===============================
R CMD BUILD
===============================
* checking for file AnVILVRS/DESCRIPTION ... OK
* preparing AnVILVRS:
* 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
* building AnVILVRS_0.99.11.tar.gz
===============================
BiocCheckGitClone('AnVILVRS')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3987/4e38554f30455635f5af273455159c5245890ef4/AnVILVRS
BiocVersion: 3.23
Package: AnVILVRS
PackageVersion: 0.99.11
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3987/4e38554f30455635f5af273455159c5245890ef4/AnVILVRS.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3987/4e38554f30455635f5af273455159c5245890ef4/AnVILVRS
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 NAMESPACE...
* 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 v1.47.18 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/3987/4e38554f30455635f5af273455159c5245890ef4/AnVILVRS.Rcheck
* using R Under development (unstable) (2026-01-15 r89304)
* 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 24.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file AnVILVRS/DESCRIPTION ... OK
* checking extension type ... Package
* this is package AnVILVRS version 0.99.11
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... 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 AnVILVRS 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [8s/8s] 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 ... [3s/3s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running tinytest.R [2s/2s]
[3s/3s] 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('AnVILVRS_0.99.11.tar.gz')
===============================
Installing AnVILVRS
Package installed successfully
AnVILVRS session metadata
sourceDir: /tmp/RtmpfkYSiJ/file344dd340b9acfe/AnVILVRS
BiocVersion: 3.23
Package: AnVILVRS
PackageVersion: 0.99.11
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3987/4e38554f30455635f5af273455159c5245890ef4/AnVILVRS.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /tmp/RtmpfkYSiJ/file344dd340b9acfe/AnVILVRS
installDir: /tmp/RtmpfkYSiJ/file344dd3710a8266
isTarBall: TRUE
platform: unix
Running BiocCheck on AnVILVRS
* 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:
GenomicVariation
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...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (75%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: 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...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
AnVILVRS.Rmd
! WARNING: Potential package installation calls found in vignette(s)
Found in files:
vignettes/AnVILVRS.Rmd (chunk no. 1, line 32, column 15)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of AnVILVRS...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid '<<-' if possible (found 3 times)
<<- in R/python.R (line 6, column 23)
<<- in R/python.R (line 16, column 29)
<<- in R/python.R (line 29, column 18)
ERROR: Avoid 'Sys.setenv' (found 2 times)
Sys.setenv() in R/install_AnVILVRS.R (line 10, column 13)
Sys.setenv() in R/install_AnVILVRS.R (line 17, column 13)
* 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:
.install_AnVILVRS() (R/install_AnVILVRS.R): 67 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
man/get_caf.Rd
man/get_pop_descriptor.Rd
man/get_seqrepo.Rd
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
install_AnVILVRS.Rd
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider multiples of 4 spaces for line indents; 6 lines (1%) are not.
First few lines:
vignettes/AnVILVRS.Rmd#L25 collapse = TRUE, ...
...
vignettes/AnVILVRS.Rmd#L178 pop_desc_file = pop_desc, toolkit_dir ...
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...
ERROR: Unable to find your email in the Support Site: HTTP 504 Gateway
Timeout.
BiocCheck v1.47.18 results
2 ERRORS | 2 WARNINGS | i 10 NOTES
i See the AnVILVRS.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.