[ Started: 2025-04-16 23:04:44 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-3.21/2025-04-16_2255/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
[2025-04-16 23:05:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-16 23:05:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 23:05:12] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-04-16 23:05:12] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-04-16 21:03:38 UTC; omnipath
[2025-04-16 23:05:12] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-04-16 23:05:12] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-16 21:04:46 UTC; unix
[2025-04-16 23:05:12] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-04-16 23:05:12] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-04-16 23:05:12] [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=2025-04-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-04-16 23:05:13] [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]
[2025-04-16 23:05:13] [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 3.6.4(2025-02-13); 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(2025-04-16); 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)
[2025-04-16 23:05:13] [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
[2025-04-16 23:05:13] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-04-16 23:05:13] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-04-16 23:05:13] [TRACE]   [OmnipathR] Contains 1 files.
[2025-04-16 23:05:13] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-04-16 23:05:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-16 23:05:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 23:05:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-04-16 23:05:13] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-04-16 23:05:13] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-16_2255/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-16 23:05:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 23:05:13] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-16_2255/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-16 23:05:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 23:05:13] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-16_2255/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-16 23:05:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 23:05:13] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-16_2255/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-16 23:05:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 23:05:13] [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
[2025-04-16 23:05:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-16 23:05:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 23:05:22] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-04-16 23:05:22] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-04-16 21:03:38 UTC; omnipath
[2025-04-16 23:05:22] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-04-16 23:05:22] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-16 21:04:46 UTC; unix
[2025-04-16 23:05:22] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-04-16 23:05:22] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-04-16 23:05:23] [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=2025-04-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-04-16 23:05:23] [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]
[2025-04-16 23:05:23] [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 3.6.4(2025-02-13); 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(2025-04-16); 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)
[2025-04-16 23:05:23] [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
[2025-04-16 23:05:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-04-16 23:05:23] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-04-16 23:05:23] [TRACE]   [OmnipathR] Contains 1 files.
[2025-04-16 23:05:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-04-16 23:05:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-16 23:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 23:05:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-04-16 23:05:23] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-04-16 23:05:23] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-16_2255/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-16 23:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 23:05:23] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-16_2255/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-16 23:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 23:05:23] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-16_2255/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-16 23:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 23:05:23] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-04-16_2255/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-16 23:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 23:05:23] [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: all_uniprots
> ### Title: A table with all UniProt records
> ### Aliases: all_uniprots
> 
> ### ** Examples
> 
> human_swissprot_entries <- all_uniprots(fields = 'id')
[2025-04-16 23:05:47] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-04-16 23:05:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-16 23:05:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 23:05:47] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-04-16 23:05:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-16 23:05:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 23:05:47] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-04-16 23:05:47] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-04-16 23:05:47] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-04-16 23:05:47] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-04-16 23:05:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-04-16 23:05:47] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-04-16 23:05:47] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-04-16 23:05:47] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-16 23:05:47] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-16 23:05:47] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-04-16 23:05:47] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-04-16 23:05:47] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-04-16 23:05:47] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-04-16 23:05:47] [TRACE]   [OmnipathR] Downloaded 30.7 Kb in 0.228014s from www.ensembl.org (134.6 Kb/s); Redirect: 0s, DNS look up: 0.009448s, Connection: 0.027986s, Pretransfer: 0.102408s, First byte at: 0.206164s
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Wed, 16 Apr 2025 21:05:47 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31436; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Thu, 17 Apr 2025 21:05:47 GMT; Set-cookie: ENSEMBL_HINX_SESSION=bc7e21b84c705a1b0c18c70c684f35ab0c60127ec160539b9f2d37bc; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Thu, 17 Apr 2025 21:05:47 GMT; Set-cookie: ENSEMBL_HINX_SESSION=bc7e21b84c705a1b0c18c70c684f35ab0c60127ec160539b9f2d37bc; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-35.ebi.ac.uk
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Response headers: [Date=Wed, 16 Apr 2025 21:05:47 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31436,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Thu, 17 Apr 2025 21:05:47 GMT,Set-cookie=ENSEMBL_HINX_SESSION=bc7e21b84c705a1b0c18c70c684f35ab0c60127ec160539b9f2d37bc; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Thu, 17 Apr 2025 21:05:47 GMT,Set-cookie=ENSEMBL_HINX_SESSION=bc7e21b84c705a1b0c18c70c684f35ab0c60127ec160539b9f2d37bc; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-35.ebi.ac.uk]
[2025-04-16 23:05:48] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 23:05:48] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-04-16 23:05:48] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 23:05:48] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-04-16 23:05:48] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.065496s from omabrowser.org (132.7 Kb/s); Redirect: 0s, DNS look up: 0.00099s, Connection: 0.012526s, Pretransfer: 0.050641s, First byte at: 0.065351s
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 16 Apr 2025 21:05:48 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-04-16 23:05:48] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 23:05:48] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-04-16 23:05:48] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`.
[2025-04-16 23:05:48] [INFO]    [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`.
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 23:05:48] [INFO]    [OmnipathR] Cache item `80e22dce504c916061293773267b3f34dea718f3` version 1: status changed from `unknown` to `started`.
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/80e22dce504c916061293773267b3f34dea718f3-1.rds`.
[2025-04-16 23:05:48] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-16 23:05:48] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-16 23:05:50] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-04-16 23:05:50] [TRACE]   [OmnipathR] Downloaded 27 bytes in 1.735505s from rest.uniprot.org (15 bytes/s); Redirect: 0s, DNS look up: 0.007952s, Connection: 0.026655s, Pretransfer: 0.098384s, First byte at: 1.73544s
[2025-04-16 23:05:50] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 05-February-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 16 Apr 2025 21:05:50 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_01; access-control-allow-origin: *; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 05-February-2025
[2025-04-16 23:06:50] [WARN]    [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true` (attempt 1/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
[2025-04-16 23:06:55] [TRACE]   [OmnipathR] Attempt 2/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`
[2025-04-16 23:06:55] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-16 23:06:55] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-16 23:06:55] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-16 23:06:57] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-04-16 23:06:57] [TRACE]   [OmnipathR] Downloaded 27 bytes in 1.973355s from rest.uniprot.org (13 bytes/s); Redirect: 0s, DNS look up: 0.007952s, Connection: 0.026604s, Pretransfer: 0.094439s, First byte at: 1.973291s
[2025-04-16 23:06:57] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 05-February-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 16 Apr 2025 21:06:57 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_01; access-control-allow-origin: *; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 05-February-2025
[2025-04-16 23:08:55] [WARN]    [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true` (attempt 2/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
[2025-04-16 23:09:00] [TRACE]   [OmnipathR] Attempt 3/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`
[2025-04-16 23:09:00] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-16 23:09:00] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-16 23:09:00] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-16 23:09:02] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-04-16 23:09:02] [TRACE]   [OmnipathR] Downloaded 27 bytes in 1.524348s from rest.uniprot.org (17 bytes/s); Redirect: 0s, DNS look up: 0.001154s, Connection: 0.019355s, Pretransfer: 0.071202s, First byte at: 1.524233s
[2025-04-16 23:09:02] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 05-February-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 16 Apr 2025 21:09:02 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_01; access-control-allow-origin: *; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 05-February-2025
[2025-04-16 23:10:54] [ERROR]   [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true` (attempt 3/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
[2025-04-16 23:10:54] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-04-16 21:03:38 UTC; omnipath
[2025-04-16 23:10:54] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-04-16 23:10:54] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-16 21:04:46 UTC; unix
[2025-04-16 23:10:54] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-04-16 23:10:54] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-04-16 23:10:54] [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; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-04-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-04-16 23:10:54] [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]
[2025-04-16 23:10:54] [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 3.6.4(2025-02-13); 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(2025-04-16); 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); selectr 0.4-2(2019-11-20); 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); vroom 1.6.5(2023-12-05); 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)
[2025-04-16 23:10:54] [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
Error in (function (con, what, n = 1L, size = NA_integer_, signed = TRUE,  : 
  Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
Calls: all_uniprots ... omnipath_cache_save -> saveRDS -> exec -> <Anonymous>
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-3.21/2025-04-16_2255/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2025-04-16 23:19:48 CEST ]