===============================
R CMD BUILD
===============================
* checking for file SEraster/DESCRIPTION ... OK
* preparing SEraster:
* 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 SEraster_0.99.3.tar.gz
===============================
BiocCheckGitClone('SEraster')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3448/114c86f08fd86cf24be1160dfc6dc9beb162463d/SEraster
BiocVersion: 3.21
Package: SEraster
PackageVersion: 0.99.3
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3448/114c86f08fd86cf24be1160dfc6dc9beb162463d/SEraster.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3448/114c86f08fd86cf24be1160dfc6dc9beb162463d/SEraster
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...
* Checking that provided CITATION file is correctly formatted...
BiocCheck v1.43.2 results
0 ERRORS | 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3448/114c86f08fd86cf24be1160dfc6dc9beb162463d/SEraster.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 SEraster/DESCRIPTION ... OK
* checking extension type ... Package
* this is package SEraster version 0.99.3
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Package suggested but not available: MERINGUE
The suggested packages are required for a complete check.
Checking can be attempted without them by setting the environment
variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
See section The DESCRIPTION file in the Writing R Extensions
manual.
* DONE
Status: 1 ERROR
See
/home/pkgbuild/packagebuilder/workers/jobs/3448/114c86f08fd86cf24be1160dfc6dc9beb162463d/SEraster.Rcheck/00check.log
for details.
===============================
BiocCheck('SEraster_0.99.3.tar.gz')
===============================
Installing SEraster
Package installed successfully
SEraster session metadata
sourceDir: /tmp/RtmpcXorVh/file1ed07170821355/SEraster
BiocVersion: 3.21
Package: SEraster
PackageVersion: 0.99.3
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3448/114c86f08fd86cf24be1160dfc6dc9beb162463d/SEraster.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/RtmpcXorVh/file1ed07170821355/SEraster
installDir: /tmp/RtmpcXorVh/file1ed07166b5b546
isTarBall: TRUE
platform: unix
Running BiocCheck on SEraster
* 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...
* 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 (38%).
* 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 SEraster...
* Checking coding practice...
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/main.R (line 621, column 13)
R/main.R (line 640, column 15)
* 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 5
functions greater than 50 lines.
The longest 5 functions are:
rasterizeMatrix() (R/main.R): 100 lines
...
plotRaster() (R/main.R): 59 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; 265 lines (21%) are > 80 characters long.
First few lines:
R/data.R#L1 #' Preprocessed MERFISH dataset of the m ...
...
vignettes/getting-started-with-SEraster.Rmd#L342
CooccurrenceAffinity::plotgg(data = ct_c ...
i NOTE: Consider multiples of 4 spaces for line indents; 265 lines (21%) are
not.
First few lines:
R/main.R#L99 ## set up parallel execution back-end ...
...
vignettes/getting-started-with-SEraster.Rmd#L241 show(plt) ...
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 | 0 WARNINGS | i 5 NOTES
i See the SEraster.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.