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R CMD BUILD
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* checking for file biotidy/DESCRIPTION ... OK
* preparing biotidy:
* 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 biotidy_0.99.1.tar.gz
===============================
BiocCheckGitClone('biotidy')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3478/c9f21840b203c6013741bff9dbad192f332ba050/biotidy
BiocVersion: 3.20
Package: biotidy
PackageVersion: 0.99.1
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3478/c9f21840b203c6013741bff9dbad192f332ba050/biotidy.BiocCheck
BiocCheckVersion: 1.41.16
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3478/c9f21840b203c6013741bff9dbad192f332ba050/biotidy
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 N: (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 v1.41.16 results
0 ERRORS | 0 WARNINGS | 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3478/c9f21840b203c6013741bff9dbad192f332ba050/biotidy.Rcheck
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file biotidy/DESCRIPTION ... OK
* this is package biotidy version 0.99.1
* 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 biotidy can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] 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 ... [0s/0s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [3s/3s] 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 ... [11s/11s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
makePerCellDF 8.31 0.412 8.723
* 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: 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3478/c9f21840b203c6013741bff9dbad192f332ba050/biotidy.Rcheck/00check.log
for details.
===============================
BiocCheck('biotidy_0.99.1.tar.gz')
===============================
Installing biotidy
Package installed successfully
biotidy session metadata
sourceDir: /tmp/RtmpAWb2uR/file7fdf84d508a02/biotidy
BiocVersion: 3.20
Package: biotidy
PackageVersion: 0.99.1
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3478/c9f21840b203c6013741bff9dbad192f332ba050/biotidy.BiocCheck
BiocCheckVersion: 1.41.16
sourceDir: /tmp/RtmpAWb2uR/file7fdf84d508a02/biotidy
installDir: /tmp/RtmpAWb2uR/file7fdf8400665bd
isTarBall: TRUE
platform: unix
Running BiocCheck on biotidy
* 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...
* 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...
i N: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
! W: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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 biotidy...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
i N: Avoid '<<-' if possible (found 1 times)
<<- in R/import-standalone-cli.R (line 88, column 25)
* Checking function lengths...
i N: The recommended function length is 50 lines or less. There are 2 functions
greater than 50 lines.
The longest 5 functions are:
obj_type_friendly() (R/import-standalone-obj-type.R): 102 lines
mock_data() (R/mock.R): 53 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
i N: 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 N: Consider shorter lines; 6 lines (0%) are > 80 characters long.
First few lines:
R/import-standalone-assert.R#L69 assert_pkg <- function(pkg, version = NU ...
...
R/mock.R#L58 SingleCellExperiment::altExp(out ...
i N: Consider multiples of 4 spaces for line indents; 71 lines (4%) are not.
First few lines:
R/makePerCellDF.R#L55 ...
...
vignettes/biotidy.Rmd#L124 use_rowdata = FALSE ...
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 v1.41.16 results
0 ERRORS | 1 WARNINGS | 6 NOTES
i See the biotidy.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.