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R CMD BUILD
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* checking for file BulkSignalR/DESCRIPTION ... OK
* preparing BulkSignalR:
* 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 BulkSignalR_0.99.9.tar.gz
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BiocCheckGitClone('BulkSignalR')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3554/4a0c97faae133ffa3f3e44ab2dd8cae8fd4a2c1e/BulkSignalR
BiocVersion: 3.21
Package: BulkSignalR
PackageVersion: 0.99.9
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3554/4a0c97faae133ffa3f3e44ab2dd8cae8fd4a2c1e/BulkSignalR.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3554/4a0c97faae133ffa3f3e44ab2dd8cae8fd4a2c1e/BulkSignalR
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
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3554/4a0c97faae133ffa3f3e44ab2dd8cae8fd4a2c1e/BulkSignalR.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 BulkSignalR/DESCRIPTION ... OK
* checking extension type ... Package
* this is package BulkSignalR version 0.99.9
* 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 28 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 BulkSignalR 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 ... [14s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/14s] OK
* checking whether the package can be unloaded cleanly ... [13s/13s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the namespace can be unloaded cleanly ... [14s/14s] OK
* checking loading without being on the library search path ... [14s/14s] OK
* checking whether startup messages can be suppressed ... [14s/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 ... [53s/54s] NOTE
Found the following calls to attach():
File BulkSignalR/R/zzz.R:
attach(myEnv, name = nameEnv)
See section Good practice in ?attach.
* checking Rd files ... [1s/1s] 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 contents of data directory ... OK
* checking data for non-ASCII characters ... [15s/16s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [183s/190s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
generateSpatialPlots 9.987 1.530 12.028
learnParameters 11.159 0.085 11.247
spatialAssociationPlot 7.851 1.510 9.472
separatedLRPlot 5.541 0.528 6.216
spatialIndexPlot 5.251 0.693 6.047
spatialPlot 4.962 0.698 5.786
spatialAssociation 4.979 0.611 5.692
spatialDiversityPlot 4.809 0.668 5.623
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [14s/14s]
[14s/15s] 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 ... [6s/6s] OK
* DONE
Status: 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3554/4a0c97faae133ffa3f3e44ab2dd8cae8fd4a2c1e/BulkSignalR.Rcheck/00check.log
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('BulkSignalR_0.99.9.tar.gz')
===============================
Installing BulkSignalR
Package installed successfully
BulkSignalR session metadata
sourceDir: /tmp/Rtmp85XGMb/file14e1e3742e5aff/BulkSignalR
BiocVersion: 3.21
Package: BulkSignalR
PackageVersion: 0.99.9
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3554/4a0c97faae133ffa3f3e44ab2dd8cae8fd4a2c1e/BulkSignalR.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/Rtmp85XGMb/file14e1e3742e5aff/BulkSignalR
installDir: /tmp/Rtmp85XGMb/file14e1e377cd1020
isTarBall: TRUE
platform: unix
Running BiocCheck on BulkSignalR
* 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...
* 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 (19%).
* 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 BulkSignalR...
* 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 are 53
functions greater than 50 lines.
The longest 5 functions are:
.downstreamRegulatedSignaling() (R/regulatedInference.R): 207 lines
...
getLRIntracellNetwork() (R/networks.R): 173 lines
* Checking man page documentation...
Local "database" is up to date.
Local "resources" are up to date.
* 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; 1 lines (0%) are > 80 characters long.
First few lines:
R/BSRInference-class.R#L913 #' bsrinf <- resetToInitialOrganism(bsri ...
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 2 NOTES
i See the BulkSignalR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.