| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-08-28 11:39 -0400 (Thu, 28 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1484/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.16.1 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: OmnipathR |
| Version: 3.16.1 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings OmnipathR_3.16.1.tar.gz |
| StartedAt: 2025-08-28 01:32:39 -0400 (Thu, 28 Aug 2025) |
| EndedAt: 2025-08-28 02:00:57 -0400 (Thu, 28 Aug 2025) |
| EllapsedTime: 1697.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings OmnipathR_3.16.1.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.16.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 ... OK
* 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
[2025-08-28 01:33:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-28 01:33:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-28 01:33:09] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-08-28 01:33:09] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-28 01:33:09] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-27
[2025-08-28 01:33:09] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-27 19:09:36 UTC; unix
[2025-08-28 01:33:09] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.1
[2025-08-28 01:33:09] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-08-28 01:33:10] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-28; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-08-28 01:33:10] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; 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=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-08-28 01:33:10] [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 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); 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 3.16.1(2025-08-27); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); 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 2.4.3(2025-08-20); 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 3.3.0(2025-06-08); 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); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-28 01:33:10] [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
[2025-08-28 01:33:10] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-28 01:33:10] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-08-28 01:33:10] [TRACE] [OmnipathR] Contains 1 files.
[2025-08-28 01:33:10] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-28 01:33:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-28 01:33:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-28 01:33:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-08-28 01:33:10] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-28 01:33:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-28 01:33:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-28 01:33:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-28 01:33:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-28 01:33:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-28 01:33:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-28 01:33:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-28 01:33:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-28 01:33:10] [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
[2025-08-28 01:33:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-28 01:33:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-28 01:33:27] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-08-28 01:33:27] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-28 01:33:27] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-27
[2025-08-28 01:33:27] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-27 19:09:36 UTC; unix
[2025-08-28 01:33:27] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.1
[2025-08-28 01:33:27] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-08-28 01:33:27] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-28; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-08-28 01:33:28] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; 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=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-08-28 01:33:28] [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 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); 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 3.16.1(2025-08-27); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); 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 2.4.3(2025-08-20); 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 3.3.0(2025-06-08); 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); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-28 01:33:28] [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
[2025-08-28 01:33:28] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-28 01:33:28] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-08-28 01:33:28] [TRACE] [OmnipathR] Contains 1 files.
[2025-08-28 01:33:28] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-28 01:33:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-28 01:33:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-28 01:33:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-08-28 01:33:28] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-28 01:33:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-28 01:33:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-28 01:33:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-28 01:33:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-28 01:33:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-28 01:33:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-28 01:33:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-28 01:33:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-28 01:33:28] [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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: organism_for
> ### Title: Make sure the resource supports the organism and it has the ID
> ### Aliases: organism_for
>
> ### ** Examples
>
> organism_for(10116, 'chalmers-gem')
Error in organism_for(10116, "chalmers-gem") :
Organism `10116` (common_name: `Norway rat - BN/NHsdMcwi`; common_name: `Norway rat - BN/NHsdMcwi`) is not supported by resource `chalmers-gem`. Supported organisms: Human, Mouse, Rat, Zebrafish, Drosophila melanogaster (Fruit fly), Caenorhabditis elegans (PRJNA13758), Caenorhabditis elegans (Nematode, N2).
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 89.771 0.037 91.010
omnipath-interactions 53.485 3.455 116.304
curated_ligrec_stats 39.556 2.853 106.337
nichenet_gr_network_omnipath 28.722 1.054 42.054
filter_extra_attrs 22.256 5.139 28.091
nichenet_signaling_network_omnipath 20.318 1.154 29.393
go_annot_download 16.619 1.381 19.093
giant_component 15.545 0.952 23.196
has_extra_attrs 12.843 1.687 20.703
extra_attrs_to_cols 12.621 1.347 13.985
extra_attr_values 11.473 1.422 16.848
omnipath_for_cosmos 11.692 0.593 21.401
find_all_paths 7.872 0.198 8.199
filter_by_resource 7.601 0.270 11.786
extra_attrs 6.603 1.051 7.689
curated_ligand_receptor_interactions 6.543 0.680 17.732
filter_intercell 6.404 0.447 17.115
hpo_download 5.162 0.251 7.774
kegg_conv 2.510 0.206 14.054
all_uniprots 1.681 0.152 13.326
ensembl_id_mapping_table 1.456 0.119 9.458
metalinksdb_sqlite 1.145 0.284 9.860
kegg_rm_prefix 1.284 0.050 6.941
kegg_link 1.119 0.141 6.333
kegg_picture 1.198 0.040 6.009
* 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
‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.16.1’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2025-08-27 15:09:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-27 15:09:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-27 15:09:50] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-08-27 15:09:50] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-27 15:09:50] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-27 [2025-08-27 15:09:50] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-27 19:09:36 UTC; unix [2025-08-27 15:09:50] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.1 [2025-08-27 15:09:50] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-08-27 15:09:50] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-27; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto] [2025-08-27 15:09:50] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; 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=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-08-27 15:09:50] [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 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); 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 3.16.1(2025-08-27); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); 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 2.4.3(2025-08-20); 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 3.3.0(2025-06-08); 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); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-27 15:09:50] [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 [2025-08-27 15:09:50] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-27 15:09:50] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-08-27 15:09:50] [TRACE] [OmnipathR] Contains 8 files. [2025-08-27 15:09:50] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-27 15:09:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-27 15:09:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-27 15:09:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-08-27 15:09:50] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-08-27 15:09:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-27 15:09:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-27 15:09:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-27 15:09:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-27 15:09:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-27 15:09:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-27 15:09:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-27 15:09:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-27 15:09:50] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-08-27 15:09:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-27 15:09:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-27 15:09:52] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-08-27 15:09:52] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-27 15:09:52] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-27 [2025-08-27 15:09:52] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-27 19:09:36 UTC; unix [2025-08-27 15:09:52] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.1 [2025-08-27 15:09:52] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-08-27 15:09:53] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-27; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto] [2025-08-27 15:09:53] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; 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=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-08-27 15:09:53] [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 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); 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 3.16.1(2025-08-27); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); 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 2.4.3(2025-08-20); 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 3.3.0(2025-06-08); 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); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-27 15:09:53] [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 [2025-08-27 15:09:53] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-27 15:09:53] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-08-27 15:09:53] [TRACE] [OmnipathR] Contains 1 files. [2025-08-27 15:09:53] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-27 15:09:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-27 15:09:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-27 15:09:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-08-27 15:09:53] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-08-27 15:09:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-27 15:09:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-27 15:09:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-27 15:09:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-27 15:09:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-27 15:09:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-27 15:09:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-27 15:09:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-27 15:09:53] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #!/usr/bin/env Rscript
>
> #
> # This file is part of the `OmnipathR` R package
> #
> # Copyright
> # 2018-2024
> # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> # File author(s): Alberto Valdeolivas
> # Dénes Türei (turei.denes@gmail.com)
> # Attila Gábor
> #
> # Distributed under the MIT (Expat) License.
> # See accompanying file `LICENSE` or find a copy at
> # https://directory.fsf.org/wiki/License:Expat
> #
> # Website: https://r.omnipathdb.org/
> # Git repo: https://github.com/saezlab/OmnipathR
> #
>
>
> library(testthat)
> library(OmnipathR)
[2025-08-28 01:46:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-28 01:46:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-28 01:46:18] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-08-28 01:46:18] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-28 01:46:18] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-27
[2025-08-28 01:46:18] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-27 19:09:36 UTC; unix
[2025-08-28 01:46:18] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.1
[2025-08-28 01:46:18] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-08-28 01:46:18] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-28; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-08-28 01:46:18] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; 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=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-08-28 01:46:18] [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); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); 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 3.16.1(2025-08-27); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); 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 2.4.3(2025-08-20); 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); testthat 3.2.3(2025-01-13); tibble 3.3.0(2025-06-08); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-28 01:46:18] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-08-28 01:46:18] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-28 01:46:18] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-08-28 01:46:18] [TRACE] [OmnipathR] Contains 3 files.
[2025-08-28 01:46:18] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-28 01:46:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-28 01:46:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-28 01:46:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-08-28 01:46:18] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-28 01:46:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-28 01:46:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-28 01:46:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-28 01:46:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-28 01:46:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-28 01:46:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-28 01:46:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-28 01:46:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-28 01:46:19] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 38 ]
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 38 ]
>
> proc.time()
user system elapsed
19.458 1.686 61.910
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.012 | 0.003 | 0.016 | |
| all_uniprots | 1.681 | 0.152 | 13.326 | |
| ancestors | 0.007 | 0.001 | 0.008 | |
| annotated_network | 1.462 | 0.160 | 4.833 | |
| annotation_categories | 89.771 | 0.037 | 91.010 | |
| annotation_resources | 0.167 | 0.009 | 0.670 | |
| annotations | 0.589 | 0.031 | 1.544 | |
| biomart_query | 1.096 | 0.068 | 3.701 | |
| bioplex1 | 0.008 | 0.001 | 0.009 | |
| bioplex2 | 0.007 | 0.001 | 0.008 | |
| bioplex3 | 0.007 | 0.001 | 0.008 | |
| bioplex_all | 0.007 | 0.001 | 0.008 | |
| bioplex_hct116_1 | 0.008 | 0.000 | 0.007 | |
| bma_motif_es | 0.596 | 0.048 | 1.530 | |
| bma_motif_vs | 0.190 | 0.008 | 0.780 | |
| chalmers_gem | 0.007 | 0.002 | 0.008 | |
| chalmers_gem_id_mapping_table | 0.008 | 0.000 | 0.008 | |
| chalmers_gem_id_type | 0.001 | 0.001 | 0.002 | |
| chalmers_gem_metabolites | 0.005 | 0.003 | 0.007 | |
| chalmers_gem_network | 0.007 | 0.001 | 0.008 | |
| chalmers_gem_raw | 0.008 | 0.000 | 0.007 | |
| chalmers_gem_reactions | 0.007 | 0.000 | 0.008 | |
| common_name | 0.027 | 0.002 | 0.030 | |
| complex_genes | 0.735 | 0.033 | 2.393 | |
| complex_resources | 0.157 | 0.002 | 0.697 | |
| complexes | 0.248 | 0.008 | 0.774 | |
| consensuspathdb_download | 0.000 | 0.000 | 0.001 | |
| consensuspathdb_raw_table | 0.009 | 0.001 | 0.009 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 6.543 | 0.680 | 17.732 | |
| curated_ligrec_stats | 39.556 | 2.853 | 106.337 | |
| database_summary | 1.436 | 0.101 | 2.726 | |
| descendants | 0.007 | 0.002 | 0.009 | |
| ensembl_dataset | 0.011 | 0.001 | 0.011 | |
| ensembl_id_mapping_table | 1.456 | 0.119 | 9.458 | |
| ensembl_id_type | 0.002 | 0.000 | 0.002 | |
| ensembl_name | 0.059 | 0.002 | 0.062 | |
| ensembl_organisms | 0.118 | 0.010 | 0.128 | |
| ensembl_organisms_raw | 0.096 | 0.013 | 0.109 | |
| ensembl_orthology | 0.000 | 0.001 | 0.001 | |
| enzsub_graph | 2.082 | 0.106 | 4.583 | |
| enzsub_resources | 0.146 | 0.004 | 0.725 | |
| enzyme_substrate | 0.967 | 0.021 | 1.574 | |
| evex_download | 0.008 | 0.000 | 0.008 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 11.473 | 1.422 | 16.848 | |
| extra_attrs | 6.603 | 1.051 | 7.689 | |
| extra_attrs_to_cols | 12.621 | 1.347 | 13.985 | |
| filter_by_resource | 7.601 | 0.270 | 11.786 | |
| filter_extra_attrs | 22.256 | 5.139 | 28.091 | |
| filter_intercell | 6.404 | 0.447 | 17.115 | |
| filter_intercell_network | 0.019 | 0.001 | 0.019 | |
| find_all_paths | 7.872 | 0.198 | 8.199 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0.001 | 0.000 | 0.000 | |
| get_ontology_db | 0.016 | 0.002 | 0.018 | |
| giant_component | 15.545 | 0.952 | 23.196 | |
| go_annot_download | 16.619 | 1.381 | 19.093 | |
| go_annot_slim | 0.001 | 0.000 | 0.000 | |
| go_ontology_download | 0.016 | 0.002 | 0.018 | |
| guide2pharma_download | 0.017 | 0.001 | 0.017 | |
| harmonizome_download | 0.016 | 0.001 | 0.018 | |
| has_extra_attrs | 12.843 | 1.687 | 20.703 | |
| hmdb_id_mapping_table | 0.017 | 0.002 | 0.018 | |
| hmdb_id_type | 0.005 | 0.000 | 0.004 | |
| hmdb_metabolite_fields | 0.000 | 0.001 | 0.002 | |
| hmdb_protein_fields | 0.000 | 0.000 | 0.001 | |
| hmdb_table | 0.016 | 0.004 | 0.019 | |
| homologene_download | 0.015 | 0.003 | 0.026 | |
| homologene_raw | 0.051 | 0.001 | 0.101 | |
| homologene_uniprot_orthology | 0.026 | 0.004 | 0.058 | |
| hpo_download | 5.162 | 0.251 | 7.774 | |
| htridb_download | 0.024 | 0.003 | 0.051 | |
| id_translation_resources | 0.001 | 0.000 | 0.001 | |
| id_types | 0.107 | 0.007 | 0.146 | |
| inbiomap_download | 0.000 | 0.000 | 0.001 | |
| inbiomap_raw | 0.001 | 0.000 | 0.000 | |
| interaction_datasets | 1.864 | 0.046 | 2.928 | |
| interaction_graph | 0.850 | 0.029 | 1.354 | |
| interaction_resources | 0.275 | 0.009 | 0.964 | |
| interaction_types | 0.085 | 0.004 | 0.090 | |
| intercell | 0.954 | 0.057 | 1.962 | |
| intercell_categories | 0.674 | 0.035 | 0.891 | |
| intercell_consensus_filter | 1.448 | 0.185 | 3.424 | |
| intercell_generic_categories | 0.046 | 0.003 | 0.049 | |
| intercell_network | 0.008 | 0.002 | 0.010 | |
| intercell_resources | 0.174 | 0.010 | 0.674 | |
| intercell_summary | 0.068 | 0.025 | 0.093 | |
| is_ontology_id | 0.000 | 0.001 | 0.001 | |
| is_swissprot | 0.037 | 0.006 | 0.043 | |
| is_trembl | 0.036 | 0.006 | 0.041 | |
| is_uniprot | 0.013 | 0.002 | 0.015 | |
| kegg_api_templates | 0.000 | 0.005 | 0.006 | |
| kegg_conv | 2.510 | 0.206 | 14.054 | |
| kegg_databases | 0.000 | 0.001 | 0.000 | |
| kegg_ddi | 1.265 | 0.070 | 3.658 | |
| kegg_find | 1.179 | 0.056 | 3.057 | |
| kegg_info | 0.019 | 0.002 | 0.035 | |
| kegg_link | 1.119 | 0.141 | 6.333 | |
| kegg_list | 0.796 | 0.049 | 1.714 | |
| kegg_open | 0.012 | 0.002 | 0.014 | |
| kegg_operations | 0.000 | 0.001 | 0.001 | |
| kegg_organism_codes | 0.029 | 0.110 | 0.138 | |
| kegg_organisms | 0.031 | 0.005 | 0.036 | |
| kegg_pathway_annotations | 0.000 | 0.000 | 0.001 | |
| kegg_pathway_download | 0.015 | 0.002 | 0.017 | |
| kegg_pathway_list | 0.013 | 0.001 | 0.014 | |
| kegg_pathways_download | 0.000 | 0.000 | 0.001 | |
| kegg_picture | 1.198 | 0.040 | 6.009 | |
| kegg_process | 0.019 | 0.001 | 0.020 | |
| kegg_query | 0.008 | 0.000 | 0.008 | |
| kegg_request | 0.061 | 0.003 | 0.064 | |
| kegg_rm_prefix | 1.284 | 0.050 | 6.941 | |
| latin_name | 0.095 | 0.003 | 0.099 | |
| load_db | 0.130 | 0.009 | 0.138 | |
| metalinksdb_sqlite | 1.145 | 0.284 | 9.860 | |
| metalinksdb_table | 0.216 | 0.023 | 0.239 | |
| metalinksdb_tables | 0.017 | 0.001 | 0.019 | |
| ncbi_taxid | 0.064 | 0.002 | 0.065 | |
| nichenet_build_model | 0.001 | 0.000 | 0.000 | |
| nichenet_expression_data | 0.009 | 0.000 | 0.009 | |
| nichenet_gr_network | 0.023 | 0.001 | 0.024 | |
| nichenet_gr_network_evex | 0.008 | 0.000 | 0.008 | |
| nichenet_gr_network_harmonizome | 0.009 | 0.000 | 0.008 | |
| nichenet_gr_network_htridb | 0.008 | 0.001 | 0.008 | |
| nichenet_gr_network_omnipath | 28.722 | 1.054 | 42.054 | |
| nichenet_gr_network_pathwaycommons | 0.015 | 0.000 | 0.015 | |
| nichenet_gr_network_regnetwork | 0.013 | 0.000 | 0.013 | |
| nichenet_gr_network_remap | 0.010 | 0.002 | 0.012 | |
| nichenet_gr_network_trrust | 0.011 | 0.000 | 0.011 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0 | 0 | 0 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.032 | 0.001 | 0.033 | |
| nichenet_lr_network_guide2pharma | 0.012 | 0.002 | 0.014 | |
| nichenet_lr_network_omnipath | 0.039 | 0.001 | 0.039 | |
| nichenet_lr_network_ramilowski | 0.013 | 0.001 | 0.014 | |
| nichenet_main | 0.000 | 0.000 | 0.001 | |
| nichenet_networks | 0.055 | 0.004 | 0.059 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.102 | 0.001 | 0.103 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.031 | 0.003 | 0.034 | |
| nichenet_signaling_network_cpdb | 0.009 | 0.002 | 0.011 | |
| nichenet_signaling_network_evex | 0.010 | 0.001 | 0.011 | |
| nichenet_signaling_network_harmonizome | 0.010 | 0.001 | 0.011 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 20.318 | 1.154 | 29.393 | |
| nichenet_signaling_network_pathwaycommons | 0.021 | 0.000 | 0.021 | |
| nichenet_signaling_network_vinayagam | 0.016 | 0.003 | 0.019 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0.001 | 0.000 | 0.001 | |
| obo_parser | 0.152 | 0.014 | 0.367 | |
| oma_code | 0.051 | 0.000 | 0.090 | |
| oma_organisms | 0.099 | 0.015 | 0.114 | |
| oma_pairwise | 0.015 | 0.002 | 0.016 | |
| oma_pairwise_genesymbols | 0.015 | 0.000 | 0.014 | |
| oma_pairwise_translated | 0.010 | 0.004 | 0.014 | |
| omnipath-interactions | 53.485 | 3.455 | 116.304 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.016 | 0.002 | 0.032 | |
| omnipath_cache_clean_db | 0.265 | 0.016 | 0.310 | |
| omnipath_cache_download_ready | 0.884 | 0.087 | 1.311 | |
| omnipath_cache_filter_versions | 0.283 | 0.019 | 0.392 | |
| omnipath_cache_get | 0.158 | 0.014 | 0.241 | |
| omnipath_cache_key | 0.002 | 0.001 | 0.002 | |
| omnipath_cache_latest_or_new | 0.115 | 0.015 | 0.187 | |
| omnipath_cache_load | 1.068 | 0.077 | 3.540 | |
| omnipath_cache_move_in | 0.360 | 0.049 | 0.572 | |
| omnipath_cache_remove | 0.206 | 0.050 | 0.321 | |
| omnipath_cache_save | 0.476 | 0.061 | 0.773 | |
| omnipath_cache_search | 0.001 | 0.000 | 0.001 | |
| omnipath_cache_set_ext | 0.175 | 0.026 | 0.282 | |
| omnipath_cache_update_status | 0.211 | 0.029 | 0.371 | |
| omnipath_cache_wipe | 0.000 | 0.000 | 0.001 | |
| omnipath_config_path | 0.001 | 0.001 | 0.006 | |
| omnipath_for_cosmos | 11.692 | 0.593 | 21.401 | |
| omnipath_load_config | 0.000 | 0.001 | 0.000 | |
| omnipath_log | 0.000 | 0.000 | 0.001 | |
| omnipath_logfile | 0.001 | 0.000 | 0.002 | |
| omnipath_msg | 0.003 | 0.002 | 0.005 | |
| omnipath_query | 3.319 | 0.130 | 3.445 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.022 | 0.003 | 0.026 | |
| omnipath_set_console_loglevel | 0.003 | 0.000 | 0.004 | |
| omnipath_set_logfile_loglevel | 0.003 | 0.000 | 0.003 | |
| omnipath_set_loglevel | 0.002 | 0.000 | 0.001 | |
| omnipath_show_db | 0.056 | 0.005 | 0.061 | |
| omnipath_unlock_cache_db | 0.000 | 0.001 | 0.001 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.000 | 0.000 | 0.001 | |
| ontology_ensure_name | 0.000 | 0.000 | 0.001 | |
| ontology_name_id | 0.000 | 0.001 | 0.001 | |