===============================
R CMD BUILD
===============================
* checking for file ‘GExPipe/DESCRIPTION’ ... OK
* preparing ‘GExPipe’:
* 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
WARNING: directory ‘GExPipe/inst/scripts’ is empty
* building ‘GExPipe_0.99.13.tar.gz’
===============================
BiocCheckGitClone('GExPipe')
===============================
── Running Git clone checks on GExPipe ─────────────────────────────────────────
* Checking valid files...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* 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()'.
===============================
R CMD CHECK
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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4162/efd0159c51dcbe6f22dbcf3deb78edc3e1142b7a/GExPipe.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: 2026-06-22 10:20:04 UTC
* using option ‘--no-vignettes’
* checking for file ‘GExPipe/DESCRIPTION’ ... OK
* this is package ‘GExPipe’ version ‘0.99.13’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 63 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 ‘GExPipe’ 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [10s/10s] 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 files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [2s/2s]
[2s/2s] 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
===============================
BiocCheck('GExPipe_0.99.13.tar.gz')
===============================
── Installing GExPipe ──────────────────────────────────────────────────────────
✔ Package installed successfully
── GExPipe session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp2UVgkv/file2489211d6b38fb/GExPipe
→ BiocVersion: 3.23
→ Package: GExPipe
→ PackageVersion: 0.99.13
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4162/efd0159c51dcbe6f22dbcf3deb78edc3e1142b7a/GExPipe.BiocCheck
→ BiocCheckVersion: 1.49.19
→ sourceDir: /tmp/Rtmp2UVgkv/file2489211d6b38fb/GExPipe
→ installDir: /tmp/Rtmp2UVgkv/file24892147af7a13
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GExPipe ────────────────────────────────────────────────
* 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...
i NOTE: Consider adding these automatically suggested biocViews:
NetworkEnrichment, Normalization
i Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* 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 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...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
Found in files:
• install() in R/gexpipe_shiny_helpers.R (line 220, column 22)
• ...
• install() in R/utils_shiny_app.R (line 836, column 20)
* Checking for library/require of GExPipe...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• utils_shiny_app.R (line 472, column 24)
• utils_shiny_app.R (line 472, column 39)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/utils_shiny_app.R (line 695, column 13)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/utils_shiny_app.R (line 850, column 13)
• R/utils_shiny_app.R (line 1065, column 36)
! WARNING: Remove set.seed usage (found 1 times)
• set.seed() in R/gexp_platform_helpers.R (line 255, column 5)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid '<<-' if possible (found 4 times)
• <<- in R/utils_shiny_app.R (line 1063, column 18)
• ...
• <<- in R/utils_shiny_app.R (line 1083, column 19)
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 28 times)
• suppressWarnings() in R/gexp_download_pipeline.R (line 741, column 69)
• ...
• suppressWarnings() in R/utils_shiny_app.R (line 927, column 11)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 34
functions greater than 50 lines.
The longest 5 functions are:
• gexp_app_head() (R/interface_app.R): 944 lines
• ...
• gexp_normalize_and_intersect() (R/gexp_normalize_pipeline.R): 285 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
• gexp_run_de.Rd
• ...
• gexpipe_wgcna_heatmap_cor.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; 826 lines (8%) are > 80 characters long.
First few lines:
• R/gexp_batch_pipeline.R#L19 #' @param expr Combined expression matri ...
• ...
• vignettes/GExPipe.Rmd#L538 | **Corporate proxy** | `Sys.setenv(http ...
i NOTE: Consider multiples of 4 spaces for line indents; 4063 lines (40%) are
not.
First few lines:
• R/dummy_imports.R#L6 affy::ReadAffy ...
• ...
• vignettes/GExPipe.Rmd#L515 decreasing = TRUE), ...
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 'gexpipe' is already in your 'Watched Tags' on the Support Site.
── BiocCheck v1.49.19 results ──────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 1 WARNINGS | i 11 NOTES
i See the GExPipe.BiocCheck folder and run
`browseVignettes(package = 'BiocCheck')`
for details.