nebbiolo1 Summary
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| Package: mobileRNA |
| Version: 0.99.17 |
| RVersion: 4.4
|
| BiocVersion: 3.19
|
| BuildCommand: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data mobileRNA |
| BuildTime: 1 minutes 21.50 seconds |
| CheckCommand: BiocCheckGitClone('mobileRNA') && /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3076/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3076/94b6b68617bd1af33c877936c0d987eb899057ea/mobileRNA.install-out.txt mobileRNA_0.99.17.tar.gz && BiocCheck('mobileRNA_0.99.17.tar.gz', `new-package`=TRUE) |
| CheckTime: 5 minutes 35.30 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 3087.93 KiB |
| BuildID:: mobileRNA_20240218222631 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: mobileRNA. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file mobileRNA/DESCRIPTION ... OK
* preparing mobileRNA:
* 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 mobileRNA_0.99.17.tar.gz
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('mobileRNA')
===============================
BiocCheckVersion: 1.39.25
BiocVersion: 3.19
Package: mobileRNA
PackageVersion: 0.99.17
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3076/94b6b68617bd1af33c877936c0d987eb899057ea/mobileRNA
platform: unix
isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
BiocCheck results
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3076/94b6b68617bd1af33c877936c0d987eb899057ea/mobileRNA.Rcheck
* using R Under development (unstable) (2024-01-16 r85808)
* 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 22.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file mobileRNA/DESCRIPTION ... OK
* checking extension type ... Package
* this is package mobileRNA version 0.99.17
* 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 mobileRNA 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 R 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 ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] 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 ... [39s/39s] 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 contents of data directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [82s/82s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
RNAdistribution 11.041 0.076 11.118
RNAdicercall 10.340 0.179 10.520
RNAsubset 10.007 0.060 10.067
RNAdifferentialAnalysis 6.017 0.147 6.165
* 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('mobileRNA_0.99.17.tar.gz')
===============================
BiocCheckVersion: 1.39.25
BiocVersion: 3.19
Package: mobileRNA
PackageVersion: 0.99.17
sourceDir: /tmp/Rtmpaznv2y/file100bf2587aab3a/mobileRNA
installDir: /tmp/Rtmpaznv2y/file100bf2668ab8e4
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3076/94b6b68617bd1af33c877936c0d987eb899057ea/mobileRNA.BiocCheck
platform: unix
isTarBall: TRUE
* Installing package...
* 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...
* NOTE: Update R version dependency from 4.3.0 to 4.4.0.
* 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 blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* NOTE: Invalid ORCID iD for Katie Jeynes-Cupper
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (34%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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 mobileRNA...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 11
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 17 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 9% of man pages use at least one of these tags.
* NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 272 lines (4%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 1960 lines
(31%) are not.
See https://contributions.bioconductor.org/r-code.html
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...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package is in the Support Site Watched Tags.
BiocCheck results
0 ERRORS | 0 WARNINGS | 13 NOTES
See the mobileRNA.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
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merida1 Summary
[top]
| Package: mobileRNA |
| Version: 0.99.17 |
| RVersion: 4.4
|
| BiocVersion: 3.19
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data mobileRNA |
| BuildTime: 3 minutes 49.79 seconds |
| CheckCommand: BiocCheckGitClone('mobileRNA') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3076/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3076/94b6b68617bd1af33c877936c0d987eb899057ea/mobileRNA.install-out.txt mobileRNA_0.99.17.tar.gz && BiocCheck('mobileRNA_0.99.17.tar.gz', `new-package`=TRUE) |
| CheckTime: 14 minutes 26.65 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh mobileRNA_0.99.17.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 1 minutes 26.18 seconds |
| PackageFileSize: 3187.04 KiB |
| BuildID:: mobileRNA_20240218222631 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: mobileRNA. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.WARNING: check time exceeded 10 min. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file mobileRNA/DESCRIPTION ... OK
* preparing mobileRNA:
* 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 mobileRNA_0.99.17.tar.gz
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('mobileRNA')
===============================
BiocCheckVersion: 1.39.25
BiocVersion: 3.19
Package: mobileRNA
PackageVersion: 0.99.17
sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3076/94b6b68617bd1af33c877936c0d987eb899057ea/mobileRNA
platform: unix
isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
BiocCheck results
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /Users/pkgbuild/packagebuilder/workers/jobs/3076/94b6b68617bd1af33c877936c0d987eb899057ea/mobileRNA.Rcheck
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option --no-vignettes
* checking for file mobileRNA/DESCRIPTION ... OK
* checking extension type ... Package
* this is package mobileRNA version 0.99.17
* 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 mobileRNA 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [23s/31s] OK
* checking whether the package can be loaded with stated dependencies ... [22s/26s] OK
* checking whether the package can be unloaded cleanly ... [22s/24s] OK
* checking whether the namespace can be loaded with stated dependencies ... [22s/25s] OK
* checking whether the namespace can be unloaded cleanly ... [23s/30s] OK
* checking loading without being on the library search path ... [23s/28s] 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 ... [83s/108s] OK
* 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 ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [194s/239s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
RNAdistribution 30.759 0.337 36.855
RNAdicercall 29.405 0.467 35.921
RNAsubset 28.994 0.314 34.009
RNAdifferentialAnalysis 15.354 0.401 21.768
RNAsummary 12.683 0.190 16.165
plotSamplePCA 6.623 0.175 8.903
RNApopulation 6.310 0.073 7.423
plotSampleDistance 5.549 0.130 8.212
* 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 ... [16s/22s] OK
* DONE
Status: OK
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('mobileRNA_0.99.17.tar.gz')
===============================
BiocCheckVersion: 1.39.25
BiocVersion: 3.19
Package: mobileRNA
PackageVersion: 0.99.17
sourceDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//RtmpBjlHmK/file93856ac4144e/mobileRNA
installDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//RtmpBjlHmK/file9385566ffcf3
BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3076/94b6b68617bd1af33c877936c0d987eb899057ea/mobileRNA.BiocCheck
platform: unix
isTarBall: TRUE
* Installing package...
* 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...
* NOTE: Update R version dependency from 4.3.0 to 4.4.0.
* 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 blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* NOTE: Invalid ORCID iD for Katie Jeynes-Cupper
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (34%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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 mobileRNA...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 11
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 17 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 9% of man pages use at least one of these tags.
* NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 272 lines (4%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 1960 lines
(31%) are not.
See https://contributions.bioconductor.org/r-code.html
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...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package is in the Support Site Watched Tags.
BiocCheck results
0 ERRORS | 0 WARNINGS | 13 NOTES
See the mobileRNA.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir mobileRNA_0.99.17.tar.gz'
>>>>>>>
* installing *source* package mobileRNA ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mobileRNA)