===============================
R CMD BUILD
===============================
* checking for file chevreul/DESCRIPTION ... OK
* preparing chevreul:
* 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 chevreul_0.99.38.tar.gz
===============================
BiocCheckGitClone('chevreul')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/5e4506fb2d18665e2ef33b196abb6bb0fbb007c6/chevreul
BiocVersion: 3.20
Package: chevreul
PackageVersion: 0.99.38
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/5e4506fb2d18665e2ef33b196abb6bb0fbb007c6/chevreul.BiocCheck
BiocCheckVersion: 1.41.16
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/5e4506fb2d18665e2ef33b196abb6bb0fbb007c6/chevreul
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
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3332/5e4506fb2d18665e2ef33b196abb6bb0fbb007c6/chevreul.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 chevreul/DESCRIPTION ... OK
* checking extension type ... Package
* this is package chevreul version 0.99.38
* 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 whether package chevreul 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 ... [20s/20s] OK
* checking whether the package can be loaded with stated dependencies ... [19s/19s] OK
* checking whether the package can be unloaded cleanly ... [19s/19s] OK
* checking whether the namespace can be loaded with stated dependencies ... [19s/19s] OK
* checking whether the namespace can be unloaded cleanly ... [19s/19s] OK
* checking loading without being on the library search path ... [19s/19s] OK
* checking whether startup messages can be suppressed ... [19s/19s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
'ExperimentHub' 'httr'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [64s/64s] NOTE
Found the following calls to data() loading into the global environment:
File chevreul/R/chevreul_app.R:
data("grch38_tx2gene")
File chevreul/R/plotting.R:
data(cc.genes.cyclone)
data("grch38")
data("grch38_tx2gene")
See section Good practice in ?data.
* 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 data sets:
'tiny_sce'
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 ... WARNING
Functions or methods with usage in Rd file 'pipe.Rd' but not in code:
'%>%'
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of data directory ... OK
* checking data for non-ASCII characters ... [10s/10s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [77s/77s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [114s/115s]
[114s/115s] 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: 2 WARNINGs, 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3332/5e4506fb2d18665e2ef33b196abb6bb0fbb007c6/chevreul.Rcheck/00check.log
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('chevreul_0.99.38.tar.gz')
===============================
Installing chevreul
Package installed successfully
chevreul session metadata
sourceDir: /tmp/RtmpEQNy4v/file3c395d2595ad45/chevreul
BiocVersion: 3.20
Package: chevreul
PackageVersion: 0.99.38
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/5e4506fb2d18665e2ef33b196abb6bb0fbb007c6/chevreul.BiocCheck
BiocCheckVersion: 1.41.16
sourceDir: /tmp/RtmpEQNy4v/file3c395d2595ad45/chevreul
installDir: /tmp/RtmpEQNy4v/file3c395d7c95e50f
isTarBall: TRUE
platform: unix
Running BiocCheck on chevreul
* 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...
! W: Package files exceed the 5MB size limit.
Files over the limit:
/tmp/RtmpEQNy4v/file3c395d2595ad45/chevreul//inst/doc/visualization.html
/tmp/RtmpEQNy4v/file3c395d2595ad45/chevreul/inst/doc/visualization.html
/tmp/RtmpEQNy4v/file3c395d2595ad45/chevreul/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 N: Consider adding these automatically suggested biocViews: Transcriptomics,
Normalization, Preprocessing, ImmunoOncology, QualityControl,
DimensionReduction, DataImport
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 (25%).
* 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 chevreul...
* Checking coding practice...
i N: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/chevreul_app.R (line 706, column 13)
...
print in R/shiny_modules.R (line 1172, column 26)
i N: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/chevreul_app.R (line 122, column 13)
R/docker_app.R (line 24, column 11)
R/minimal_chevreul_app.R (line 26, column 11)
i N: Avoid the use of 'paste' in condition signals
Found in files:
R/project_management.R (line 79, column 9)
R/wiggleplotr.R (line 58, column 13)
i N: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/utils.R (line 158, column 25)
R/utils.R (line 158, column 71)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i N: The recommended function length is 50 lines or less. There are 23
functions greater than 50 lines.
The longest 5 functions are:
chevreulApp() (R/chevreul_app.R): 599 lines
...
server() (R/minimal_chevreul_app.R): 212 lines
* Checking man page documentation...
E: At least 80% of man pages documenting exported objects must have runnable
examples.
The following pages do not:
annotate_cell_cycle.Rd
...
update_project_db.Rd
i N: Usage of dontrun / donttest tags found in man page examples. 14% of man
pages use at least one of these tags.
Found in files:
build_bigwig_db.Rd
...
update_project_db.Rd
* 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 N: Consider shorter lines; 343 lines (5%) are > 80 characters long.
First few lines:
R/chevreul_app.R#L581 object()[, colname ...
...
vignettes/visualization.Rmd#L31 crop = NULL, ## Related to https://s ...
i N: Consider 4 spaces instead of tabs; 57 lines (1%) contain tabs.
First few lines:
R/chevreul_app.R#L19 data_env <- new.env(parent = emptyenv() ...
...
R/zzz.R#L12 ...
i N: Consider multiples of 4 spaces for line indents; 67 lines (1%) are not.
First few lines:
R/chevreul_app.R#L16 diffex_scheme ...
...
vignettes/visualization.Rmd#L142 ...
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
1 ERRORS | 1 WARNINGS | 10 NOTES
i See the chevreul.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.