===============================
R CMD BUILD
===============================
* checking for file chevreuldata/DESCRIPTION ... OK
* preparing chevreuldata:
* 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 chevreuldata_0.99.25.tar.gz
===============================
BiocCheckGitClone('chevreuldata')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/c9380612e642d3093b2421d3db4176abfd01a963/chevreuldata
BiocVersion: 3.21
Package: chevreuldata
PackageVersion: 0.99.25
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/c9380612e642d3093b2421d3db4176abfd01a963/chevreuldata.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/c9380612e642d3093b2421d3db4176abfd01a963/chevreuldata
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/c9380612e642d3093b2421d3db4176abfd01a963/chevreuldata.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 chevreuldata/DESCRIPTION ... OK
* this is package chevreuldata version 0.99.25
* 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 chevreuldata can be installed ... WARNING
Found the following significant warnings:
Warning: previous export 'human_gene_transcript_sce' is being replaced
See /home/pkgbuild/packagebuilder/workers/jobs/3332/c9380612e642d3093b2421d3db4176abfd01a963/chevreuldata.Rcheck/00install.out for details.
* 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 ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] NOTE
Warning: previous export 'human_gene_transcript_sce' is being replaced
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [4s/4s] OK
* checking whether startup messages can be suppressed ... [4s/4s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: SingleCellExperiment
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 ... [12s/12s] 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 ... ERROR
TIMEOUT: R CMD check exceeded 15 mins
===============================
BiocCheck('chevreuldata_0.99.25.tar.gz')
===============================
Installing chevreuldata
Package installed successfully
chevreuldata session metadata
sourceDir: /tmp/RtmpA5WzaP/file3c605a3db31a66/chevreuldata
BiocVersion: 3.21
Package: chevreuldata
PackageVersion: 0.99.25
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/c9380612e642d3093b2421d3db4176abfd01a963/chevreuldata.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/RtmpA5WzaP/file3c605a3db31a66/chevreuldata
installDir: /tmp/RtmpA5WzaP/file3c605a4b459127
isTarBall: TRUE
platform: unix
Running BiocCheck on chevreuldata
* 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...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
i NOTE: Consider adding these automatically suggested biocViews:
ThirdPartyClient, DataImport, GUI
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 (67%).
* 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 chevreuldata...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
Warning: previous export 'human_gene_transcript_sce' is being replaced
* Checking package NEWS...
* Checking unit tests...
i NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 11 lines (5%) are > 80 characters long.
First few lines:
vignettes/human_gene_transcript_sce.Rmd#L31 crop = NULL ## Related to
https://st ...
...
vignettes/human_gene_transcript_sce.Rmd#L177 ```{r vignetteBiblio, results =
"asis", ...
i NOTE: Consider multiples of 4 spaces for line indents; 2 lines (1%) are not.
First few lines:
vignettes/human_gene_transcript_sce.Rmd#L65 install.packages("BiocManager")
...
vignettes/human_gene_transcript_sce.Rmd#L66 } ...
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 4 NOTES
i See the chevreuldata.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.