===============================
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
* 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_0.99.2.tar.gz’
===============================
BiocCheckGitClone('GSEAlens')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4251/b968bbf7a6890c2465be5167b91d67d05c3746c4/GSEAlens
→ BiocVersion: 3.23
→ Package: GSEAlens
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4251/b968bbf7a6890c2465be5167b91d67d05c3746c4/GSEAlens.BiocCheck
→ BiocCheckVersion: 1.49.6
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4251/b968bbf7a6890c2465be5167b91d67d05c3746c4/GSEAlens
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/4251/b968bbf7a6890c2465be5167b91d67d05c3746c4/GSEAlens/.gitignore'
✖ ERROR: System files found that should not be Git tracked.
• GSEAlen.Rproj
* 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 v1.49.6 results ───────────────────────────────────────────────────
✖ 1 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/b968bbf7a6890c2465be5167b91d67d05c3746c4/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: 2026-05-19 13:25:43 UTC
* using option ‘--no-vignettes’
* checking for file ‘GSEAlens/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GSEAlens’ version ‘0.99.2’
* 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 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 ... NOTE
Namespace in Imports field not imported from: ‘enrichit’
All declared Imports should be used.
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [32s/32s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [10s/10s]
[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: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4251/b968bbf7a6890c2465be5167b91d67d05c3746c4/GSEAlens.Rcheck/00check.log’
for details.
===============================
BiocCheck('GSEAlens_0.99.2.tar.gz')
===============================
── Installing GSEAlens ─────────────────────────────────────────────────────────
✔ Package installed successfully
── GSEAlens session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpNy8h6Q/file24c2f76f15b03/GSEAlens
→ BiocVersion: 3.23
→ Package: GSEAlens
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4251/b968bbf7a6890c2465be5167b91d67d05c3746c4/GSEAlens.BiocCheck
→ BiocCheckVersion: 1.49.6
→ sourceDir: /tmp/RtmpNy8h6Q/file24c2f76f15b03/GSEAlens
→ installDir: /tmp/RtmpNy8h6Q/file24c2f57abe46a
→ 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
* 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 158, column 15)
• ...
• utils-core-genes.R (line 343, 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 642, column 7)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/04_calculation.R (line 202, column 18)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/00_class_validations.R (line 123, column 7)
• ...
• R/utils-accessors.R (line 496, column 29)
! WARNING: Remove set.seed usage (found 4 times)
• set.seed() in R/08_shiny_mod_data_prep.R (line 402, column 9)
• ...
• set.seed() in R/utils_hubgene.R (line 393, 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 267, column 13)
• suppressWarnings() in R/utils-core-genes.R (line 190, 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): 698 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/inspect_gsea_env.Rd
• ...
• man/visualization.Rd
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• pipe.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#L289 `batch_calc_gsea` 函数返回的
`GseaRes` 对象包含以下 ...
i NOTE: Consider multiples of 4 spaces for line indents; 4731 lines (38%) are
not.
First few lines:
• R/00_class_validations.R#L33 structure( ...
• ...
• vignettes/GSEAlens-vignette-zh.Rmd#L262 ...
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 v1.49.6 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | i 15 NOTES
i See the GSEAlens.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.