===============================
R CMD BUILD
===============================
* checking for file ‘ReducedExperiment/DESCRIPTION’ ... OK
* preparing ‘ReducedExperiment’:
* checking DESCRIPTION meta-information ... OK
* installing the package 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
* building ‘ReducedExperiment_0.99.3.tar.gz’
===============================
BiocCheckGitClone('ReducedExperiment')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3592/bc7c6edb3e99c028b8a8e581fbdb9d30387bf250/ReducedExperiment
→ BiocVersion: 3.21
→ Package: ReducedExperiment
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3592/bc7c6edb3e99c028b8a8e581fbdb9d30387bf250/ReducedExperiment.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3592/bc7c6edb3e99c028b8a8e581fbdb9d30387bf250/ReducedExperiment
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.43.2 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3592/bc7c6edb3e99c028b8a8e581fbdb9d30387bf250/ReducedExperiment.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReducedExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ReducedExperiment’ version ‘0.99.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 ‘ReducedExperiment’ 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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘BiocGenerics:::replaceSlots’
‘SummarizedExperiment:::.SummarizedExperiment.charbound’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [31s/31s] 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 ... [108s/108s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
identify_modules 14.540 0.143 14.685
run_wgcna 13.934 0.119 14.056
module_preservation 8.943 1.307 10.251
plot_module_preservation 7.176 0.175 7.352
get_msigdb_t2g 4.796 0.259 5.055
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [88s/88s]
[88s/88s] 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 ... [6s/6s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3592/bc7c6edb3e99c028b8a8e581fbdb9d30387bf250/ReducedExperiment.Rcheck/00check.log’
for details.
===============================
BiocCheck('ReducedExperiment_0.99.3.tar.gz')
===============================
── Installing ReducedExperiment ────────────────────────────────────────────────
✔ Package installed successfully
── ReducedExperiment session metadata ──────────────────────────────────────────
→ sourceDir: /tmp/Rtmpk2ze4O/file2828027d1d9741/ReducedExperiment
→ BiocVersion: 3.21
→ Package: ReducedExperiment
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3592/bc7c6edb3e99c028b8a8e581fbdb9d30387bf250/ReducedExperiment.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /tmp/Rtmpk2ze4O/file2828027d1d9741/ReducedExperiment
→ installDir: /tmp/Rtmpk2ze4O/file2828026f2efedc
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ReducedExperiment ──────────────────────────────────────
* 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 4.5.0.
* 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: Sequencing,
Coverage
i Search 'biocViews' at https://contributions.bioconductor.org
* 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 (30%).
* Checking for pinned package versions in DESCRIPTION...
* 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 ReducedExperiment...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• modules.R (line 218, column 45)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in vignettes/ReducedExperiment.Rmd
i NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 12
functions greater than 50 lines.
The longest 5 functions are:
• _anonymous_.587() (R/methods-ReducedExperiment.R): 65 lines
• ...
• .stability_ica() (R/factors.R): 56 lines
* Checking man page documentation...
* 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; 46 lines (1%) are > 80 characters long.
First few lines:
• R/factors.R#L18 #' @param center_X If `TRUE`, X is cente ...
• ...
• vignettes/ReducedExperiment.Rmd#L187 
for details.