===============================
R CMD BUILD
===============================
* checking for file GSEAlens/DESCRIPTION ... OK
* preparing GSEAlens:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... OK
Warning: inst/doc files
GSEAlens-vignette-en.html, GSEAlens-vignette-zh.html
ignored as vignettes have been rebuilt.
Run R CMD build with --no-build-vignettes to prevent rebuilding.
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted LazyData from DESCRIPTION
* building GSEAlens_0.99.0.tar.gz
===============================
BiocCheckGitClone('GSEAlens')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4251/GSEAlens_20260518181354/GSEAlens
BiocVersion: 3.23
Package: GSEAlens
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4251/GSEAlens_20260518181354/GSEAlens.BiocCheck
BiocCheckVersion: 1.49.6
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4251/GSEAlens_20260518181354/GSEAlens
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
ERROR: Remove 'doc' folder from the package source
* Checking if DESCRIPTION is well formatted...
* Checking for remote package usage...
* Checking NAMESPACE...
* Checking for valid maintainer...
ERROR: Use Authors@R field not Author/Maintainer fields. Do not use both.
* 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 v1.49.6 results
2 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/4251/GSEAlens_20260518181354/GSEAlens.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: 2026-05-18 18:16:56 UTC
* using option --no-vignettes
* checking for file GSEAlens/DESCRIPTION ... OK
* checking extension type ... Package
* this is package GSEAlens version 0.99.0
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 34 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 GSEAlens 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 ... NOTE
License stub is invalid DCF.
* 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 ... [10s/10s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [10s/10s] 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 ... [42s/42s] NOTE
.gsea_nb_core: no visible binding for global variable fc
Undefined global functions or variables:
fc
* 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 ... WARNING
Undocumented arguments in Rd file 'create_gsea_env.Rd'
backend_info contrast_registry de_store expr_bundle geneset
raw_obj
Undocumented arguments in Rd file 'create_gsea_res.Rd'
metadata backend_info contrast_registry de_store
expr_bundle geneset_info results
Undocumented arguments in Rd file 'create_gsea_task.Rd'
gsea_res meta
Undocumented arguments in Rd file 'get_sample_meta.Rd'
obj
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter Writing R documentation files in the Writing R
Extensions manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from inst/doc ... OK
* checking files in vignettes ... OK
* checking examples ... [19s/19s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [11s/11s]
[11s/11s] 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 ... [4s/4s] OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/4251/GSEAlens_20260518181354/GSEAlens.Rcheck/00check.log
for details.
===============================
BiocCheck('GSEAlens_0.99.0.tar.gz')
===============================
Installing GSEAlens
Package installed successfully
GSEAlens session metadata
sourceDir: /tmp/RtmpNtk81i/file2c64f07ac6c48d/GSEAlens
BiocVersion: 3.23
Package: GSEAlens
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4251/GSEAlens_20260518181354/GSEAlens.BiocCheck
BiocCheckVersion: 1.49.6
sourceDir: /tmp/RtmpNtk81i/file2c64f07ac6c48d/GSEAlens
installDir: /tmp/RtmpNtk81i/file2c64f06d451f2a
isTarBall: TRUE
platform: unix
Running BiocCheck on GSEAlens
* 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 4.5.0 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 if 'Package:' field matches directory / tarball...
* 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 (22%).
* 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...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
GSEAlens-vignette-en.Rmd
GSEAlens-vignette-zh.Rmd
ERROR: Package installation calls found in vignette(s)
Found in files:
vignettes/GSEAlens-vignette-en.Rmd (chunk no. 2, line 42, column 5)
...
vignettes/GSEAlens-vignette-zh.Rmd (chunk no. 2, line 45, column 16)
! WARNING: Potential package installation calls found in vignette(s)
Found in files:
vignettes/GSEAlens-vignette-en.Rmd (chunk no. 2, line 42, column 5)
vignettes/GSEAlens-vignette-zh.Rmd (chunk no. 2, line 42, column 5)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found in files:
vignettes/GSEAlens-vignette-en.Rmd (chunk no. 3, line 82, column 18)
vignettes/GSEAlens-vignette-zh.Rmd (chunk no. 3, line 82, column 18)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of GSEAlens...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
R/01_backends.R (line 52, column 19)
...
R/vis-gsea-core.R (line 203, column 22)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
02_setup.R (line 153, column 15)
...
utils-core-genes.R (line 318, column 40)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/03_pathways.R (line 212, column 7)
...
cat() in R/16_shiny_mod_hubgene_vis.R (line 641, column 7)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/04_calculation.R (line 197, column 18)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/00_class_validations.R (line 81, column 7)
...
R/utils-accessors.R (line 495, column 29)
! WARNING: Remove set.seed usage (found 4 times)
set.seed() in R/08_shiny_mod_data_prep.R (line 403, column 9)
...
set.seed() in R/utils_hubgene.R (line 376, column 3)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in vignettes/GSEAlens-vignette-en.Rmd
i Found @ in vignettes/GSEAlens-vignette-zh.Rmd
i NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
i NOTE: Avoid '<<-' if possible (found 3 times)
<<- in R/08_shiny_mod_data_prep.R (line 366, column 29)
<<- in R/13_shiny_mod_pathway_relation.R (line 654, column 17)
<<- in R/13_shiny_mod_pathway_relation.R (line 738, column 15)
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
suppressWarnings() in R/04_calculation.R (line 262, column 13)
suppressWarnings() in R/utils-core-genes.R (line 170, column 10)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 57
functions greater than 50 lines.
The longest 5 functions are:
mod_quadrant_server() (R/10_shiny_mod_quadrant.R): 1088 lines
...
mod_data_prep_server() (R/08_shiny_mod_data_prep.R): 699 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
man/create_gsea_env.Rd
...
man/visualization.Rd
ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
batch_calc_gsea.Rd
...
validate_param.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 15% of man
pages use at least one of these tags.
Found in files:
build_gsea_pathways.Rd
...
setup_gsea_env.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
build_gsea_pathways.Rd
...
setup_gsea_env.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; 711 lines (6%) are > 80 characters long.
First few lines:
R/00_class_validations.R#L2 #' @description Define GseaEnv, GseaRes, ...
...
vignettes/GSEAlens-vignette-zh.Rmd#L298 `batch_calc_gsea`
`GseaRes` ...
i NOTE: Consider multiples of 4 spaces for line indents; 4740 lines (38%) are
not.
First few lines:
R/00_class_validations.R#L17 structure( ...
...
vignettes/GSEAlens-vignette-zh.Rmd#L271 ...
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...
ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
i Maintainer is registered at support site.
ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
BiocCheck v1.49.6 results
4 ERRORS | 4 WARNINGS | i 16 NOTES
i See the GSEAlens.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.