| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-08-11 11:40 -0400 (Mon, 11 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
| 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 3.16.0 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| 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: 3.16.0 |
| 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_3.16.0.tar.gz |
| StartedAt: 2025-08-11 00:58:13 -0400 (Mon, 11 Aug 2025) |
| EndedAt: 2025-08-11 01:23:08 -0400 (Mon, 11 Aug 2025) |
| EllapsedTime: 1495.2 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_3.16.0.tar.gz
###
##############################################################################
##############################################################################
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.16.0’
* 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
[2025-08-11 00:58:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-11 00:58:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 00:58:43] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-08-11 00:58:43] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-11 00:58:43] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-10
[2025-08-11 00:58:43] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-10 19:07:46 UTC; unix
[2025-08-11 00:58:43] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-08-11 00:58:43] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-08-11 00:58:43] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-11; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-08-11 00:58:43] [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]
[2025-08-11 00:58:43] [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); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); 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 1.4.2(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 3.16.0(2025-08-10); 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 2.4.2(2025-07-18); 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 0.52(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 2.3.3(2025-05-13)
[2025-08-11 00:58:43] [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
[2025-08-11 00:58:43] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-11 00:58:43] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-08-11 00:58:43] [TRACE] [OmnipathR] Contains 1 files.
[2025-08-11 00:58:43] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-11 00:58:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-11 00:58:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 00:58:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-08-11 00:58:43] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-11 00:58:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-11 00:58:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 00:58:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-11 00:58:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 00:58:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-11 00:58:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 00:58:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-11 00:58:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 00:58:44] [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
[2025-08-11 00:59:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-11 00:59:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 00:59:00] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-08-11 00:59:00] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-11 00:59:00] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-10
[2025-08-11 00:59:00] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-10 19:07:46 UTC; unix
[2025-08-11 00:59:00] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-08-11 00:59:00] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-08-11 00:59:00] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-11; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-08-11 00:59:01] [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]
[2025-08-11 00:59:01] [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); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); 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 1.4.2(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 3.16.0(2025-08-10); 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 2.4.2(2025-07-18); 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 0.52(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 2.3.3(2025-05-13)
[2025-08-11 00:59:01] [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
[2025-08-11 00:59:01] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-11 00:59:01] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-08-11 00:59:01] [TRACE] [OmnipathR] Contains 1 files.
[2025-08-11 00:59:01] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-11 00:59:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-11 00:59:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 00:59:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-08-11 00:59:01] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-11 00:59:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-11 00:59:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 00:59:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-11 00:59:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 00:59:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-11 00:59:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 00:59:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-11 00:59:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 00:59:01] [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: metalinksdb_sqlite
> ### Title: Open MetalinksDB as an SQLite3 connection
> ### Aliases: metalinksdb_sqlite
>
> ### ** Examples
>
> con <- metalinksdb_sqlite()
[2025-08-11 01:06:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-11 01:06:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 01:06:49] [INFO] [OmnipathR] Looking up in cache `metalinksdb.sqlite`: key=e2682a205032a8eff5e0533edafd2730b9eb450c, no version available.
[2025-08-11 01:06:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-11 01:06:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 01:06:49] [INFO] [OmnipathR] Created new version for cache record e2682a205032a8eff5e0533edafd2730b9eb450c: version 1.
[2025-08-11 01:06:49] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/e2682a205032a8eff5e0533edafd2730b9eb450c-1
[2025-08-11 01:06:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-11 01:06:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 01:06:49] [INFO] [OmnipathR] Looking up in cache `https://figshare.com/ndownloader/files/47567597`: key=7b250a38d14fd754d28d2b7803ee3069659251ec, no version available.
[2025-08-11 01:06:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-11 01:06:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 01:06:50] [INFO] [OmnipathR] Created new version for cache record 7b250a38d14fd754d28d2b7803ee3069659251ec: version 1.
[2025-08-11 01:06:50] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7b250a38d14fd754d28d2b7803ee3069659251ec-1
[2025-08-11 01:06:50] [INFO] [OmnipathR] Retrieving URL: `https://figshare.com/ndownloader/files/47567597`
[2025-08-11 01:06:50] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-08-11 01:06:50] [TRACE] [OmnipathR] Attempt 1/3: `https://figshare.com/ndownloader/files/47567597`
[2025-08-11 01:06:50] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://figshare.com/ndownloader/files/47567597`.
[2025-08-11 01:06:50] [TRACE] [OmnipathR] HTTP headers: <NULL>
[2025-08-11 01:06:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-08-11 01:06:50] [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]
[2025-08-11 01:06:50] [TRACE] [OmnipathR] HTTP headers: []
[2025-08-11 01:06:50] [TRACE] [OmnipathR] Sending HTTP request.
[2025-08-11 01:06:50] [WARN] [OmnipathR] Failed to download `https://figshare.com/ndownloader/files/47567597` (attempt 1/3); error: HTTP 403 Forbidden.
[2025-08-11 01:06:55] [TRACE] [OmnipathR] Attempt 2/3: `https://figshare.com/ndownloader/files/47567597`
[2025-08-11 01:06:55] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://figshare.com/ndownloader/files/47567597`.
[2025-08-11 01:06:55] [TRACE] [OmnipathR] HTTP headers: <NULL>
[2025-08-11 01:06:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-08-11 01:06:56] [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]
[2025-08-11 01:06:56] [TRACE] [OmnipathR] HTTP headers: []
[2025-08-11 01:06:56] [TRACE] [OmnipathR] Sending HTTP request.
[2025-08-11 01:06:56] [WARN] [OmnipathR] Failed to download `https://figshare.com/ndownloader/files/47567597` (attempt 2/3); error: HTTP 403 Forbidden.
[2025-08-11 01:07:01] [TRACE] [OmnipathR] Attempt 3/3: `https://figshare.com/ndownloader/files/47567597`
[2025-08-11 01:07:01] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://figshare.com/ndownloader/files/47567597`.
[2025-08-11 01:07:01] [TRACE] [OmnipathR] HTTP headers: <NULL>
[2025-08-11 01:07:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-08-11 01:07:01] [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]
[2025-08-11 01:07:01] [TRACE] [OmnipathR] HTTP headers: []
[2025-08-11 01:07:01] [TRACE] [OmnipathR] Sending HTTP request.
[2025-08-11 01:07:01] [ERROR] [OmnipathR] Failed to download `https://figshare.com/ndownloader/files/47567597` (attempt 3/3); error: HTTP 403 Forbidden.
[2025-08-11 01:07:01] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-11 01:07:01] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-10
[2025-08-11 01:07:01] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-10 19:07:46 UTC; unix
[2025-08-11 01:07:01] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-08-11 01:07:01] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-08-11 01:07:02] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-11; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-08-11 01:07:02] [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]
[2025-08-11 01:07:03] [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 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); 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 1.4.2(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 3.16.0(2025-08-10); 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 2.4.2(2025-07-18); 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 3.3.0(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); utf8 1.2.6(2025-06-08); 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 2.3.3(2025-05-13)
[2025-08-11 01:07:03] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
Error in req_perform(., path = path) : HTTP 403 Forbidden.
Calls: metalinksdb_sqlite ... sqlite_downloader -> %>% -> download_to_cache -> download_base
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 84.789 0.065 86.310
curated_ligrec_stats 37.798 3.319 104.211
filter_extra_attrs 20.835 3.886 25.677
go_annot_download 12.612 0.908 13.481
extra_attr_values 11.026 1.322 14.823
extra_attrs_to_cols 11.075 1.178 12.299
giant_component 9.033 0.478 12.234
has_extra_attrs 6.934 1.315 8.272
filter_by_resource 6.764 0.297 9.149
extra_attrs 5.904 1.032 7.121
curated_ligand_receptor_interactions 6.162 0.573 15.552
filter_intercell 5.261 0.287 9.102
kegg_conv 1.819 0.168 11.796
all_uniprots 1.574 0.184 13.128
kegg_picture 1.523 0.039 5.362
ensembl_id_mapping_table 1.413 0.120 8.937
kegg_rm_prefix 1.185 0.065 6.438
kegg_link 0.974 0.059 6.730
* 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 ‘3.16.0’ ** 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 [2025-08-10 15:07:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-10 15:07:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-10 15:07:59] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-08-10 15:07:59] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-10 15:07:59] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-10 [2025-08-10 15:07:59] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-10 19:07:46 UTC; unix [2025-08-10 15:07:59] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-08-10 15:07:59] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-08-10 15:07:59] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-10; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto] [2025-08-10 15:08:00] [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] [2025-08-10 15:08:00] [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); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); 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 1.4.2(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 3.16.0(2025-08-10); 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 2.4.2(2025-07-18); 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 0.52(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 2.3.3(2025-05-13) [2025-08-10 15:08:00] [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 [2025-08-10 15:08:00] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-10 15:08:00] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-08-10 15:08:00] [TRACE] [OmnipathR] Contains 8 files. [2025-08-10 15:08:00] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-10 15:08:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-10 15:08:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-10 15:08:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-08-10 15:08:00] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-08-10 15:08:00] [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). [2025-08-10 15:08:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-10 15:08:00] [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). [2025-08-10 15:08:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-10 15:08:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-10 15:08:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-10 15:08:00] [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). [2025-08-10 15:08:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-10 15:08:00] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-08-10 15:08:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-10 15:08:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-10 15:08:02] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-08-10 15:08:02] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-10 15:08:02] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-10 [2025-08-10 15:08:02] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-10 19:07:46 UTC; unix [2025-08-10 15:08:02] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-08-10 15:08:02] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-08-10 15:08:02] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-10; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto] [2025-08-10 15:08:02] [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] [2025-08-10 15:08:03] [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); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); 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 1.4.2(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 3.16.0(2025-08-10); 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 2.4.2(2025-07-18); 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 0.52(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 2.3.3(2025-05-13) [2025-08-10 15:08:03] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-08-10 15:08:03] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-10 15:08:03] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-08-10 15:08:03] [TRACE] [OmnipathR] Contains 1 files. [2025-08-10 15:08:03] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-10 15:08:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-10 15:08:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-10 15:08:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-08-10 15:08:03] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-08-10 15:08:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-10 15:08:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-10 15:08:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-10 15:08:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-10 15:08:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-10 15:08:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-10 15:08:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-10 15:08:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-10 15:08:03] [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.
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> #!/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)
[2025-08-11 01:07:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-11 01:07:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 01:07:13] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-08-11 01:07:13] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-11 01:07:13] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-10
[2025-08-11 01:07:13] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-10 19:07:46 UTC; unix
[2025-08-11 01:07:13] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-08-11 01:07:13] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-08-11 01:07:14] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-11; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-08-11 01:07:14] [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]
[2025-08-11 01:07:14] [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); brio 1.1.5(2024-04-24); 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 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); 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 1.4.2(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 3.16.0(2025-08-10); 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 2.4.2(2025-07-18); 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 0.52(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 2.3.3(2025-05-13)
[2025-08-11 01:07:14] [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
[2025-08-11 01:07:14] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-11 01:07:14] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-08-11 01:07:14] [TRACE] [OmnipathR] Contains 57 files.
[2025-08-11 01:07:14] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-11 01:07:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-11 01:07:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 01:07:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-08-11 01:07:14] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-11 01:07:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-11 01:07:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 01:07:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-11 01:07:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 01:07:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-11 01:07:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 01:07:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-11 01:07:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-11 01:07:15] [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
27.494 3.261 63.429
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.000 | 0.000 | 0.001 | |
| all_uniprot_acs | 0.013 | 0.004 | 0.017 | |
| all_uniprots | 1.574 | 0.184 | 13.128 | |
| ancestors | 0.007 | 0.001 | 0.009 | |
| annotated_network | 1.443 | 0.129 | 4.308 | |
| annotation_categories | 84.789 | 0.065 | 86.310 | |
| annotation_resources | 0.152 | 0.012 | 0.871 | |
| annotations | 0.574 | 0.066 | 1.268 | |
| biomart_query | 1.028 | 0.074 | 3.691 | |
| bioplex1 | 0.007 | 0.001 | 0.008 | |
| bioplex2 | 0.007 | 0.001 | 0.008 | |
| bioplex3 | 0.006 | 0.001 | 0.007 | |
| bioplex_all | 0.006 | 0.002 | 0.008 | |
| bioplex_hct116_1 | 0.008 | 0.001 | 0.008 | |
| bma_motif_es | 0.550 | 0.053 | 1.473 | |
| bma_motif_vs | 0.272 | 0.007 | 0.866 | |
| chalmers_gem | 0.007 | 0.001 | 0.008 | |
| chalmers_gem_id_mapping_table | 0.006 | 0.001 | 0.008 | |
| chalmers_gem_id_type | 0.002 | 0.000 | 0.002 | |
| chalmers_gem_metabolites | 0.007 | 0.001 | 0.007 | |
| chalmers_gem_network | 0.008 | 0.000 | 0.008 | |
| chalmers_gem_raw | 0.007 | 0.001 | 0.007 | |
| chalmers_gem_reactions | 0.007 | 0.000 | 0.008 | |
| common_name | 0.035 | 0.000 | 0.035 | |
| complex_genes | 0.664 | 0.025 | 2.473 | |
| complex_resources | 0.136 | 0.001 | 0.890 | |
| complexes | 0.287 | 0.011 | 0.841 | |
| consensuspathdb_download | 0.000 | 0.000 | 0.001 | |
| consensuspathdb_raw_table | 0.008 | 0.001 | 0.009 | |
| cosmos_pkn | 0.000 | 0.000 | 0.001 | |
| curated_ligand_receptor_interactions | 6.162 | 0.573 | 15.552 | |
| curated_ligrec_stats | 37.798 | 3.319 | 104.211 | |
| database_summary | 1.443 | 0.086 | 2.785 | |
| descendants | 0.010 | 0.001 | 0.011 | |
| ensembl_dataset | 0.012 | 0.001 | 0.013 | |
| ensembl_id_mapping_table | 1.413 | 0.120 | 8.937 | |
| ensembl_id_type | 0.002 | 0.000 | 0.002 | |
| ensembl_name | 0.056 | 0.001 | 0.056 | |
| ensembl_organisms | 0.115 | 0.009 | 0.124 | |
| ensembl_organisms_raw | 0.101 | 0.007 | 0.108 | |
| ensembl_orthology | 0.001 | 0.000 | 0.001 | |
| enzsub_graph | 2.015 | 0.095 | 4.041 | |
| enzsub_resources | 0.144 | 0.000 | 0.769 | |
| enzyme_substrate | 0.957 | 0.020 | 1.496 | |
| evex_download | 0.008 | 0.000 | 0.008 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 11.026 | 1.322 | 14.823 | |
| extra_attrs | 5.904 | 1.032 | 7.121 | |
| extra_attrs_to_cols | 11.075 | 1.178 | 12.299 | |
| filter_by_resource | 6.764 | 0.297 | 9.149 | |
| filter_extra_attrs | 20.835 | 3.886 | 25.677 | |
| filter_intercell | 5.261 | 0.287 | 9.102 | |
| filter_intercell_network | 0.017 | 0.001 | 0.019 | |
| find_all_paths | 4.710 | 0.146 | 4.858 | |
| from_evidences | 0.000 | 0.000 | 0.001 | |
| get_db | 0.001 | 0.000 | 0.001 | |
| get_ontology_db | 0.008 | 0.001 | 0.009 | |
| giant_component | 9.033 | 0.478 | 12.234 | |
| go_annot_download | 12.612 | 0.908 | 13.481 | |
| go_annot_slim | 0.000 | 0.000 | 0.001 | |
| go_ontology_download | 0.009 | 0.001 | 0.010 | |
| guide2pharma_download | 0.009 | 0.000 | 0.009 | |
| harmonizome_download | 0.009 | 0.000 | 0.009 | |
| has_extra_attrs | 6.934 | 1.315 | 8.272 | |
| hmdb_id_mapping_table | 0.010 | 0.000 | 0.009 | |
| hmdb_id_type | 0.003 | 0.000 | 0.002 | |
| hmdb_metabolite_fields | 0.002 | 0.000 | 0.001 | |
| hmdb_protein_fields | 0.001 | 0.000 | 0.000 | |
| hmdb_table | 0.010 | 0.000 | 0.009 | |
| homologene_download | 0.008 | 0.000 | 0.009 | |
| homologene_raw | 0.019 | 0.002 | 0.021 | |
| homologene_uniprot_orthology | 0.009 | 0.000 | 0.009 | |
| hpo_download | 2.994 | 0.201 | 3.492 | |
| htridb_download | 0.017 | 0.002 | 0.018 | |
| id_translation_resources | 0.001 | 0.000 | 0.000 | |
| id_types | 0.071 | 0.011 | 0.083 | |
| inbiomap_download | 0.000 | 0.001 | 0.000 | |
| inbiomap_raw | 0.000 | 0.000 | 0.001 | |
| interaction_datasets | 1.365 | 0.058 | 1.911 | |
| interaction_graph | 0.616 | 0.014 | 1.356 | |
| interaction_resources | 0.274 | 0.010 | 1.064 | |
| interaction_types | 0.131 | 0.004 | 0.220 | |
| intercell | 1.132 | 0.072 | 2.150 | |
| intercell_categories | 1.008 | 0.074 | 1.349 | |
| intercell_consensus_filter | 2.304 | 0.193 | 4.733 | |
| intercell_generic_categories | 0.105 | 0.006 | 0.111 | |
| intercell_network | 0.019 | 0.004 | 0.022 | |
| intercell_resources | 0.193 | 0.016 | 0.848 | |
| intercell_summary | 0.109 | 0.031 | 0.172 | |
| is_ontology_id | 0.001 | 0.001 | 0.001 | |
| is_swissprot | 0.060 | 0.001 | 0.090 | |
| is_trembl | 0.068 | 0.001 | 0.100 | |
| is_uniprot | 0.025 | 0.005 | 0.062 | |
| kegg_api_templates | 0.004 | 0.003 | 0.014 | |
| kegg_conv | 1.819 | 0.168 | 11.796 | |
| kegg_databases | 0.001 | 0.000 | 0.001 | |
| kegg_ddi | 0.899 | 0.060 | 2.182 | |
| kegg_find | 0.873 | 0.044 | 2.335 | |
| kegg_info | 0.013 | 0.002 | 0.013 | |
| kegg_link | 0.974 | 0.059 | 6.730 | |
| kegg_list | 1.902 | 0.087 | 3.484 | |
| kegg_open | 0.026 | 0.002 | 0.028 | |
| kegg_operations | 0.000 | 0.001 | 0.000 | |
| kegg_organism_codes | 0.026 | 0.115 | 0.142 | |
| kegg_organisms | 0.050 | 0.006 | 0.056 | |
| kegg_pathway_annotations | 0.000 | 0.000 | 0.001 | |
| kegg_pathway_download | 0.021 | 0.003 | 0.025 | |
| kegg_pathway_list | 0.018 | 0.003 | 0.021 | |
| kegg_pathways_download | 0.000 | 0.001 | 0.001 | |
| kegg_picture | 1.523 | 0.039 | 5.362 | |
| kegg_process | 0.042 | 0.003 | 0.091 | |
| kegg_query | 0.015 | 0.000 | 0.029 | |
| kegg_request | 0.113 | 0.011 | 0.161 | |
| kegg_rm_prefix | 1.185 | 0.065 | 6.438 | |
| latin_name | 0.111 | 0.004 | 0.154 | |
| load_db | 0.125 | 0.018 | 0.144 | |