===============================
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_0.99.4.tar.gz’
===============================
BiocCheckGitClone('rigvf')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3757/ce1c15fad780cd296df07292cdc5f97b8f103b5e/rigvf
→ BiocVersion: 3.21
→ Package: rigvf
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3757/ce1c15fad780cd296df07292cdc5f97b8f103b5e/rigvf.BiocCheck
→ BiocCheckVersion: 1.43.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3757/ce1c15fad780cd296df07292cdc5f97b8f103b5e/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/ce1c15fad780cd296df07292cdc5f97b8f103b5e/rigvf.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 ‘0.99.4’
* 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/ce1c15fad780cd296df07292cdc5f97b8f103b5e/rigvf.Rcheck/00check.log’
for details.
===============================
BiocCheck('rigvf_0.99.4.tar.gz')
===============================
── Installing rigvf ────────────────────────────────────────────────────────────
✔ Package installed successfully
── rigvf session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp6bKDAH/file45bad757320e/rigvf
→ BiocVersion: 3.21
→ Package: rigvf
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3757/ce1c15fad780cd296df07292cdc5f97b8f103b5e/rigvf.BiocCheck
→ BiocCheckVersion: 1.43.12
→ sourceDir: /tmp/Rtmp6bKDAH/file45bad757320e/rigvf
→ installDir: /tmp/Rtmp6bKDAH/file45bad321a07f1
→ 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 4.6.0.
* 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...
* 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...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.43.12 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 5 NOTES
i See the rigvf.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.