===============================
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_0.99.2.tar.gz
===============================
BiocCheckGitClone('GOaGO')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4121/e25c394c51ce82e1e285718b9a82cf7ad2f853cf/GOaGO
BiocVersion: 3.23
Package: GOaGO
PackageVersion: 0.99.2
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4121/e25c394c51ce82e1e285718b9a82cf7ad2f853cf/GOaGO.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4121/e25c394c51ce82e1e285718b9a82cf7ad2f853cf/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 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 v1.47.18 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/e25c394c51ce82e1e285718b9a82cf7ad2f853cf/GOaGO.Rcheck
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file GOaGO/DESCRIPTION ... OK
* this is package GOaGO version 0.99.2
* 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] 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 ... [23s/23s] NOTE
.sortedResult: no visible binding for global variable Count
.sortedResult: no visible binding for global variable ID
.sortedResult: no visible binding for global variable Description
DotPlot: no visible binding for global variable .data
DotPlot: no visible binding for global variable Description
GOaGO: no visible binding for global variable geneID
GOaGO: no visible binding for global variable ID
GOaGO: no visible binding for global variable ..cols
GOaGO: no visible binding for global variable FoldEnrichment
GOaGO: no visible binding for global variable PairRatio
GOaGO: no visible binding for global variable BgRatio
GOaGO: no visible binding for global variable pvalue
RidgePlot: no visible binding for global variable Count
RidgePlot: no visible binding for global variable Description
uniqueGenePairs: no visible binding for global variable gid1
uniqueGenePairs: no visible binding for global variable geneID1
uniqueGenePairs: no visible binding for global variable geneID2
uniqueGenePairs: no visible binding for global variable gid2
uniqueGenePairs: no visible binding for global variable pairID
uniqueGenePairs: no visible binding for global variable .I
Undefined global functions or variables:
..cols .I .data BgRatio Count Description FoldEnrichment ID PairRatio
geneID geneID1 geneID2 gid1 gid2 pairID pvalue
* 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [461s/366s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
show-methods 50.894 2.426 43.219
DotPlot 45.079 1.921 37.938
GOaGO 42.317 2.606 34.553
RidgePlot 42.275 2.029 34.702
as.data.frame-methods 41.231 2.859 34.501
genePairs 40.646 2.242 33.555
as.data.table-methods 40.289 2.128 33.080
organism-methods 39.905 2.365 33.058
termGenePairs 40.375 1.887 33.108
keyType 39.978 2.263 32.827
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [57s/50s]
[57s/50s] 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: 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/4121/e25c394c51ce82e1e285718b9a82cf7ad2f853cf/GOaGO.Rcheck/00check.log
for details.
===============================
BiocCheck('GOaGO_0.99.2.tar.gz')
===============================
Installing GOaGO
Package installed successfully
GOaGO session metadata
sourceDir: /tmp/Rtmpp0WHzP/file1398ac2947373b/GOaGO
BiocVersion: 3.23
Package: GOaGO
PackageVersion: 0.99.2
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4121/e25c394c51ce82e1e285718b9a82cf7ad2f853cf/GOaGO.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /tmp/Rtmpp0WHzP/file1398ac2947373b/GOaGO
installDir: /tmp/Rtmpp0WHzP/file1398ac61729b3f
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 (55%).
* 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): 189 lines
* Checking man page documentation...
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 77 lines (7%) are > 80 characters long.
First few lines:
vignettes/GOaGO.Rmd#L13 %\VignetteIndexEntry{Gene Ontology enr ...
...
vignettes/GOaGO.Rmd#L308 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 v1.47.18 results
0 ERRORS | 0 WARNINGS | i 6 NOTES
i See the GOaGO.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.