===============================
R CMD BUILD
===============================
* checking for file chevreuldata/DESCRIPTION ... OK
* preparing chevreuldata:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building human_gene_transcript_sce.Rmd using rmarkdown
Quitting from lines 92-93 [unnamed-chunk-1] (human_gene_transcript_sce.Rmd)
Error: processing vignette 'human_gene_transcript_sce.Rmd' failed with diagnostics:
failed to load resource
name: EH9452
title: human_gene_transcript_sce
reason: error in evaluating the argument 'x' in selecting a method for function 'get': error reading from connection
--- failed re-building human_gene_transcript_sce.Rmd
SUMMARY: processing the following file failed:
human_gene_transcript_sce.Rmd
Error: Vignette re-building failed.
Execution halted
===============================
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_0.99.0.tar.gz
===============================
BiocCheckGitClone('chevreuldata')
===============================
sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3332/chevreuldata_20240805135355/chevreuldata
BiocVersion: 3.20
Package: chevreuldata
PackageVersion: 0.99.0
BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3332/chevreuldata_20240805135355/chevreuldata.BiocCheck
BiocCheckVersion: 1.41.10
sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3332/chevreuldata_20240805135355/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...
* 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 results
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /Users/pkgbuild/packagebuilder/workers/jobs/3332/chevreuldata_20240805135355/chevreuldata.Rcheck
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option --no-vignettes
* checking for file chevreuldata/DESCRIPTION ... OK
* this is package chevreuldata version 0.99.0
* 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 serialization versions ... OK
* checking whether package chevreuldata can be installed ... ERROR
Installation failed.
See /Users/pkgbuild/packagebuilder/workers/jobs/3332/chevreuldata_20240805135355/chevreuldata.Rcheck/00install.out for details.
* DONE
Status: 1 ERROR
See
/Users/pkgbuild/packagebuilder/workers/jobs/3332/chevreuldata_20240805135355/chevreuldata.Rcheck/00check.log
for details.
===============================
BiocCheck('chevreuldata_0.99.0.tar.gz')
===============================
* Installing package...
sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpofGbWN/file9c3641822e55/chevreuldata
BiocVersion: 3.20
Package: chevreuldata
PackageVersion: 0.99.0
BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3332/chevreuldata_20240805135355/chevreuldata.BiocCheck
BiocCheckVersion: 1.41.10
sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpofGbWN/file9c3641822e55/chevreuldata
installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpofGbWN/file9c3649aff00c
isTarBall: TRUE
platform: unix
* 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...
* NOTE: Consider adding these automatically suggested biocViews:
ThirdPartyClient, DataImport, GUI
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...
Bioconductor dependencies found in Imports & Depends (50%).
* 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...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 11 lines (6%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 2 lines
(1%) are not.
See https://contributions.bioconductor.org/r-code.html
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...
Unable to connect to the Bioc-devel mailing list: HTTP 502 Bad
Gateway.
* Checking for support site registration...
Maintainer is registered at support site.
Package is in the Support Site Watched Tags.
BiocCheck results
0 ERRORS | 0 WARNINGS | 3 NOTES
See the chevreuldata.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir chevreuldata_0.99.0.tar.gz'
>>>>>>>
* installing *source* package chevreuldata ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package chevreuldata
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (chevreuldata)