===============================
R CMD BUILD
===============================
* checking for file chevreulProcess/DESCRIPTION ... OK
* preparing chevreulProcess:
* 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
* looking to see if a data/datalist file should be added
* building chevreulProcess_0.99.7.tar.gz
===============================
BiocCheckGitClone('chevreulProcess')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/1a882aa16d360860755e3f79ec2c6ac9cc9ba4b2/chevreulProcess
BiocVersion: 3.21
Package: chevreulProcess
PackageVersion: 0.99.7
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/1a882aa16d360860755e3f79ec2c6ac9cc9ba4b2/chevreulProcess.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/1a882aa16d360860755e3f79ec2c6ac9cc9ba4b2/chevreulProcess
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/3332/1a882aa16d360860755e3f79ec2c6ac9cc9ba4b2/chevreulProcess.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 chevreulProcess/DESCRIPTION ... OK
* checking extension type ... Package
* this is package chevreulProcess version 0.99.7
* 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'
ERROR
Namespace dependencies missing from DESCRIPTION Imports/Depends entries:
'EnhancedVolcano', 'EnrichmentBrowser', 'forcats', 'future', 'readr',
'rlang'
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
See section The DESCRIPTION file in the Writing R Extensions
manual.
* DONE
Status: 1 ERROR
See
/home/pkgbuild/packagebuilder/workers/jobs/3332/1a882aa16d360860755e3f79ec2c6ac9cc9ba4b2/chevreulProcess.Rcheck/00check.log
for details.
===============================
BiocCheck('chevreulProcess_0.99.7.tar.gz')
===============================
Installing chevreulProcess
Package installed successfully
chevreulProcess session metadata
sourceDir: /tmp/RtmpezOT2D/fileaa7055b5d9745/chevreulProcess
BiocVersion: 3.21
Package: chevreulProcess
PackageVersion: 0.99.7
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/1a882aa16d360860755e3f79ec2c6ac9cc9ba4b2/chevreulProcess.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/RtmpezOT2D/fileaa7055b5d9745/chevreulProcess
installDir: /tmp/RtmpezOT2D/fileaa7052593cfda
isTarBall: TRUE
platform: unix
Running BiocCheck on chevreulProcess
* 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: ImmunoOncology
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 (38%).
* 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 chevreulProcess...
* Checking coding practice...
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/wiggleplotr.R (line 54, column 13)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/utils.R (line 169, column 25)
R/utils.R (line 170, column 28)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 2
functions greater than 50 lines.
The longest 5 functions are:
sce_de() (R/cluster.R): 68 lines
record_experiment_data() (R/utils.R): 51 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
integration_workflow.Rd
...
reintegrate_sce.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; 9 lines (0%) are > 80 characters long.
First few lines:
R/pipeline.R#L27 sce_integrate <- function(sce_list, reso ...
...
R/utils.R#L45 metadata(object)[["experiment"]] ...
i NOTE: Consider multiples of 4 spaces for line indents; 76 lines (4%) are not.
First few lines:
R/cluster.R#L22 diffex_scheme ...
...
R/workflow.R#L43 ...
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 8 NOTES
i See the chevreulProcess.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.