===============================
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_0.99.50.tar.gz’
===============================
BiocCheckGitClone('chevreul')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/f7a54ca42dbee39e4cf8ff8b5b5550d38ee0bed6/chevreul
→ BiocVersion: 3.20
→ Package: chevreul
→ PackageVersion: 0.99.50
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/f7a54ca42dbee39e4cf8ff8b5b5550d38ee0bed6/chevreul.BiocCheck
→ BiocCheckVersion: 1.41.16
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/f7a54ca42dbee39e4cf8ff8b5b5550d38ee0bed6/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/f7a54ca42dbee39e4cf8ff8b5b5550d38ee0bed6/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 ‘0.99.50’
* 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 ... [19s/19s] 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 ... [20s/20s] OK
* checking loading without being on the library search path ... [20s/20s] OK
* checking whether startup messages can be suppressed ... [18s/18s] 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 ... [65s/65s] NOTE
minimalChevreulApp : server: no visible global function definition for
'bject_pipeline'
Undefined global functions or variables:
bject_pipeline
* 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 ... WARNING
Undocumented arguments in Rd file 'object_cluster.Rd'
‘ustom_clust’
Documented arguments not in \usage in Rd file 'object_cluster.Rd':
‘custom_clust’
Undocumented arguments in Rd file 'plot_readcount.Rd'
‘...’
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 ... [9s/9s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [72s/72s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [30s/30s]
[30s/30s] 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 WARNING, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3332/f7a54ca42dbee39e4cf8ff8b5b5550d38ee0bed6/chevreul.Rcheck/00check.log’
for details.
===============================
BiocCheck('chevreul_0.99.50.tar.gz')
===============================
── Installing chevreul ─────────────────────────────────────────────────────────
✔ Package installed successfully
── chevreul session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpzxHnyn/file27df526e743dd/chevreul
→ BiocVersion: 3.20
→ Package: chevreul
→ PackageVersion: 0.99.50
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/f7a54ca42dbee39e4cf8ff8b5b5550d38ee0bed6/chevreul.BiocCheck
→ BiocCheckVersion: 1.41.16
→ sourceDir: /tmp/RtmpzxHnyn/file27df526e743dd/chevreul
→ installDir: /tmp/RtmpzxHnyn/file27df5277bb460d
→ 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/RtmpzxHnyn/file27df526e743dd/chevreul//inst/doc/visualization.html
• /tmp/RtmpzxHnyn/file27df526e743dd/chevreul/inst/doc/visualization.html
• /tmp/RtmpzxHnyn/file27df526e743dd/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...
* 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 711, column 13)
• ...
• print in R/shiny_modules.R (line 1312, column 26)
i N: Avoid the use of 'paste' in condition signals
Found in files:
• R/wiggleplotr.R (line 50, column 13)
i N: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/utils.R (line 171, column 25)
• R/utils.R (line 172, column 28)
* 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 25
functions greater than 50 lines.
The longest 5 functions are:
• chevreulApp() (R/chevreul_app.R): 602 lines
• ...
• server() (R/docker_app.R): 215 lines
* Checking man page documentation...
i N: Consider adding runnable examples to man pages that document exported
objects.
• build_bigwig_db.Rd
• ...
• minimalChevreulApp.Rd
i N: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
Found in files:
• chevreulApp.Rd
• dockerChevreulApp.Rd
• minimalChevreulApp.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; 93 lines (1%) are > 80 characters long.
First few lines:
• R/docker_app.R#L336 organism = m ...
• ...
• vignettes/visualization.Rmd#L31 crop = NULL, ## Related to https://s ...
i N: Consider multiples of 4 spaces for line indents; 303 lines (4%) are not.
First few lines:
• R/chevreul_app.R#L16 diffex_scheme ...
• ...
• vignettes/visualization.Rmd#L140 ...
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 | • 8 NOTES
i See the chevreul.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.