===============================
R CMD BUILD
===============================
* checking for file ‘GOaGO/DESCRIPTION’ ... OK
* preparing ‘GOaGO’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘GOaGO_0.99.4.tar.gz’
===============================
BiocCheckGitClone('GOaGO')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4121/baf845aca70cb6d218636adc1fbd5644131102f1/GOaGO
→ BiocVersion: 3.23
→ Package: GOaGO
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4121/baf845aca70cb6d218636adc1fbd5644131102f1/GOaGO.BiocCheck
→ BiocCheckVersion: 1.47.26
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4121/baf845aca70cb6d218636adc1fbd5644131102f1/GOaGO
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for remote package usage...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.47.26 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4121/baf845aca70cb6d218636adc1fbd5644131102f1/GOaGO.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-22 09:43:41 UTC
* using option ‘--no-vignettes’
* checking for file ‘GOaGO/DESCRIPTION’ ... OK
* this is package ‘GOaGO’ version ‘0.99.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GOaGO’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [9s/9s] OK
* checking use of S3 registration ... OK
* 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 ... [26s/26s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [2s/2s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [478s/411s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
termGenePairs 46.188 5.985 45.725
DotPlot 45.665 2.198 38.524
RidgePlot 45.846 1.861 38.150
GOaGO 41.665 2.019 34.484
as.data.frame-methods 36.394 2.845 32.608
organism-methods 35.075 2.236 41.943
show-methods 33.709 1.918 40.270
as.data.table-methods 29.536 2.855 33.044
genePairs 28.770 2.110 31.012
keyType 28.062 2.646 30.681
annotateAnchors 6.341 0.833 7.070
annotateInteractions 3.418 0.218 5.293
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [80s/74s]
[80s/74s] 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 ... [3s/3s] OK
* DONE
Status: OK
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('GOaGO_0.99.4.tar.gz')
===============================
── Installing GOaGO ────────────────────────────────────────────────────────────
✔ Package installed successfully
── GOaGO session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpBsAGV8/file29602b5b8071d9/GOaGO
→ BiocVersion: 3.23
→ Package: GOaGO
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4121/baf845aca70cb6d218636adc1fbd5644131102f1/GOaGO.BiocCheck
→ BiocCheckVersion: 1.47.26
→ sourceDir: /tmp/RtmpBsAGV8/file29602b5b8071d9/GOaGO
→ installDir: /tmp/RtmpBsAGV8/file29602b57d62476
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GOaGO ──────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 4.4.0 to 4.6.0
* 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...
* 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...
i Bioconductor dependencies found in Imports & Depends (64%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of GOaGO...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
• suppressMessages() in R/termGenePairs.R (line 33, column 9)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
The longest 5 functions are:
• GOaGO() (R/GOaGO.R): 202 lines
* Checking man page documentation...
* 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; 93 lines (6%) are > 80 characters long.
First few lines:
• vignettes/GOaGO.Rmd#L13 %\VignetteIndexEntry{Gene Ontology enr ...
• ...
• vignettes/GOaGO.Rmd#L362 We hope that GO-a-GO will be useful for ...
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 if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.47.26 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 5 NOTES
i See the GOaGO.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.