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R CMD BUILD
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* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘GSEAlens_0.99.33.tar.gz’
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BiocCheckGitClone('GSEAlens')
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── Running Git clone checks on GSEAlens ────────────────────────────────────────
* Checking valid files...
* Checking for inst/doc folders...
* Checking DESCRIPTION readability...
* Checking for valid use of maintainer fields...
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R CMD CHECK
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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4251/GSEAlens_20260721103608/GSEAlens.Rcheck’
* using R version 4.6.1 (2026-06-24)
* 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: 2026-07-21 14:39:05 UTC
* using option ‘--no-vignettes’
* checking for file ‘GSEAlens/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GSEAlens’ version ‘0.99.33’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 33 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 ... INFO
installed size is 10.6Mb
sub-directories of 1Mb or more:
data 9.7Mb
* 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 ... [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 ... [46s/46s] 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 ... [9s/9s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [56s/82s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
batch_calc_gsea 5.426 0.513 31.252
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [72s/72s]
[72s/72s] 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 ... [5s/5s] OK
* DONE
Status: OK
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BiocCheck('GSEAlens_0.99.33.tar.gz')
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── Installing GSEAlens ─────────────────────────────────────────────────────────
✔ Package installed successfully
── GSEAlens session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpwpP7dj/file26b0b8b85ed03/GSEAlens
→ BiocVersion: 3.23
→ Package: GSEAlens
→ PackageVersion: 0.99.33
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4251/GSEAlens_20260721103608/GSEAlens.BiocCheck
→ BiocCheckVersion: 1.49.29
→ sourceDir: /tmp/RtmpwpP7dj/file26b0b8b85ed03/GSEAlens
→ installDir: /tmp/RtmpwpP7dj/file26b0b825aecd0d/lib
→ 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...
* 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 if 'Package:' field matches directory / tarball...
* Checking for Version: field...
* Checking DESCRIPTION readability...
* Checking validity of DESCRIPTION fields...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for whitespace in DESCRIPTION field names...
* Checking for proper Description: field...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (21%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i 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 CITATION...
i (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()'.
* 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 GSEAlens...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print in R/10_shiny_mod_quadrant.R (line 3087, column 22)
• ...
• print in R/16_shiny_mod_hubgene_vis.R (line 2271, column 22)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/01_backends.R (line 63, column 13)
• ...
• R/utils-accessors.R (line 501, column 29)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 31 times)
• suppressWarnings() in R/04_calculation.R (line 201, column 16)
• ...
• suppressWarnings() in R/utils-core-genes.R (line 405, column 15)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 98
functions greater than 50 lines.
The longest 5 functions are:
• mod_quadrant_server() (R/10_shiny_mod_quadrant.R): 3883 lines
• ...
• mod_hubgene_vis_server() (R/16_shiny_mod_hubgene_vis.R): 1866 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• build_gsea_pathways.Rd
• ...
• generate_joint_canvas_code.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
Found in files:
• build_gsea_pathways.Rd
• ...
• generate_joint_canvas_code.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• build_gsea_pathways.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; 1421 lines (5%) are > 80 characters long.
First few lines:
• R/00_class_validations.R#L3 #' @description Define GseaEnv, GseaRes, ...
• ...
• vignettes/GSEAlens.Rmd#L465 The `GseaTask` object returned by the `e ...
i NOTE: Consider multiples of 4 spaces for line indents; 182 lines (1%) are
not.
First few lines:
• vignettes/GSEAlens-preprocessing-zh.Rmd#L76 gene_id =
SummarizedExperiment::rowDat ...
• ...
• vignettes/GSEAlens.Rmd#L377 Gene-node size is unaffected (always ` ...
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 'gsealens' is already in your 'Watched Tags' on the Support Site.
── BiocCheck v1.49.29 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 9 NOTES
i See the GSEAlens.BiocCheck folder and run
`browseVignettes(package = 'BiocCheck')`
for details.