===============================
R CMD BUILD
===============================
* checking for file chevreulShiny/DESCRIPTION ... OK
* preparing chevreulShiny:
* 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 chevreulShiny_0.99.5.tar.gz
===============================
BiocCheckGitClone('chevreulShiny')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/c3f9a913eca9a184a4baf3e2dcb63de88aa18036/chevreulShiny
BiocVersion: 3.21
Package: chevreulShiny
PackageVersion: 0.99.5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/c3f9a913eca9a184a4baf3e2dcb63de88aa18036/chevreulShiny.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/c3f9a913eca9a184a4baf3e2dcb63de88aa18036/chevreulShiny
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/c3f9a913eca9a184a4baf3e2dcb63de88aa18036/chevreulShiny.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 chevreulShiny/DESCRIPTION ... OK
* checking extension type ... Package
* this is package chevreulShiny version 0.99.5
* 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'
INFO
Imports includes 33 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.
* 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 chevreulShiny can be installed ... WARNING
Found the following significant warnings:
Note: possible error in 'genes_to_transcripts(gene, ': unused argument (organism)
See /home/pkgbuild/packagebuilder/workers/jobs/3332/c3f9a913eca9a184a4baf3e2dcb63de88aa18036/chevreulShiny.Rcheck/00install.out for details.
Information on the location(s) of code generating the Notes can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to yes.
* 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 ... [15s/15s] OK
* checking whether the package can be loaded with stated dependencies ... [16s/16s] OK
* checking whether the package can be unloaded cleanly ... [15s/15s] OK
* checking whether the namespace can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the namespace can be unloaded cleanly ... [15s/15s] 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 ... NOTE
Namespaces in Imports field not imported from:
'ExperimentHub' 'wiggleplotr'
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 ... [49s/49s] NOTE
chevreulApp : server: no visible global function definition for
'subset_by_meta'
dockerChevreulApp : server: no visible global function definition for
'subset_by_meta'
get_transcripts_from_sce: possible error in genes_to_transcripts(gene,
organism): unused argument (organism)
minimalChevreulApp : server: no visible global function definition for
'subset_by_meta'
Undefined global functions or variables:
subset_by_meta
* 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 contents of data directory ... OK
* checking data for non-ASCII characters ... [8s/8s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [23s/23s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [19s/19s]
[19s/19s] 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: 1 WARNING, 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3332/c3f9a913eca9a184a4baf3e2dcb63de88aa18036/chevreulShiny.Rcheck/00check.log
for details.
===============================
BiocCheck('chevreulShiny_0.99.5.tar.gz')
===============================
Installing chevreulShiny
Package installed successfully
chevreulShiny session metadata
sourceDir: /tmp/Rtmp2MkWSa/file3c8f29ae58524/chevreulShiny
BiocVersion: 3.21
Package: chevreulShiny
PackageVersion: 0.99.5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/c3f9a913eca9a184a4baf3e2dcb63de88aa18036/chevreulShiny.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/Rtmp2MkWSa/file3c8f29ae58524/chevreulShiny
installDir: /tmp/Rtmp2MkWSa/file3c8f293128f9b7
isTarBall: TRUE
platform: unix
Running BiocCheck on chevreulShiny
* 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 (21%).
* 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 chevreulShiny...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/chevreul_app.R (line 609, column 13)
print() in R/shiny_modules.R (line 994, column 13)
print in R/shiny_modules.R (line 1402, column 30)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/wiggleplotr.R (line 21, column 13)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/utils.R (line 70, column 25)
R/utils.R (line 71, 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 30
functions greater than 50 lines.
The longest 5 functions are:
chevreulApp() (R/chevreul_app.R): 592 lines
...
server() (R/docker_app.R): 205 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; 72 lines (1%) are > 80 characters long.
First few lines:
R/chevreul_app.R#L216 h3(paste0("chevreul vers ...
...
vignettes/shiny_app.Rmd#L134 * p_val_adj : Adjusted p-value, based o ...
i NOTE: Consider multiples of 4 spaces for line indents; 132 lines (3%) are
not.
First few lines:
R/chevreul_app.R#L26 function(preset_project, ...
...
vignettes/shiny_app.Rmd#L216 * Regressing feature expression as wel ...
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 chevreulShiny.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.