===============================
R CMD BUILD
===============================
* checking for file scrapbook/DESCRIPTION ... OK
* preparing scrapbook:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed 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
* creating default NAMESPACE file
* building scrapbook_0.99.2.tar.gz
===============================
BiocCheckGitClone('scrapbook')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4074/841244b0467026cd97c6bedc831cc636afc3edc4/scrapbook
BiocVersion: 3.23
Package: scrapbook
PackageVersion: 0.99.2
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4074/841244b0467026cd97c6bedc831cc636afc3edc4/scrapbook.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4074/841244b0467026cd97c6bedc831cc636afc3edc4/scrapbook
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
Warning in file(con, "r") :
cannot open file '/home/pkgbuild/packagebuilder/workers/jobs/4074/841244b0467026cd97c6bedc831cc636afc3edc4/scrapbook/NAMESPACE': No such file or directory
Error in file(con, "r") : cannot open the connection
Calls: BiocCheckGitClone -> checkNAMESPACE -> readLines -> file
Execution halted
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/4074/841244b0467026cd97c6bedc831cc636afc3edc4/scrapbook.Rcheck
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file scrapbook/DESCRIPTION ... OK
* this is package scrapbook version 0.99.2
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
'AnnotationHub', 'BiocStyle', 'bluster', 'cluster',
'DropletTestFiles', 'DropletUtils', 'dynamicTreeCut', 'edgeR',
'ggplot2', 'gridExtra', 'msigdbr', 'pheatmap', 'scater', 'scrapper',
'scRNAseq', 'TENxPBMCData'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 scrapbook can be installed ... OK
* 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 whether the package can be loaded ... [15s/15s] OK
* checking whether the package can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the package can be unloaded cleanly ... [15s/15s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [15s/15s] OK
* checking use of S3 registration ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in vignettes ... OK
* checking examples ... NONE
* 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 ... [2s/2s] OK
* DONE
Status: OK
===============================
BiocCheck('scrapbook_0.99.2.tar.gz')
===============================
Installing scrapbook
Package installed successfully
scrapbook session metadata
sourceDir: /tmp/RtmpUaGdvo/file10555512a01b72/scrapbook
BiocVersion: 3.23
Package: scrapbook
PackageVersion: 0.99.2
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4074/841244b0467026cd97c6bedc831cc636afc3edc4/scrapbook.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /tmp/RtmpUaGdvo/file10555512a01b72/scrapbook
installDir: /tmp/RtmpUaGdvo/file10555566674499
isTarBall: TRUE
platform: unix
Running BiocCheck on scrapbook
* 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...
Workflow
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
Warning in readLines(con) :
URL 'http://bioconductor.org/js/versions.js': Timeout of 60 seconds was reached
* 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 (44%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
stub.Rmd
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/stub.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of scrapbook...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
Warning: replacing previous import scater::aggregateAcrossCells by scrapper::aggregateAcrossCells when loading scrapbook
Warning: replacing previous import scater::normalizeCounts by scrapper::normalizeCounts when loading scrapbook
* 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 multiples of 4 spaces for line indents; 16 lines (35%) are
not.
First few lines:
scrapbook/NAMESPACE#L9 AnnotationHub, ...
...
scrapbook/NAMESPACE#L24 TENxPBMCData ...
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...
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/bioc/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository https://bioconductor.org/packages/3.23/bioc
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/data/annotation/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository
https://bioconductor.org/packages/3.23/data/annotation
* 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 v1.47.18 results
0 ERRORS | 0 WARNINGS | i 5 NOTES
i See the scrapbook.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.