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R CMD BUILD
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* checking for file chevreulPlot/DESCRIPTION ... OK
* preparing chevreulPlot:
* 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
* looking to see if a data/datalist file should be added
* building chevreulPlot_0.99.7.tar.gz
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BiocCheckGitClone('chevreulPlot')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/3c9a5049e44d4e93817c00d4dab5c2a0b5982273/chevreulPlot
BiocVersion: 3.21
Package: chevreulPlot
PackageVersion: 0.99.7
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/3c9a5049e44d4e93817c00d4dab5c2a0b5982273/chevreulPlot.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/3c9a5049e44d4e93817c00d4dab5c2a0b5982273/chevreulPlot
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 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 v1.43.2 results
0 ERRORS | 0 WARNINGS | i 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/3332/3c9a5049e44d4e93817c00d4dab5c2a0b5982273/chevreulPlot.Rcheck
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file chevreulPlot/DESCRIPTION ... OK
* checking extension type ... Package
* this is package chevreulPlot version 0.99.7
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
INFO
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 whether package chevreulPlot can be installed ... OK
* checking installed package size ... INFO
installed size is 12.5Mb
sub-directories of 1Mb or more:
data 4.6Mb
extdata 7.7Mb
* 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 ... [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 ... [15s/15s] OK
* checking whether the namespace can be unloaded cleanly ... [16s/16s] OK
* checking loading without being on the library search path ... [16s/16s] OK
* checking whether startup messages can be suppressed ... [15s/15s] 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 ... [47s/48s] 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 ... WARNING
Undocumented code objects:
'plotly_settings'
All user-level objects in a package should have documentation entries.
See chapter Writing R documentation files in the Writing R
Extensions manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in Rd file 'plot_colData_on_embedding.Rd':
pt.size
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter Writing R documentation files in the Writing R
Extensions manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of data directory ... OK
* checking data for non-ASCII characters ... [8s/8s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [30s/30s] ERROR
Running examples in chevreulPlot-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_gene_coverage_by_var
> ### Title: Plot BigWig Coverage for Genes of Interest by a Given Variable
> ### Aliases: plot_gene_coverage_by_var
>
> ### ** Examples
>
> tiny_sce <- tiny_sce[,c("ds20181001-0001", "ds20181001-0173")]
Error: object 'tiny_sce' not found
Execution halted
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [19s/19s]
[20s/20s] OK
* 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 ... [3s/3s] OK
* DONE
Status: 1 ERROR, 2 WARNINGs
See
/home/pkgbuild/packagebuilder/workers/jobs/3332/3c9a5049e44d4e93817c00d4dab5c2a0b5982273/chevreulPlot.Rcheck/00check.log
for details.
===============================
BiocCheck('chevreulPlot_0.99.7.tar.gz')
===============================
Installing chevreulPlot
Package installed successfully
chevreulPlot session metadata
sourceDir: /tmp/RtmppmfnaX/file3cf0cdfd5a501/chevreulPlot
BiocVersion: 3.21
Package: chevreulPlot
PackageVersion: 0.99.7
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/3c9a5049e44d4e93817c00d4dab5c2a0b5982273/chevreulPlot.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/RtmppmfnaX/file3cf0cdfd5a501/chevreulPlot
installDir: /tmp/RtmppmfnaX/file3cf0cd5aff8121
isTarBall: TRUE
platform: unix
Running BiocCheck on chevreulPlot
* 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...
i NOTE: Update R version dependency from 4.4.0 to 4.5.0.
* Checking package size...
* Checking individual file sizes...
! WARNING: Package files exceed the 5MB size limit.
Files over the limit:
/tmp/RtmppmfnaX/file3cf0cdfd5a501/chevreulPlot//inst/doc/visualization.html
/tmp/RtmppmfnaX/file3cf0cdfd5a501/chevreulPlot/inst/doc/visualization.html
/tmp/RtmppmfnaX/file3cf0cdfd5a501/chevreulPlot/inst/doc/visualization.html
* 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...
i NOTE: Consider adding these automatically suggested biocViews: ImmunoOncology
i Search 'biocViews' at https://contributions.bioconductor.org
* 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 (29%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/chevreulPlot.Rmd
vignettes/visualization.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of chevreulPlot...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/plotting.R (line 111, column 5)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 4
functions greater than 50 lines.
The longest 5 functions are:
plot_gene_coverage_by_var() (R/wiggleplotr.R): 109 lines
...
plot_transcript_composition() (R/plotting.R): 60 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 9 lines (1%) are > 80 characters long.
First few lines:
R/globals.R#L1 utils::globalVariables(c(".", "Cluster", ...
...
vignettes/visualization.Rmd#L119 plotted using `plot_marker_features`. Th ...
i NOTE: Consider multiples of 4 spaces for line indents; 57 lines (4%) are not.
First few lines:
R/plotting.R#L39 embedding = "UMAP", ...
...
vignettes/visualization.Rmd#L139 ...
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 v1.43.2 results
0 ERRORS | 1 WARNINGS | i 7 NOTES
i See the chevreulPlot.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.