1] [2025-04-23 22:56:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:07] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`. [2025-04-23 22:56:07] [SUCCESS] [OmnipathR] Downloaded 26412 intercellular communication role records. [2025-04-23 22:56:07] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:56:07] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:56:07] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-23 22:56:07] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-04-23 22:56:07] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-23 22:56:07] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache. [2025-04-23 22:56:07] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:56:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein] [2025-04-23 22:56:07] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:56:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions] [2025-04-23 22:56:07] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:56:07] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:56:07] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-04-23 22:56:07] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-04-23 22:56:07] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-04-23 22:56:07] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-04-23 22:56:07] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-04-23 22:56:07] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-04-23 22:56:07] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-04-23 22:56:07] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:56:07] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:56:07] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:56:08] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:56:08] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.088776s from omnipathdb.org (176.5 Kb/s); Redirect: 0s, DNS look up: 0.000935s, Connection: 0.017843s, Pretransfer: 0.053673s, First byte at: 0.08847s [2025-04-23 22:56:08] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:56:07 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:56:07 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:56:08] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-04-23 22:56:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:08] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`. [2025-04-23 22:56:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2025-04-23 22:56:08] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2025-04-23 22:56:08] [INFO] [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1] [2025-04-23 22:56:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:08] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`. [2025-04-23 22:56:09] [SUCCESS] [OmnipathR] Downloaded 30053 interactions. [2025-04-23 22:56:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:56:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations] [2025-04-23 22:56:09] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:56:09] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:56:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-23 22:56:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:09] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-04-23 22:56:09] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-04-23 22:56:09] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-04-23 22:56:09] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-04-23 22:56:09] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-04-23 22:56:09] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-04-23 22:56:09] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-04-23 22:56:09] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:56:09] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:56:09] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:56:09] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:56:09] [TRACE] [OmnipathR] Downloaded 13.1 Kb in 0.117666s from omnipathdb.org (111.4 Kb/s); Redirect: 0s, DNS look up: 0.001012s, Connection: 0.019549s, Pretransfer: 0.069177s, First byte at: 0.117416s [2025-04-23 22:56:09] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:56:09 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:56:09 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:56:10] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-04-23 22:56:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:10] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`. [2025-04-23 22:56:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2025-04-23 22:56:10] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2025-04-23 22:56:10] [INFO] [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1] [2025-04-23 22:56:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:10] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`. [2025-04-23 22:56:10] [SUCCESS] [OmnipathR] Downloaded 1144 annotation records. [2025-04-23 22:56:10] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:56:10] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations] [2025-04-23 22:56:10] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:56:10] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:56:10] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-23 22:56:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:10] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-04-23 22:56:10] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-04-23 22:56:10] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-04-23 22:56:10] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-04-23 22:56:10] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-04-23 22:56:10] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-04-23 22:56:10] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-04-23 22:56:10] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:56:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:56:10] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:56:10] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:56:10] [TRACE] [OmnipathR] Downloaded 12.1 Kb in 0.116586s from omnipathdb.org (103.7 Kb/s); Redirect: 0s, DNS look up: 0.000963s, Connection: 0.022156s, Pretransfer: 0.073441s, First byte at: 0.116321s [2025-04-23 22:56:10] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:56:10 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:56:10 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:56:10] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-04-23 22:56:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:10] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`. [2025-04-23 22:56:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2025-04-23 22:56:10] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2025-04-23 22:56:10] [INFO] [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1] [2025-04-23 22:56:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:10] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`. [2025-04-23 22:56:10] [SUCCESS] [OmnipathR] Downloaded 1080 annotation records. [2025-04-23 22:56:11] [TRACE] [OmnipathR] Bypassing call: `simplify_intercell_network(.)`. [2025-04-23 22:56:11] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2025-04-23 22:56:11] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:56:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions] [2025-04-23 22:56:11] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:56:11] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:56:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-23 22:56:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:11] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-04-23 22:56:11] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-04-23 22:56:11] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-04-23 22:56:11] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-04-23 22:56:11] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-04-23 22:56:11] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-04-23 22:56:11] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-04-23 22:56:11] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:56:11] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:56:11] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:56:11] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:56:11] [TRACE] [OmnipathR] Downloaded 11.7 Kb in 0.095713s from omnipathdb.org (122.3 Kb/s); Redirect: 0s, DNS look up: 0.000988s, Connection: 0.02122s, Pretransfer: 0.054248s, First byte at: 0.095455s [2025-04-23 22:56:11] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:56:11 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:56:11 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:56:11] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-04-23 22:56:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:11] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`. [2025-04-23 22:56:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2025-04-23 22:56:11] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2025-04-23 22:56:11] [INFO] [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1] [2025-04-23 22:56:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:11] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`. [2025-04-23 22:56:11] [SUCCESS] [OmnipathR] Downloaded 322 interactions. [2025-04-23 22:56:12] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:56:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2025-04-23 22:56:12] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:56:12] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:56:12] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-23 22:56:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:12] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-23 22:56:12] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-23 22:56:12] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-23 22:56:12] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-23 22:56:12] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-23 22:56:12] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-23 22:56:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-23 22:56:12] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:56:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:56:12] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:56:12] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:56:12] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.098649s from omnipathdb.org (158.8 Kb/s); Redirect: 0s, DNS look up: 0.000988s, Connection: 0.020999s, Pretransfer: 0.056644s, First byte at: 0.098296s [2025-04-23 22:56:12] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:56:12 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:56:12 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:56:12] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-23 22:56:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:12] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2025-04-23 22:56:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-04-23 22:56:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-04-23 22:56:13] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2025-04-23 22:56:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:13] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2025-04-23 22:56:13] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records. [2025-04-23 22:56:13] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:56:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2025-04-23 22:56:13] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:56:13] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:56:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-23 22:56:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-04-23 22:56:13] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-04-23 22:56:13] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-04-23 22:56:13] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-04-23 22:56:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-04-23 22:56:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-04-23 22:56:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-04-23 22:56:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-23 22:56:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-23 22:56:13] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-23 22:56:13] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-23 22:56:13] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.108003s from omnipathdb.org (145.1 Kb/s); Redirect: 0s, DNS look up: 0.000965s, Connection: 0.019967s, Pretransfer: 0.071026s, First byte at: 0.107678s [2025-04-23 22:56:13] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 20:56:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 21:56:13 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-23 22:56:14] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-04-23 22:56:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:14] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`. [2025-04-23 22:56:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2025-04-23 22:56:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2025-04-23 22:56:14] [INFO] [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1] [2025-04-23 22:56:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 22:56:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:14] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`. [2025-04-23 22:56:14] [SUCCESS] [OmnipathR] Downloaded 2029 annotation records. [2025-04-23 22:56:15] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:56:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2025-04-23 22:56:15] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:56:15] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:56:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-23 22:56:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-23 22:56:16] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-04-23 22:56:16] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-23 22:56:16] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache. [2025-04-23 22:56:16] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-23 22:56:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2025-04-23 22:56:16] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-23 22:56:16] [TRACE] [OmnipathR] Orthology targets: [2025-04-23 22:56:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-23 22:56:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 22:56:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-04-23 22:56:16] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2025-04-23 22:56:16] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-04-23 22:56:16] [SUCCESS] [OmnipathR] Loaded 2029 annotation records from cache. --- finished re-building ‘paths.Rmd’ SUMMARY: processing the following file failed: ‘omnipath_intro.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-23_2227/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2025-04-23 22:56:25 CEST ]