===============================
R CMD BUILD
===============================
* checking for file ‘homosapienDEE2CellScore/DESCRIPTION’ ... OK
* preparing ‘homosapienDEE2CellScore’:
* 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 ‘homosapienDEE2CellScore_0.99.9.tar.gz’
===============================
BiocCheckGitClone('homosapienDEE2CellScore')
===============================
─ BiocCheckVersion: 1.39.23
─ BiocVersion: 3.19
─ Package: homosapienDEE2CellScore
─ PackageVersion: 0.99.9
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3101/a17b80f3678952edbc38a014a0bf2cfbebf39a1a/homosapienDEE2CellScore
─ 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...
* 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 ‘/home/pkgbuild/packagebuilder/workers/jobs/3101/a17b80f3678952edbc38a014a0bf2cfbebf39a1a/homosapienDEE2CellScore.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘homosapienDEE2CellScore/DESCRIPTION’ ... OK
* this is package ‘homosapienDEE2CellScore’ version ‘0.99.9’
* 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 ‘homosapienDEE2CellScore’ 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [10s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/10s] OK
* checking whether the package can be unloaded cleanly ... [9s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [10s/10s] OK
* checking whether startup messages can be suppressed ... [10s/10s] 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 ... [32s/33s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'buildData.Rd':
\examples lines wider than 100 characters:
# To build a restricted set of data, with a cached metadata file, only running deseq2 normalisation, to "data_PASS_deseq2.csv" and "dat ... [TRUNCATED]
homosapienDEE2CellScore::buildData(metadata=metadata, accessions=as.list(unique(cols$SRR_accession)[c(1,3)]), build_deseq2=TRUE, build_ ... [TRUNCATED]
processed_data <- homosapienDEE2CellScore::buildData(metadata=metadata, accessions=as.list(unique(cols$SRR_accession)[c(1,3)]), build_d ... [TRUNCATED]
Rd file 'cols.Rd':
\examples lines wider than 100 characters:
liver_cell_accessions <- homosapienDEE2CellScore::cols$SRR_accession[homosapienDEE2CellScore::cols$cell_type == "liver"]
Rd file 'readInSEZip.Rd':
\examples lines wider than 100 characters:
# We can read in a small SummarizedExperiment containing a subset of the built data stored directly in the package like so
small_data <- readInSEZip(system.file("ASmallSummarizedExperiment.zip", package="homosapienDEE2CellScore"))
Rd file 'srx_agg_se.Rd':
\examples lines wider than 100 characters:
small_data <- readInSEZip(system.file("ASmallSummarizedExperiment.zip", package="homosapienDEE2CellScore"))
Rd file 'writeOutSEZip.Rd':
\examples lines wider than 100 characters:
accessions_of_interest <- buildData(accessions=as.list(unique(cols$SRR_accession)[c(1,3)]), write_files=FALSE, build_raw=TRUE, build_de ... [TRUNCATED]
These lines will be truncated in the PDF manual.
* 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 ... [46s/515s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
buildData 13.139 1.707 190.643
writeOutSEZip 6.630 0.640 152.138
buildRaw 4.582 0.664 152.590
* 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/3101/a17b80f3678952edbc38a014a0bf2cfbebf39a1a/homosapienDEE2CellScore.Rcheck/00check.log’
for details.
===============================
BiocCheck('homosapienDEE2CellScore_0.99.9.tar.gz')
===============================
─ BiocCheckVersion: 1.39.23
─ BiocVersion: 3.19
─ Package: homosapienDEE2CellScore
─ PackageVersion: 0.99.9
─ sourceDir: /tmp/RtmpGUrODL/file3f0cde5fc23f41/homosapienDEE2CellScore
─ installDir: /tmp/RtmpGUrODL/file3f0cde194e77f9
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3101/a17b80f3678952edbc38a014a0bf2cfbebf39a1a/homosapienDEE2CellScore.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...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
ExperimentData
* 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:
ExpressionData
Search 'biocViews' at https://contributions.bioconductor.org
* 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 recommended DESCRIPTION fields...
* NOTE: Provide 'URL', 'BugReports', 'Date' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (78%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of homosapienDEE2CellScore...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
is 1 function greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* Checking unit tests...
* 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...
* NOTE: Consider shorter lines; 149 lines (26%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 175 lines
(31%) 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...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package is in the Support Site Watched Tags.
─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 14 NOTES
See the homosapienDEE2CellScore.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.