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###
### Running command:
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###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings OmnipathR_3.17.4.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'OmnipathR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OmnipathR' version '3.17.4'
* 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 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 ... NOTE
[2025-07-24 04:53:42] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-24 04:53:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-24 04:53:42] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-24 04:53:42] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-07-24 04:53:42] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-07-23
[2025-07-24 04:53:42] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-07-23 19:54:48 UTC; windows
[2025-07-24 04:53:42] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-07-24 04:53:42] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpQhDV42/file13cd867566539". Did you mean command "update"?
Warning in system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=",  :
  running command '"quarto" TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpQhDV42/file13cd867566539 -V' had status 1
[2025-07-24 04:53:44] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-07-24; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-07-24 04:53:44] [INFO]    [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-07-24 04:53:44] [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 3.17.4(2025-07-23); 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)
[2025-07-24 04:53:44] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-07-24 04:53:44] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-07-24 04:53:44] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-24 04:53:44] [TRACE]   [OmnipathR] Contains 1 files.
[2025-07-24 04:53:44] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-07-24 04:53:44] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-24 04:53:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-24 04:53:44] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-24 04:53:44] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-07-24 04:53:44] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-07-24 04:53:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-24 04:53:44] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-07-24 04:53:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-24 04:53:44] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-07-24 04:53:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-24 04:53:44] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-07-24 04:53:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-24 04:53:44] [TRACE]   [OmnipathR] Cache locked: FALSE

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-07-24 04:53:58] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-24 04:53:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-24 04:53:58] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-24 04:53:58] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-07-24 04:53:58] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-07-23
[2025-07-24 04:53:58] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-07-23 19:54:48 UTC; windows
[2025-07-24 04:53:58] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-07-24 04:53:58] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmp6f0J6w/file1408869277ded". Did you mean command "update"?
[2025-07-24 04:53:59] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-07-24; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-07-24 04:53:59] [INFO]    [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-07-24 04:54:00] [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 3.17.4(2025-07-23); 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)
[2025-07-24 04:54:00] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-07-24 04:54:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-07-24 04:54:00] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-24 04:54:00] [TRACE]   [OmnipathR] Contains 1 files.
[2025-07-24 04:54:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-07-24 04:54:00] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-24 04:54:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-24 04:54:00] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-24 04:54:00] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-07-24 04:54:00] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-07-24 04:54:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-24 04:54:00] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-07-24 04:54:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-24 04:54:00] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-07-24 04:54:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-24 04:54:00] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-07-24 04:54:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-24 04:54:00] [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 ... NOTE
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmpk3PHAO/filed185f2412ba". Did you mean command "update"?
* checking S3 generic/method consistency ... WARNING
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmpo5qQgv/filea10c42cd5d3c". Did you mean command "preview"?
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
* checking replacement functions ... WARNING
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpiOLFeC/filee454746c1970". Did you mean command "preview"?
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... NOTE
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmpo1pYEZ/file76101a85a95". Did you mean command "update"?
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
[2025-07-24 04:54:26] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-24 04:54:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-24 04:54:26] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-24 04:54:26] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-07-24 04:54:26] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-07-23
[2025-07-24 04:54:26] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-07-23 19:54:48 UTC; windows
[2025-07-24 04:54:26] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-07-24 04:54:26] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpMVAzeo/file2276847ea1697". Did you mean command "preview"?
[2025-07-24 04:54:28] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-07-24; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-07-24 04:54:28] [INFO]    [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-07-24 04:54:28] [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 2.3.2(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 3.17.4(2025-07-23); 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)
[2025-07-24 04:54:28] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-07-24 04:54:28] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-07-24 04:54:28] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-24 04:54:28] [TRACE]   [OmnipathR] Contains 1 files.
[2025-07-24 04:54:28] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-07-24 04:54:28] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-24 04:54:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-24 04:54:28] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-24 04:54:28] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-07-24 04:54:28] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-07-24 04:54:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-24 04:54:28] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-07-24 04:54:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-24 04:54:28] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-07-24 04:54:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-24 04:54:28] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-07-24 04:54:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-24 04:54:28] [TRACE]   [OmnipathR] Cache locked: FALSE
taxon_names_table: no visible binding for global variable
  'latin_name_uniprot'
taxon_names_table: no visible binding for global variable
  'latin_name_ensembl'
taxon_names_table: no visible binding for global variable
  'latin_name_oma'
taxon_names_table: no visible binding for global variable
  'common_name_ensembl'
taxon_names_table: no visible binding for global variable
  'common_name_uniprot'
Undefined global functions or variables:
  common_name_ensembl common_name_uniprot latin_name_ensembl
  latin_name_oma latin_name_uniprot
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmp6pEfuh/fileeecc56c3327". Did you mean command "update"?
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpumDBGG/file185987dd31ecb". Did you mean command "update"?
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpctCUAP/filec55c2dca5c2e". Did you mean command "create"?
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpigOlOA/file6984ac7e48". Did you mean command "create"?
* checking Rd \usage sections ... NOTE
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmp4GPCsO/filea2dc7f5d7dcb". Did you mean command "update"?
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
annotation_categories                82.14   0.03   83.04
curated_ligrec_stats                 40.93   1.70  101.99
omnipath-interactions                33.08   1.27   60.56
all_uniprots                         27.51   2.26   50.44
uniprot_organisms                    23.98   2.19   27.27
filter_extra_attrs                   24.04   0.59   44.66
nichenet_gr_network_omnipath         21.51   1.39   26.78
go_annot_download                    17.65   1.24   17.74
nichenet_signaling_network_omnipath  14.95   1.17   29.86
with_extra_attrs                     13.97   0.46   15.01
giant_component                      13.78   0.57   26.73
extra_attrs_to_cols                  12.68   0.32   13.08
extra_attr_values                    12.44   0.35   13.38
pivot_annotations                    11.37   0.82   23.38
omnipath_for_cosmos                  10.56   0.39   18.19
filter_by_resource                    9.11   0.39   10.09
has_extra_attrs                       8.70   0.15   22.20
translate_ids_multi                   8.23   0.21   15.11
filter_intercell                      7.60   0.66   12.54
find_all_paths                        7.70   0.19    8.00
curated_ligand_receptor_interactions  7.01   0.39   16.47
static_table                          6.89   0.42    7.80
print_interactions                    6.44   0.16    9.94
extra_attrs                           6.12   0.21    6.36
signed_ptms                           5.18   0.02    5.79
pubmed_open                           4.33   0.50    7.88
ensembl_id_mapping_table              2.39   0.09   10.09
kegg_conv                             1.56   0.06    9.22
translate_ids                         1.32   0.17   21.92
uniprot_full_id_mapping_table         1.13   0.14   15.90
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 6 NOTEs
See
  'F:/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck/00check.log'
for details.