Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/transmogR
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo1 Linux (Ubuntu 22.04.3 LTS)/x86_64   OK     OK     skipped     OK  
merida1 macOS 12.7.1 Monterey/x86_64   OK     WARNINGS     OK     OK  

nebbiolo1 Summary

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Package: transmogR
Version: 0.99.2
RVersion: 4.4
BiocVersion: 3.19
BuildCommand: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data transmogR
BuildTime: 1 minutes 7.78 seconds
CheckCommand: BiocCheckGitClone('transmogR') && /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3277/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3277/96b04d1457b97e47d2ca38d3533d3ee84d505378/transmogR.install-out.txt transmogR_0.99.2.tar.gz && BiocCheck('transmogR_0.99.2.tar.gz', `new-package`=TRUE)
CheckTime: 5 minutes 35.40 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 537.10 KiB
BuildID:: transmogR_20240212153559
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: transmogR. 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 ‘transmogR/DESCRIPTION’ ... OK
* preparing ‘transmogR’:
* 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 ‘transmogR_0.99.2.tar.gz’


nebbiolo1 CHECK output

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===============================

 BiocCheckGitClone('transmogR')

===============================

─ BiocCheckVersion: 1.39.23
─ BiocVersion: 3.19
─ Package: transmogR
─ PackageVersion: 0.99.2
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3277/96b04d1457b97e47d2ca38d3533d3ee84d505378/transmogR
─ 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...
    * 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 results ──
0 ERRORS | 0 WARNINGS | 1 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




===============================

 R CMD CHECK

===============================

* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3277/96b04d1457b97e47d2ca38d3533d3ee84d505378/transmogR.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 ‘transmogR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘transmogR’ version ‘0.99.2’
* 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 serialization versions ... OK
* checking whether package ‘transmogR’ 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/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] OK
* checking loading without being on the library search path ... [12s/12s] 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 ... [42s/42s] 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 ... [35s/35s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [38s/38s]
 [38s/38s] 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('transmogR_0.99.2.tar.gz')

===============================

─ BiocCheckVersion: 1.39.23
─ BiocVersion: 3.19
─ Package: transmogR
─ PackageVersion: 0.99.2
─ sourceDir: /tmp/Rtmpcyw6Dy/file187e1bc3400ff/transmogR
─ installDir: /tmp/Rtmpcyw6Dy/file187e1b67250197
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3277/96b04d1457b97e47d2ca38d3533d3ee84d505378/transmogR.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...
* 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...
    * NOTE: Consider adding these automatically suggested biocViews:
      Coverage, VariantAnnotation, SequenceMatching, DataImport
Search 'biocViews' at https://contributions.bioconductor.org
* 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
    * NOTE: Provide 'Date' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (60%).
* 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 transmogR...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 5 functions greater than 50 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...
    * NOTE: Consider shorter lines; 8 lines (0%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 1 lines
      (0%) 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 | 5 NOTES

See the transmogR.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

nebbiolo1 BUILD BIN output

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merida1 Summary

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Package: transmogR
Version: 0.99.2
RVersion: 4.4
BiocVersion: 3.19
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data transmogR
BuildTime: 2 minutes 43.62 seconds
CheckCommand: BiocCheckGitClone('transmogR') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3277/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3277/96b04d1457b97e47d2ca38d3533d3ee84d505378/transmogR.install-out.txt transmogR_0.99.2.tar.gz && BiocCheck('transmogR_0.99.2.tar.gz', `new-package`=TRUE)
CheckTime: 12 minutes 28.36 seconds
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh transmogR_0.99.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir
BuildBinTime: 1 minutes 28.90 seconds
PackageFileSize: 571.05 KiB
BuildID:: transmogR_20240212153559
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: transmogR. 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 ‘transmogR/DESCRIPTION’ ... OK
* preparing ‘transmogR’:
* 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 ‘transmogR_0.99.2.tar.gz’


merida1 CHECK output

[top]

===============================

 BiocCheckGitClone('transmogR')

===============================

─ BiocCheckVersion: 1.39.23
─ BiocVersion: 3.19
─ Package: transmogR
─ PackageVersion: 0.99.2
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3277/96b04d1457b97e47d2ca38d3533d3ee84d505378/transmogR
─ 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...
    * 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 results ──
0 ERRORS | 0 WARNINGS | 1 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




===============================

 R CMD CHECK

===============================

* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3277/96b04d1457b97e47d2ca38d3533d3ee84d505378/transmogR.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 ‘transmogR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘transmogR’ version ‘0.99.2’
* 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 serialization versions ... OK
* checking whether package ‘transmogR’ 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 ... [27s/29s] OK
* checking whether the package can be loaded with stated dependencies ... [26s/29s] OK
* checking whether the package can be unloaded cleanly ... [26s/28s] OK
* checking whether the namespace can be loaded with stated dependencies ... [26s/28s] OK
* checking whether the namespace can be unloaded cleanly ... [27s/29s] OK
* checking loading without being on the library search path ... [27s/29s] 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 ... [76s/82s] 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 files in ‘vignettes’ ... OK
* checking examples ... [62s/68s] OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
sjFromExons         10.116  0.564  11.824
genomogrify-methods  6.495  0.422   7.844
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [81s/88s]
 [81s/88s] 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 ... [12s/13s] OK
* DONE

Status: OK

 WARNING: R CMD check exceeded 10 min requirement






===============================

 BiocCheck('transmogR_0.99.2.tar.gz')

===============================

─ BiocCheckVersion: 1.39.23
─ BiocVersion: 3.19
─ Package: transmogR
─ PackageVersion: 0.99.2
─ sourceDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//Rtmp2yKcw3/file94e83e1f741c/transmogR
─ installDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//Rtmp2yKcw3/file94e8737e8e10
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3277/96b04d1457b97e47d2ca38d3533d3ee84d505378/transmogR.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...
* 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...
    * NOTE: Consider adding these automatically suggested biocViews:
      Coverage, VariantAnnotation, SequenceMatching, DataImport
Search 'biocViews' at https://contributions.bioconductor.org
* 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
    * NOTE: Provide 'Date' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (60%).
* 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 transmogR...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 5 functions greater than 50 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...
    * NOTE: Consider shorter lines; 8 lines (0%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 1 lines
      (0%) 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 | 5 NOTES

See the transmogR.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 transmogR_0.99.2.tar.gz'
>>>>>>> 

* installing *source* package ‘transmogR’ ...
** using staged installation
** R
** 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 (transmogR)