===============================
R CMD BUILD
===============================
* checking for file rigvf/DESCRIPTION ... OK
* preparing rigvf:
* 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 rigvf_0.99.3.tar.gz
===============================
BiocCheckGitClone('rigvf')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3757/3661534ed539e2a083260ba5b84835235a19dee0/rigvf
BiocVersion: 3.21
Package: rigvf
PackageVersion: 0.99.3
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3757/3661534ed539e2a083260ba5b84835235a19dee0/rigvf.BiocCheck
BiocCheckVersion: 1.43.12
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3757/3661534ed539e2a083260ba5b84835235a19dee0/rigvf
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* 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 v1.43.12 results
0 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/3757/3661534ed539e2a083260ba5b84835235a19dee0/rigvf.Rcheck
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file rigvf/DESCRIPTION ... OK
* this is package rigvf version 0.99.3
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Namespace dependency missing from DESCRIPTION Imports/Depends entries: methods
See section The DESCRIPTION file in the Writing R Extensions
manual.
* DONE
Status: 1 ERROR
See
/home/pkgbuild/packagebuilder/workers/jobs/3757/3661534ed539e2a083260ba5b84835235a19dee0/rigvf.Rcheck/00check.log
for details.
===============================
BiocCheck('rigvf_0.99.3.tar.gz')
===============================
Installing rigvf
Package installed successfully
rigvf session metadata
sourceDir: /tmp/RtmpLr6cPt/file37941422d4bd22/rigvf
BiocVersion: 3.21
Package: rigvf
PackageVersion: 0.99.3
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3757/3661534ed539e2a083260ba5b84835235a19dee0/rigvf.BiocCheck
BiocCheckVersion: 1.43.12
sourceDir: /tmp/RtmpLr6cPt/file37941422d4bd22/rigvf
installDir: /tmp/RtmpLr6cPt/file37941451007f17
isTarBall: TRUE
platform: unix
Running BiocCheck on rigvf
* 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 4.1.0 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...
* 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 (25%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* 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 rigvf...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid '<<-' if possible (found 2 times)
<<- in R/zzz.R (line 4, column 17)
<<- in R/zzz.R (line 9, column 24)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
The longest 5 functions are:
variant_genes() (R/catalog_queries.R): 52 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; 10 lines (1%) are > 80 characters long.
First few lines:
R/catalog_queries.R#L60 #' @param page integer(1) when there are ...
...
vignettes/rigvf.Rmd#L229 ```{r plotgardener, fig.alt="Manhattan o ...
i NOTE: Consider multiples of 4 spaces for line indents; 29 lines (3%) are not.
First few lines:
vignettes/rigvf.Rmd#L12 collapse = TRUE, ...
...
vignettes/rigvf.Rmd#L242 sigVal = -log10(5e-8), sigLine = 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...
ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
BiocCheck v1.43.12 results
2 ERRORS | 0 WARNINGS | i 5 NOTES
i See the rigvf.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.