===============================
R CMD BUILD
===============================
* checking for file chevreul/DESCRIPTION ... OK
* preparing chevreul:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building chevreul_0.99.1.tar.gz
===============================
BiocCheckGitClone('chevreul')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/10a54255356fc2608801d8407953253890e352dd/chevreul
BiocVersion: 3.21
Package: chevreul
PackageVersion: 0.99.1
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/10a54255356fc2608801d8407953253890e352dd/chevreul.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/10a54255356fc2608801d8407953253890e352dd/chevreul
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...
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 v1.43.2 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/3332/10a54255356fc2608801d8407953253890e352dd/chevreul.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 chevreul/DESCRIPTION ... OK
* this is package chevreul version 0.99.1
* 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 serialization versions ... OK
* checking whether package chevreul can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [15s/15s] OK
* checking whether the package can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the package can be unloaded cleanly ... [15s/15s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [15s/15s] OK
* checking whether startup messages can be suppressed ... [15s/15s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
cli crayon rstudioapi
Namespaces in Imports field not imported from:
chevreulPlot chevreulProcess chevreulShiny
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [2s/2s] 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 ... WARNING
Undocumented code objects:
'check_loaded' 'chevreul_attach' 'chevreul_detach' 'is_attached'
'msg' 'package_version' 'pkgs' 'text_col'
All user-level objects in a package should have documentation entries.
See chapter Writing R documentation files in the Writing R
Extensions manual.
* 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 ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
chevreul.Rmd
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... [17s/17s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [15s/15s]
[15s/15s] OK
* checking package vignettes ... NOTE
Package has vignettes subdirectory but apparently no vignettes.
Perhaps the VignetteBuilder information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... [3s/3s] OK
* DONE
Status: 3 WARNINGs, 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3332/10a54255356fc2608801d8407953253890e352dd/chevreul.Rcheck/00check.log
for details.
===============================
BiocCheck('chevreul_0.99.1.tar.gz')
===============================
Installing chevreul
Package installed successfully
chevreul session metadata
sourceDir: /tmp/RtmprcNS3o/file39f8f618b8d6cb/chevreul
BiocVersion: 3.21
Package: chevreul
PackageVersion: 0.99.1
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/10a54255356fc2608801d8407953253890e352dd/chevreul.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/RtmprcNS3o/file39f8f618b8d6cb/chevreul
installDir: /tmp/RtmprcNS3o/file39f8f64f227e66
isTarBall: TRUE
platform: unix
Running BiocCheck on chevreul
* 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...
* 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...
ERROR: Add biocViews other than Software
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...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ERROR: 'VignetteEngine' specified but not in the DESCRIPTION.
Add 'VignetteEngine' to DESCRIPTION from the following:
vignettes/chevreul.Rmd
* Checking whether vignette is built with 'R CMD build'...
ERROR: Vignette must be built by 'R CMD build'. Please see the `Vignette
Checks` section of the BiocCheck vignette.
* Checking package installation calls in R code...
* Checking for library/require of chevreul...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/hello.R (line 17, column 5)
* Checking parsed R code in R directory, examples, vignettes...
* 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:
chevreul_attach() (R/attach.R): 51 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
man/chevreul_packages.Rd
man/hello.Rd
* 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; 8 lines (3%) are > 80 characters long.
First few lines:
R/attach.R#L22 # Return a character string containi ...
...
vignettes/chevreul.Rmd#L54 We hope that `r Biocpkg("chevreul")` wil ...
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
3 ERRORS | 2 WARNINGS | i 3 NOTES
i See the chevreul.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.