Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* 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_0.99.0.tar.gz

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 BiocCheckGitClone('ReducedExperiment')

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 sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3592/ReducedExperiment_20241114182055/ReducedExperiment
 BiocVersion: 3.21
 Package: ReducedExperiment
 PackageVersion: 0.99.0
 BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3592/ReducedExperiment_20241114182055/ReducedExperiment.BiocCheck
 BiocCheckVersion: 1.43.2
 sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3592/ReducedExperiment_20241114182055/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')




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 R CMD CHECK

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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3592/ReducedExperiment_20241114182055/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 0.99.0
* 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 ... [10s/10s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] 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 ... [28s/28s] 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 ... [114s/114s] OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
enrichment               13.475  1.006  14.243
identify_modules         14.174  0.160  14.335
run_wgcna                13.663  0.132  13.796
estimate_stability        9.656  0.515  10.171
module_preservation       6.918  0.047   6.965
plot_module_preservation  6.532  0.005   6.536
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running testthat.R [170s/170s]
 [171s/170s] 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: 1 NOTE
See
  /home/pkgbuild/packagebuilder/workers/jobs/3592/ReducedExperiment_20241114182055/ReducedExperiment.Rcheck/00check.log
for details.

 WARNING: R CMD check exceeded 10 min requirement






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 BiocCheck('ReducedExperiment_0.99.0.tar.gz')

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 Installing ReducedExperiment 
 Package installed successfully
 ReducedExperiment session metadata 
 sourceDir: /tmp/RtmpRpakyK/file4d82e48f252f/ReducedExperiment
 BiocVersion: 3.21
 Package: ReducedExperiment
 PackageVersion: 0.99.0
 BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3592/ReducedExperiment_20241114182055/ReducedExperiment.BiocCheck
 BiocCheckVersion: 1.43.2
 sourceDir: /tmp/RtmpRpakyK/file4d82e48f252f/ReducedExperiment
 installDir: /tmp/RtmpRpakyK/file4d82e1311b93
 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; 43 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 ![](https://raw.githubusercontent.com/ja
  ...
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 v1.43.2 results 
 0 ERRORS |  0 WARNINGS | i 6 NOTES
i See the ReducedExperiment.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.