===============================
R CMD BUILD
===============================
* checking for file sosta/DESCRIPTION ... OK
* preparing sosta:
* 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 sosta_0.99.2.tar.gz
===============================
BiocCheckGitClone('sosta')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3584/496ff575d5f15ca761b7ea3633412af4d4095bfb/sosta
BiocVersion: 3.21
Package: sosta
PackageVersion: 0.99.2
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3584/496ff575d5f15ca761b7ea3633412af4d4095bfb/sosta.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3584/496ff575d5f15ca761b7ea3633412af4d4095bfb/sosta
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
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3584/496ff575d5f15ca761b7ea3633412af4d4095bfb/sosta.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 sosta/DESCRIPTION ... OK
* this is package sosta version 0.99.2
* 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'
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 sosta 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 ... [11s/11s] 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 ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [11s/11s] 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 ... [33s/33s] 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 ... 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 ... [105s/110s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SPE2ppp 12.222 0.850 13.803
estimateReconstructionParametersSPE 9.535 0.512 10.310
shapeIntensityImage 8.940 0.366 9.958
reconstructShapeDensity 8.137 0.418 8.782
reconstructShapeDensitySPE 6.972 0.315 7.514
meanShapeMetrics 6.909 0.370 7.508
reconstructShapeDensityImage 6.008 0.404 8.909
totalShapeMetrics 6.018 0.218 6.462
getDimXY 5.445 0.210 5.882
findIntensityThreshold 4.918 0.231 5.373
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [42s/43s]
[42s/43s] 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: OK
===============================
BiocCheck('sosta_0.99.2.tar.gz')
===============================
Installing sosta
Package installed successfully
sosta session metadata
sourceDir: /tmp/Rtmp1T2vJM/file3b57c03f3dfdb2/sosta
BiocVersion: 3.21
Package: sosta
PackageVersion: 0.99.2
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3584/496ff575d5f15ca761b7ea3633412af4d4095bfb/sosta.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/Rtmp1T2vJM/file3b57c03f3dfdb2/sosta
installDir: /tmp/Rtmp1T2vJM/file3b57c020704567
isTarBall: TRUE
platform: unix
Running BiocCheck on sosta
* 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 4.0.0 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 (15%).
* 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 sosta...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
The longest 5 functions are:
estimateReconstructionParametersSPE() (R/reconstructShapePPP.R): 53 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; 60 lines (4%) are > 80 characters long.
First few lines:
R/calculateMetrics.R#L27 stopifnot("'sfPoly' must be of type ...
...
vignettes/IMC_DiabetesIslets_Vignette.Rmd#L260 We can use boxplots to
investigate diffe ...
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 3 NOTES
i See the sosta.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.