===============================
R CMD BUILD
===============================
* checking for file ‘scFeatures/DESCRIPTION’ ... OK
* preparing ‘scFeatures’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
TIMEOUT: R CMD build exceeded 15 mins
===============================
R CMD BUILD
===============================
* checking for file ‘scFeatures/DESCRIPTION’ ... OK
* preparing ‘scFeatures’:
* 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 ‘scFeatures_0.99.12.tar.gz’
===============================
BiocCheckGitClone('scFeatures')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: scFeatures
─ PackageVersion: 0.99.12
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2815/6e25d84e72962c63fddc5ef711d194c1df88596a/scFeatures
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2815/6e25d84e72962c63fddc5ef711d194c1df88596a/scFeatures.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scFeatures/DESCRIPTION’ ... OK
* this is package ‘scFeatures’ version ‘0.99.12’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Namespace dependencies missing from DESCRIPTION Imports/Depends entries:
'SingleCellSignalR', 'plyr'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2815/6e25d84e72962c63fddc5ef711d194c1df88596a/scFeatures.Rcheck/00check.log’
for details.
===============================
BiocCheck('scFeatures_0.99.12.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: scFeatures
─ PackageVersion: 0.99.12
─ sourceDir: /tmp/RtmpTMwupK/file2aa4e645bcc08/scFeatures
─ installDir: /tmp/RtmpTMwupK/file2aa4e20054f8a
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2815/6e25d84e72962c63fddc5ef711d194c1df88596a/scFeatures.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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...
* NOTE: Update R version dependency from 4.2.0 to 4.3.0.
* 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...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
Warning: replacing previous import 'dplyr::rename' by 'plyr::rename' when loading 'scFeatures'
Warning: replacing previous import 'dplyr::count' by 'plyr::count' when loading 'scFeatures'
Warning: replacing previous import 'dplyr::failwith' by 'plyr::failwith' when loading 'scFeatures'
Warning: replacing previous import 'dplyr::id' by 'plyr::id' when loading 'scFeatures'
Warning: replacing previous import 'dplyr::summarize' by 'plyr::summarize' when loading 'scFeatures'
Warning: replacing previous import 'dplyr::summarise' by 'plyr::summarise' when loading 'scFeatures'
Warning: replacing previous import 'dplyr::mutate' by 'plyr::mutate' when loading 'scFeatures'
Warning: replacing previous import 'dplyr::desc' by 'plyr::desc' when loading 'scFeatures'
Warning: replacing previous import 'dplyr::arrange' by 'plyr::arrange' when loading 'scFeatures'
* WARNING: Import SingleCellSignalR, parallel, plyr in DESCRIPTION
as well as NAMESPACE.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
* WARNING: Vignette set global option 'eval=FALSE'
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
Error in parse(outfile, keep.source = TRUE) :
/tmp/RtmpTMwupK/file2aa4e78d3294/parseFile.tmp:11:1: unexpected symbol
10: system.file("extdata", "example_scrnaseq.rds", package = "scFeatures")
11: data
^
Calls: BiocCheck -> BiocCheckRun -> parseFiles -> parseFile -> parse
Execution halted