===============================
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_0.99.16.tar.gz
===============================
BiocCheckGitClone('homosapienDEE2CellScore')
===============================
BiocCheckVersion: 1.39.27
BiocVersion: 3.19
Package: homosapienDEE2CellScore
PackageVersion: 0.99.16
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3101/53e49439ecd15d4dceb494a77f84387c79a44412/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/3101/53e49439ecd15d4dceb494a77f84387c79a44412/homosapienDEE2CellScore.Rcheck
* using R Under development (unstable) (2024-03-18 r86148)
* 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 homosapienDEE2CellScore/DESCRIPTION ... OK
* this is package homosapienDEE2CellScore version 0.99.16
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [10s/10s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/10s] 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 ... [31s/31s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
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 ... [35s/422s] ERROR
Running examples in homosapienDEE2CellScore-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: readInSEFolder
> ### Title: readInSEFolder read a SummarizedExperiment in from a folder
> ### Aliases: readInSEFolder
>
> ### ** Examples
>
> # We can read in a small SummarizedExperiment containing a
> # subset of the built data stored directly in the package like so
> small_data <- readInSEFolder(
+ folder_name=system.file("ExampleSummarisedExperimentFolder", package="homosapienDEE2CellScore"))
Error in readInSEFolder(folder_name = system.file("ExampleSummarisedExperimentFolder", :
could not find function "readInSEFolder"
Execution halted
* 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 ERROR, 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3101/53e49439ecd15d4dceb494a77f84387c79a44412/homosapienDEE2CellScore.Rcheck/00check.log
for details.
===============================
BiocCheck('homosapienDEE2CellScore_0.99.16.tar.gz')
===============================
BiocCheckVersion: 1.39.27
BiocVersion: 3.19
Package: homosapienDEE2CellScore
PackageVersion: 0.99.16
sourceDir: /tmp/RtmpXr0vxJ/file349f0d35d191b4/homosapienDEE2CellScore
installDir: /tmp/RtmpXr0vxJ/file349f0dc957edd
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3101/53e49439ecd15d4dceb494a77f84387c79a44412/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...
* 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' 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...
* 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...
* 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; 162 lines (26%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 175 lines
(28%) 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 | 0 WARNINGS | 12 NOTES
See the homosapienDEE2CellScore.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.