[ Started: 2025-02-18 00:16:54 CET ]
[ OmnipathR v3.15.9 for BioC-3.21 from https://github.com/saezlab/OmnipathR@devel (0a92537 2025-02-13 19:46:14) ]

Loading required package: BiocCheck
── Installing OmnipathR ────────────────────────────────────────────────────────
✔ Package installed successfully
── OmnipathR session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpGEMzEf/file18f58a482a5f4e/OmnipathR
→ BiocVersion: 3.21
→ Package: OmnipathR
→ PackageVersion: 3.15.9
→ BiocCheckDir: /mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.BiocCheck
→ BiocCheckVersion: 1.43.4
→ sourceDir: /tmp/RtmpGEMzEf/file18f58a482a5f4e/OmnipathR
→ installDir: /tmp/RtmpGEMzEf/file18f58a45e0bfbe
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on OmnipathR ──────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.0 to 4.5.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
ℹ NOTE: Consider adding these automatically suggested biocViews: GenePrediction
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking package installation calls in R code...
* Checking for library/require of OmnipathR...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/annotations.R (line 135, column 9)
• ...
• print() in R/uniprot.R (line 31, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/adecorate.R (line 38, column 23)
• ...
• R/tbl_attrs.R (line 97, column 17)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
Found in files:
• misc.R (line 1102, column 24)
• misc.R (line 1109, column 28)
! WARNING: .Deprecated / .Defunct usage (found 27 times)
• .Deprecated() in R/annotations.R (line 180, column 5)
• ...
• .Deprecated() in R/resources.R (line 97, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 9 times)
• suppressWarnings() in R/cache.R (line 66, column 5)
• ...
• suppressWarnings() in R/tfcensus.R (line 48, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 77
functions greater than 50 lines.
The longest 5 functions are:
• homology_translate() (R/homology.R): 220 lines
• ...
• filter_intercell_network() (R/intercell.R): 160 lines
* Checking man page documentation...
[2025-02-18 00:17:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:17:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:17:41] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:17:41] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-17 23:16:41 UTC; omnipath
[2025-02-18 00:17:41] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-18 00:17:41] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-17 23:16:57 UTC; unix
[2025-02-18 00:17:41] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-18 00:17:41] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-18 00:17:41] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=en_GB.UTF-8; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-18; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-18 00:17:41] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-18 00:17:41] [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
[2025-02-18 00:17:41] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-18 00:17:41] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:17:41] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-18 00:17:41] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-18 00:17:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:17:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:17:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:17:41] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-18 00:17:41] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpGEMzEf/file18f58a45e0bfbe/lib/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-18 00:17:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:17:41] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpGEMzEf/file18f58a45e0bfbe/lib/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-18 00:17:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:17:41] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpGEMzEf/file18f58a45e0bfbe/lib/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-18 00:17:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:17:41] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpGEMzEf/file18f58a45e0bfbe/lib/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-18 00:17:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:17:41] [TRACE]   [OmnipathR] Cache locked: FALSE
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
• ambiguity.Rd
• ...
• unnest_evidences.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 14% of man
pages use at least one of these tags.
Found in files:
• consensuspathdb_download.Rd
• ...
• unnest_evidences.Rd
ℹ NOTE: Use donttest instead of dontrun.
Found in files:
• consensuspathdb_download.Rd
• ...
• unnest_evidences.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 62 lines (0%) are > 80 characters long.
First few lines:
• R/annotations.R#L38 #' \url{https://archive.omnipathdb.org/o ...
• ...
• vignettes/omnipath_intro.Rmd#L765 `r BiocStyle::Biocpkg("OmnipathR")` prov
  ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 81 lines (0%) are not.
First few lines:
• R/chalmers_gem.R#L123 slice(metabolites, ...
• ...
• vignettes/drug_targets.Rmd#L158 print(all(drug_targets$in_OP)) ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
ℹ NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel
mailing list (requires admin credentials). Subscribe here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
ℹ Maintainer is registered at support site.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.43.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 3 WARNINGS | ℹ 12 NOTES
ℹ See the OmnipathR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.
[ Finished: 2025-02-18 00:17:45 CET ]