[ Started: 2025-04-26 22:38:35 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-3.21/2025-04-26_2228/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 [2025-04-26 22:39:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:39:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:39:04] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-04-26 22:39:04] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-26 20:37:30 UTC; omnipath [2025-04-26 22:39:04] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-04-26 22:39:04] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-26 20:38:38 UTC; unix [2025-04-26 22:39:04] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.99 [2025-04-26 22:39:04] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-04-26 22:39:04] [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=2025-04-26; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-04-26 22:39:04] [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] [2025-04-26 22:39:04] [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(2025-04-26); 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) [2025-04-26 22:39:04] [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 [2025-04-26 22:39:04] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-26 22:39:04] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-04-26 22:39:04] [TRACE] [OmnipathR] Contains 1 files. [2025-04-26 22:39:04] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-26 22:39:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:39:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:39:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-04-26 22:39:04] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-04-26 22:39:04] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-26_2228/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-26 22:39:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:39:04] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-26_2228/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-26 22:39:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:39:04] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-26_2228/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-26 22:39:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:39:04] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-26_2228/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-26 22:39:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:39:04] [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 [2025-04-26 22:39:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:39:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:39:14] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-04-26 22:39:14] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-26 20:37:30 UTC; omnipath [2025-04-26 22:39:14] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-04-26 22:39:14] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-26 20:38:38 UTC; unix [2025-04-26 22:39:14] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.99 [2025-04-26 22:39:14] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-04-26 22:39:14] [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=2025-04-26; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-04-26 22:39:14] [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] [2025-04-26 22:39:14] [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(2025-04-26); 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) [2025-04-26 22:39:14] [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 [2025-04-26 22:39:14] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-26 22:39:14] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-04-26 22:39:14] [TRACE] [OmnipathR] Contains 1 files. [2025-04-26 22:39:14] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-26 22:39:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:39:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:39:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-04-26 22:39:14] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-04-26 22:39:14] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-26_2228/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-26 22:39:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:39:14] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-26_2228/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-26 22:39:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:39:14] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-26_2228/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-26 22:39:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:39:14] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-26_2228/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-26 22:39:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:39:14] [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 ... ERROR Running examples in ‘OmnipathR-Ex.R’ failed The error most likely occurred in: > ### Name: curated_ligrec_stats > ### Title: Statistics about literature curated ligand-receptor interactions > ### Aliases: curated_ligrec_stats > > ### ** Examples > > clr <- curated_ligrec_stats() Warning in import_post_translational_interactions(resources = ., ...) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020],query_type=interactions] [2025-04-26 22:41:09] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:09] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:10] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:10] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:10] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`. [2025-04-26 22:41:10] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:10] [SUCCESS] [OmnipathR] Loaded 4568 interactions from cache. Warning in (function (...) : 'function (...) { .Deprecated("post_translational") post_translational(...) }' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:10] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:10] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,fields=extra_attrs,query_type=interactions] [2025-04-26 22:41:10] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:10] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:10] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:10] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-26 22:41:10] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`. [2025-04-26 22:41:10] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-26 22:41:10] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-04-26 22:41:10] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache. Warning in (function (...) : 'function (...) { .Deprecated("post_translational") post_translational(...) }' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:10] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:10] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,fields=extra_attrs,query_type=interactions] [2025-04-26 22:41:10] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:10] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:10] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:10] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-26 22:41:10] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`. [2025-04-26 22:41:10] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-26 22:41:10] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-04-26 22:41:11] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache. Warning in (function (...) : 'function (...) { .Deprecated("post_translational") post_translational(...) }' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:11] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=talklr,fields=extra_attrs,query_type=interactions] [2025-04-26 22:41:11] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:11] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:11] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-26 22:41:11] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`. [2025-04-26 22:41:11] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-26 22:41:11] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-04-26 22:41:11] [SUCCESS] [OmnipathR] Loaded 2484 interactions from cache. Warning in (function (...) : 'function (...) { .Deprecated("post_translational") post_translational(...) }' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:12] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,fields=extra_attrs,query_type=interactions] [2025-04-26 22:41:12] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:12] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:12] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:12] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-26 22:41:12] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`. [2025-04-26 22:41:12] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-26 22:41:12] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-04-26 22:41:12] [SUCCESS] [OmnipathR] Loaded 1894 interactions from cache. [2025-04-26 22:41:12] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,query_type=interactions] [2025-04-26 22:41:12] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:12] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:12] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:12] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:12] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`. [2025-04-26 22:41:12] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:12] [SUCCESS] [OmnipathR] Loaded 1796 interactions from cache. [2025-04-26 22:41:12] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_function,query_type=annotations] [2025-04-26 22:41:12] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:12] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:12] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:12] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2025-04-26 22:41:12] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`. [2025-04-26 22:41:12] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2025-04-26 22:41:12] [SUCCESS] [OmnipathR] Loaded 2001 annotation records from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:13] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,query_type=interactions] [2025-04-26 22:41:13] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:13] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:13] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:13] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:13] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-26 22:41:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-26 22:41:13] [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] [2025-04-26 22:41:13] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-26 22:41:13] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.106854s from omnipathdb.org (146.6 Kb/s); Redirect: 0s, DNS look up: 0.000919s, Connection: 0.021299s, Pretransfer: 0.065546s, First byte at: 0.106523s [2025-04-26 22:41:13] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 26 Apr 2025 20:41:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 26 Apr 2025 21:41:13 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-26 22:41:13] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:13] [INFO] [OmnipathR] Cache item `afe18d85fba82fa7d5f390113de328e13aa85e89` version 1: status changed from `unknown` to `started`. [2025-04-26 22:41:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`. [2025-04-26 22:41:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`. [2025-04-26 22:41:13] [INFO] [OmnipathR] Download ready [key=afe18d85fba82fa7d5f390113de328e13aa85e89, version=1] [2025-04-26 22:41:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:13] [INFO] [OmnipathR] Cache item `afe18d85fba82fa7d5f390113de328e13aa85e89` version 1: status changed from `started` to `ready`. [2025-04-26 22:41:13] [SUCCESS] [OmnipathR] Downloaded 2879 interactions. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:13] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,query_type=interactions] [2025-04-26 22:41:13] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:13] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:13] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`. [2025-04-26 22:41:13] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:14] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:14] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,query_type=interactions] [2025-04-26 22:41:14] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:14] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:14] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:14] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`. [2025-04-26 22:41:14] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:14] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache. Warning in (function (...) : 'function (...) { .Deprecated("post_translational") post_translational(...) }' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:14] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,fields=extra_attrs,query_type=interactions] [2025-04-26 22:41:14] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:14] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:14] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-26 22:41:14] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`. [2025-04-26 22:41:14] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-26 22:41:14] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-04-26 22:41:14] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:14] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,query_type=interactions] [2025-04-26 22:41:14] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:14] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:15] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-26 22:41:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-26 22:41:15] [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] [2025-04-26 22:41:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-26 22:41:15] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.112411s from omnipathdb.org (139.4 Kb/s); Redirect: 0s, DNS look up: 0.000796s, Connection: 0.020402s, Pretransfer: 0.072725s, First byte at: 0.112104s [2025-04-26 22:41:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 26 Apr 2025 20:41:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 26 Apr 2025 21:41:15 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-26 22:41:15] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:15] [INFO] [OmnipathR] Cache item `c8350370602bcfe8ed14bda96cb9bd68770c1e66` version 1: status changed from `unknown` to `started`. [2025-04-26 22:41:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`. [2025-04-26 22:41:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`. [2025-04-26 22:41:15] [INFO] [OmnipathR] Download ready [key=c8350370602bcfe8ed14bda96cb9bd68770c1e66, version=1] [2025-04-26 22:41:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:15] [INFO] [OmnipathR] Cache item `c8350370602bcfe8ed14bda96cb9bd68770c1e66` version 1: status changed from `started` to `ready`. [2025-04-26 22:41:15] [SUCCESS] [OmnipathR] Downloaded 3765 interactions. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:15] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,query_type=interactions] [2025-04-26 22:41:15] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:15] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:15] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`. [2025-04-26 22:41:15] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:15] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:15] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,query_type=interactions] [2025-04-26 22:41:15] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:15] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:16] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`. [2025-04-26 22:41:16] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:16] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache. Warning in (function (...) : 'function (...) { .Deprecated("post_translational") post_translational(...) }' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:16] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,fields=extra_attrs,query_type=interactions] [2025-04-26 22:41:16] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:16] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-26 22:41:16] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`. [2025-04-26 22:41:16] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-26 22:41:16] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-04-26 22:41:16] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:16] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellTalkDB,query_type=interactions] [2025-04-26 22:41:16] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:16] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:17] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:17] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:17] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-26 22:41:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-26 22:41:17] [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] [2025-04-26 22:41:17] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-26 22:41:17] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.0826s from omnipathdb.org (189.7 Kb/s); Redirect: 0s, DNS look up: 0.000963s, Connection: 0.016909s, Pretransfer: 0.05021s, First byte at: 0.082327s [2025-04-26 22:41:17] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 26 Apr 2025 20:41:17 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 26 Apr 2025 21:41:17 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-26 22:41:17] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:17] [INFO] [OmnipathR] Cache item `8158e608d1fd5182b9aa0a24a07fc739c59a1bf8` version 1: status changed from `unknown` to `started`. [2025-04-26 22:41:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`. [2025-04-26 22:41:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`. [2025-04-26 22:41:17] [INFO] [OmnipathR] Download ready [key=8158e608d1fd5182b9aa0a24a07fc739c59a1bf8, version=1] [2025-04-26 22:41:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:17] [INFO] [OmnipathR] Cache item `8158e608d1fd5182b9aa0a24a07fc739c59a1bf8` version 1: status changed from `started` to `ready`. [2025-04-26 22:41:17] [SUCCESS] [OmnipathR] Downloaded 3473 interactions. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:17] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellTalkDB,query_type=interactions] [2025-04-26 22:41:17] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:17] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:17] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:17] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`. [2025-04-26 22:41:17] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:17] [SUCCESS] [OmnipathR] Loaded 3473 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:17] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellTalkDB,query_type=interactions] [2025-04-26 22:41:17] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:17] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:18] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`. [2025-04-26 22:41:18] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:18] [SUCCESS] [OmnipathR] Loaded 3473 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:18] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellTalkDB,query_type=interactions] [2025-04-26 22:41:18] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:18] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:18] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`. [2025-04-26 22:41:18] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:18] [SUCCESS] [OmnipathR] Loaded 3473 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:18] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,query_type=interactions] [2025-04-26 22:41:18] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:18] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:18] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:18] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:18] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:18] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:18] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:18] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-26 22:41:18] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-26 22:41:18] [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] [2025-04-26 22:41:19] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-26 22:41:19] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.096401s from omnipathdb.org (162.5 Kb/s); Redirect: 0s, DNS look up: 0.000906s, Connection: 0.021402s, Pretransfer: 0.054635s, First byte at: 0.096105s [2025-04-26 22:41:19] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 26 Apr 2025 20:41:18 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 26 Apr 2025 21:41:18 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-26 22:41:19] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:19] [INFO] [OmnipathR] Cache item `641434253ee9e555515168e62fe5c7e36a8596c6` version 1: status changed from `unknown` to `started`. [2025-04-26 22:41:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`. [2025-04-26 22:41:19] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`. [2025-04-26 22:41:19] [INFO] [OmnipathR] Download ready [key=641434253ee9e555515168e62fe5c7e36a8596c6, version=1] [2025-04-26 22:41:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:19] [INFO] [OmnipathR] Cache item `641434253ee9e555515168e62fe5c7e36a8596c6` version 1: status changed from `started` to `ready`. [2025-04-26 22:41:19] [SUCCESS] [OmnipathR] Downloaded 1894 interactions. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:19] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:19] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,query_type=interactions] [2025-04-26 22:41:19] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:19] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:19] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:19] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`. [2025-04-26 22:41:19] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:19] [SUCCESS] [OmnipathR] Loaded 1894 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:19] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:19] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,query_type=interactions] [2025-04-26 22:41:19] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:19] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:19] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:19] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`. [2025-04-26 22:41:19] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:19] [SUCCESS] [OmnipathR] Loaded 1894 interactions from cache. Warning in (function (...) : 'function (...) { .Deprecated("post_translational") post_translational(...) }' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:19] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:19] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,fields=extra_attrs,query_type=interactions] [2025-04-26 22:41:19] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:19] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:20] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-26 22:41:20] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`. [2025-04-26 22:41:20] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-04-26 22:41:20] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-04-26 22:41:20] [SUCCESS] [OmnipathR] Loaded 1894 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:20] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellCall,query_type=interactions] [2025-04-26 22:41:20] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:20] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:20] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:20] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:20] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:20] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:20] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:20] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:20] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-26 22:41:20] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-26 22:41:20] [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] [2025-04-26 22:41:20] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-26 22:41:20] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.10604s from omnipathdb.org (147.7 Kb/s); Redirect: 0s, DNS look up: 0.001002s, Connection: 0.019432s, Pretransfer: 0.068619s, First byte at: 0.105743s [2025-04-26 22:41:20] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 26 Apr 2025 20:41:20 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 26 Apr 2025 21:41:20 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-26 22:41:20] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:20] [INFO] [OmnipathR] Cache item `af0debe0cdd22707b097cd388dfd1398cccb76c8` version 1: status changed from `unknown` to `started`. [2025-04-26 22:41:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`. [2025-04-26 22:41:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`. [2025-04-26 22:41:20] [INFO] [OmnipathR] Download ready [key=af0debe0cdd22707b097cd388dfd1398cccb76c8, version=1] [2025-04-26 22:41:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:20] [INFO] [OmnipathR] Cache item `af0debe0cdd22707b097cd388dfd1398cccb76c8` version 1: status changed from `started` to `ready`. [2025-04-26 22:41:20] [SUCCESS] [OmnipathR] Downloaded 1000 interactions. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:20] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellCall,query_type=interactions] [2025-04-26 22:41:20] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:20] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:21] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`. [2025-04-26 22:41:21] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:21] [SUCCESS] [OmnipathR] Loaded 1000 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:21] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellCall,query_type=interactions] [2025-04-26 22:41:21] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:21] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:21] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`. [2025-04-26 22:41:21] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:21] [SUCCESS] [OmnipathR] Loaded 1000 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:21] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellCall,query_type=interactions] [2025-04-26 22:41:21] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:21] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:21] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`. [2025-04-26 22:41:21] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:21] [SUCCESS] [OmnipathR] Loaded 1000 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:21] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=connectomeDB2020,query_type=interactions] [2025-04-26 22:41:21] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:21] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:21] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:21] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:21] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:21] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:21] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:21] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:21] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-26 22:41:21] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-26 22:41:21] [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] [2025-04-26 22:41:22] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-26 22:41:22] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.102199s from omnipathdb.org (153.3 Kb/s); Redirect: 0s, DNS look up: 0.000995s, Connection: 0.023029s, Pretransfer: 0.056793s, First byte at: 0.101872s [2025-04-26 22:41:22] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 26 Apr 2025 20:41:22 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 26 Apr 2025 21:41:22 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-26 22:41:22] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:22] [INFO] [OmnipathR] Cache item `d08eb76734c005daabb6eb3c832a55e330672026` version 1: status changed from `unknown` to `started`. [2025-04-26 22:41:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`. [2025-04-26 22:41:22] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`. [2025-04-26 22:41:22] [INFO] [OmnipathR] Download ready [key=d08eb76734c005daabb6eb3c832a55e330672026, version=1] [2025-04-26 22:41:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:22] [INFO] [OmnipathR] Cache item `d08eb76734c005daabb6eb3c832a55e330672026` version 1: status changed from `started` to `ready`. [2025-04-26 22:41:22] [SUCCESS] [OmnipathR] Downloaded 2313 interactions. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:22] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=connectomeDB2020,query_type=interactions] [2025-04-26 22:41:22] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:22] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:22] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:22] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`. [2025-04-26 22:41:22] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:22] [SUCCESS] [OmnipathR] Loaded 2313 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:22] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=connectomeDB2020,query_type=interactions] [2025-04-26 22:41:22] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:22] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:23] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:23] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`. [2025-04-26 22:41:23] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:23] [SUCCESS] [OmnipathR] Loaded 2313 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:23] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=connectomeDB2020,query_type=interactions] [2025-04-26 22:41:23] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:23] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:23] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:23] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`. [2025-04-26 22:41:23] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:23] [SUCCESS] [OmnipathR] Loaded 2313 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:23] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Guide2Pharma,query_type=interactions] [2025-04-26 22:41:23] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:23] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:23] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:23] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:23] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:23] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:23] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:23] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:23] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:23] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-26 22:41:23] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-26 22:41:23] [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] [2025-04-26 22:41:23] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-26 22:41:23] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.102025s from omnipathdb.org (153.6 Kb/s); Redirect: 0s, DNS look up: 0.001034s, Connection: 0.022986s, Pretransfer: 0.057784s, First byte at: 0.101662s [2025-04-26 22:41:23] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 26 Apr 2025 20:41:23 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 26 Apr 2025 21:41:23 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-26 22:41:24] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:24] [INFO] [OmnipathR] Cache item `11b0dd49c2e8541d966f577a8aacd52c71112987` version 1: status changed from `unknown` to `started`. [2025-04-26 22:41:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`. [2025-04-26 22:41:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`. [2025-04-26 22:41:24] [INFO] [OmnipathR] Download ready [key=11b0dd49c2e8541d966f577a8aacd52c71112987, version=1] [2025-04-26 22:41:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:24] [INFO] [OmnipathR] Cache item `11b0dd49c2e8541d966f577a8aacd52c71112987` version 1: status changed from `started` to `ready`. [2025-04-26 22:41:24] [SUCCESS] [OmnipathR] Downloaded 672 interactions. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:24] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Guide2Pharma,query_type=interactions] [2025-04-26 22:41:24] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:24] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:24] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:24] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:24] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`. [2025-04-26 22:41:24] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:24] [SUCCESS] [OmnipathR] Loaded 672 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:24] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Guide2Pharma,query_type=interactions] [2025-04-26 22:41:24] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:24] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:24] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:24] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:24] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`. [2025-04-26 22:41:24] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:24] [SUCCESS] [OmnipathR] Loaded 672 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:24] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Guide2Pharma,query_type=interactions] [2025-04-26 22:41:24] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:24] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:24] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:24] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:24] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`. [2025-04-26 22:41:24] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:24] [SUCCESS] [OmnipathR] Loaded 672 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:24] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Baccin2019,query_type=interactions] [2025-04-26 22:41:24] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:24] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:25] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:25] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:25] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:25] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:25] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:25] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:25] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-26 22:41:25] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-26 22:41:25] [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] [2025-04-26 22:41:25] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-26 22:41:25] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095048s from omnipathdb.org (164.8 Kb/s); Redirect: 0s, DNS look up: 0.000924s, Connection: 0.020744s, Pretransfer: 0.053972s, First byte at: 0.094748s [2025-04-26 22:41:25] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 26 Apr 2025 20:41:25 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 26 Apr 2025 21:41:25 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-26 22:41:25] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:25] [INFO] [OmnipathR] Cache item `f963006a054fdbb2fcbd5a63e731087e21fb4b31` version 1: status changed from `unknown` to `started`. [2025-04-26 22:41:25] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`. [2025-04-26 22:41:25] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`. [2025-04-26 22:41:25] [INFO] [OmnipathR] Download ready [key=f963006a054fdbb2fcbd5a63e731087e21fb4b31, version=1] [2025-04-26 22:41:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:25] [INFO] [OmnipathR] Cache item `f963006a054fdbb2fcbd5a63e731087e21fb4b31` version 1: status changed from `started` to `ready`. [2025-04-26 22:41:25] [SUCCESS] [OmnipathR] Downloaded 1676 interactions. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:25] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:25] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Baccin2019,query_type=interactions] [2025-04-26 22:41:25] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:25] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:25] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`. [2025-04-26 22:41:25] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:25] [SUCCESS] [OmnipathR] Loaded 1676 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:25] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:25] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Baccin2019,query_type=interactions] [2025-04-26 22:41:25] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:25] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:26] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:26] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:26] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`. [2025-04-26 22:41:26] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:26] [SUCCESS] [OmnipathR] Loaded 1676 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:26] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:26] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Baccin2019,query_type=interactions] [2025-04-26 22:41:26] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:26] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:26] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:26] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:26] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`. [2025-04-26 22:41:26] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:26] [SUCCESS] [OmnipathR] Loaded 1676 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:26] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:26] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Kirouac2010,query_type=interactions] [2025-04-26 22:41:26] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:26] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:26] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:26] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:26] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:26] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:26] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:26] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:26] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:26] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:26] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-26 22:41:26] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-26 22:41:26] [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] [2025-04-26 22:41:26] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-26 22:41:26] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.088886s from omnipathdb.org (176.3 Kb/s); Redirect: 0s, DNS look up: 0.000939s, Connection: 0.018784s, Pretransfer: 0.052422s, First byte at: 0.088584s [2025-04-26 22:41:26] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 26 Apr 2025 20:41:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 26 Apr 2025 21:41:26 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-26 22:41:26] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:26] [INFO] [OmnipathR] Cache item `e59c495f650b38ab64da89e0da5af6ff096901b8` version 1: status changed from `unknown` to `started`. [2025-04-26 22:41:27] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`. [2025-04-26 22:41:27] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`. [2025-04-26 22:41:27] [INFO] [OmnipathR] Download ready [key=e59c495f650b38ab64da89e0da5af6ff096901b8, version=1] [2025-04-26 22:41:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:27] [INFO] [OmnipathR] Cache item `e59c495f650b38ab64da89e0da5af6ff096901b8` version 1: status changed from `started` to `ready`. [2025-04-26 22:41:27] [SUCCESS] [OmnipathR] Downloaded 152 interactions. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:27] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Kirouac2010,query_type=interactions] [2025-04-26 22:41:27] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:27] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:27] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`. [2025-04-26 22:41:27] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:27] [SUCCESS] [OmnipathR] Loaded 152 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:27] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Kirouac2010,query_type=interactions] [2025-04-26 22:41:27] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:27] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:27] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`. [2025-04-26 22:41:27] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:27] [SUCCESS] [OmnipathR] Loaded 152 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:27] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Kirouac2010,query_type=interactions] [2025-04-26 22:41:27] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:27] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:27] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`. [2025-04-26 22:41:27] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:27] [SUCCESS] [OmnipathR] Loaded 152 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:27] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Ramilowski2015,query_type=interactions] [2025-04-26 22:41:27] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:27] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:27] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:27] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:27] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:27] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:27] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:27] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:27] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-26 22:41:27] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-26 22:41:28] [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] [2025-04-26 22:41:28] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-26 22:41:28] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.09266s from omnipathdb.org (169.1 Kb/s); Redirect: 0s, DNS look up: 0.000923s, Connection: 0.020338s, Pretransfer: 0.053234s, First byte at: 0.092366s [2025-04-26 22:41:28] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 26 Apr 2025 20:41:28 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 26 Apr 2025 21:41:28 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-26 22:41:28] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:28] [INFO] [OmnipathR] Cache item `78bff68f8413d6211070111914db1b8b2b98ad54` version 1: status changed from `unknown` to `started`. [2025-04-26 22:41:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`. [2025-04-26 22:41:28] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`. [2025-04-26 22:41:28] [INFO] [OmnipathR] Download ready [key=78bff68f8413d6211070111914db1b8b2b98ad54, version=1] [2025-04-26 22:41:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:28] [INFO] [OmnipathR] Cache item `78bff68f8413d6211070111914db1b8b2b98ad54` version 1: status changed from `started` to `ready`. [2025-04-26 22:41:28] [SUCCESS] [OmnipathR] Downloaded 1946 interactions. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:28] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Ramilowski2015,query_type=interactions] [2025-04-26 22:41:28] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:28] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:28] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:28] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`. [2025-04-26 22:41:28] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:28] [SUCCESS] [OmnipathR] Loaded 1946 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:28] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Ramilowski2015,query_type=interactions] [2025-04-26 22:41:28] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:28] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:29] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`. [2025-04-26 22:41:29] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:29] [SUCCESS] [OmnipathR] Loaded 1946 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:29] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Ramilowski2015,query_type=interactions] [2025-04-26 22:41:29] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:29] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:29] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`. [2025-04-26 22:41:29] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:29] [SUCCESS] [OmnipathR] Loaded 1946 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:29] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=scConnect,query_type=interactions] [2025-04-26 22:41:29] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:29] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:29] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:29] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-26 22:41:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-26 22:41:29] [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] [2025-04-26 22:41:29] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-26 22:41:29] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.087521s from omnipathdb.org (179 Kb/s); Redirect: 0s, DNS look up: 0.00089s, Connection: 0.01849s, Pretransfer: 0.051908s, First byte at: 0.087225s [2025-04-26 22:41:29] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 26 Apr 2025 20:41:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 26 Apr 2025 21:41:29 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-26 22:41:29] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:29] [INFO] [OmnipathR] Cache item `4d3e24d35f89a47701b9f0e9d5da90ec2aee0874` version 1: status changed from `unknown` to `started`. [2025-04-26 22:41:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`. [2025-04-26 22:41:29] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`. [2025-04-26 22:41:29] [INFO] [OmnipathR] Download ready [key=4d3e24d35f89a47701b9f0e9d5da90ec2aee0874, version=1] [2025-04-26 22:41:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-26 22:41:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:30] [INFO] [OmnipathR] Cache item `4d3e24d35f89a47701b9f0e9d5da90ec2aee0874` version 1: status changed from `started` to `ready`. [2025-04-26 22:41:30] [SUCCESS] [OmnipathR] Downloaded 479 interactions. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:30] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=scConnect,query_type=interactions] [2025-04-26 22:41:30] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:30] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:30] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:30] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:30] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`. [2025-04-26 22:41:30] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:30] [SUCCESS] [OmnipathR] Loaded 479 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:30] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=scConnect,query_type=interactions] [2025-04-26 22:41:30] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:30] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:30] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:30] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:30] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`. [2025-04-26 22:41:30] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:30] [SUCCESS] [OmnipathR] Loaded 479 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:30] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=scConnect,query_type=interactions] [2025-04-26 22:41:30] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:30] [TRACE] [OmnipathR] Orthology targets: Warning in readLines(con = path, encoding = encoding) : incomplete final line found on 'https://omnipathdb.org/resources' [2025-04-26 22:41:30] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-26 22:41:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-26 22:41:30] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:30] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`. [2025-04-26 22:41:30] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-26 22:41:30] [SUCCESS] [OmnipathR] Loaded 479 interactions from cache. Warning in import_post_translational_interactions(resources = resource) : 'import_post_translational_interactions' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-04-26 22:41:30] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-26 22:41:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=talklr,query_type=interactions] [2025-04-26 22:41:30] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-26 22:41:30] [TRACE] [OmnipathR] Orthology targets: Warning in file(con, "r") : URL 'https://omnipathdb.org/resources': Timeout of 60 seconds was reached Error in `map()`: ℹ In index: 12. Caused by error in `map()`: ℹ In index: 1. Caused by error in `file()`: ! cannot open the connection to 'https://omnipathdb.org/resources' Backtrace: ▆ 1. ├─OmnipathR::curated_ligrec_stats() 2. │ └─... %>% unnest_wider(col = data) 3. ├─OmnipathR:::unnest_wider(., col = data) 4. │ └─base::eval(call[[tbl_name]], parent.frame()) 5. │ └─base::eval(call[[tbl_name]], parent.frame()) 6. ├─tibble::tibble(resource = names(.), data = .) 7. │ └─tibble:::tibble_quos(xs, .rows, .name_repair) 8. │ └─rlang::eval_tidy(xs[[j]], mask) 9. ├─rlang::set_names(map(., stats_one_resource, curated), .) 10. ├─purrr::map(., stats_one_resource, curated) 11. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 12. │ ├─purrr:::with_indexed_errors(...) 13. │ │ └─base::withCallingHandlers(...) 14. │ ├─purrr:::call_with_cleanup(...) 15. │ └─OmnipathR (local) .f(.x[[i]], ...) 16. │ └─... %>% ... 17. ├─purrr::map(., nrow) 18. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 19. │ └─purrr:::vctrs_vec_compat(.x, .purrr_user_env) 20. ├─rlang::set_names(...) 21. ├─purrr::map(...) 22. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 23. │ ├─purrr:::with_indexed_errors(...) 24. │ │ └─base::withCallingHandlers(...) 25. │ ├─purrr:::call_with_cleanup(...) 26. │ └─OmnipathR (local) .f(.x[[i]], ...) 27. │ └─get(sprintf("%s_one_resource", field))(resource, curated) 28. │ └─OmnipathR::import_post_translational_interactions(resources = resource) 29. │ └─OmnipathR::post_translational(...) 30. │ ├─rlang::exec(omnipath_query, !!!args) 31. │ └─OmnipathR (local) ``(resources = "talklr", query_type = "interactions", datasets = ``) 32. │ └─environment() %>% as.list %>% c(list(...)) %>% ... 33. ├─OmnipathR:::omnipath_check_param(.) 34. │ └─OmnipathR::resources(param$query_type) 35. │ └─OmnipathR:::safe_json(path = resources_url) 36. │ └─base::readLines(con = path, encoding = encoding) 37. │ └─base::file(con, "r") 38. └─base::.handleSimpleError(...) 39. └─purrr (local) h(simpleError(msg, call)) 40. └─cli::cli_abort(...) 41. └─rlang::abort(...) Execution halted * 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 ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-26_2228/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2025-04-26 22:51:24 CEST ]