Bioconductor Single Package Builder - Build History

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

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo2 Linux (Ubuntu 22.04.3 LTS)/x86_64   OK     ERROR     skipped     OK  
lconway macOS 12.7.1 Monterey/x86_64   OK     ERROR     OK     OK  

nebbiolo2 Summary

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Package: PRONE
Version: 0.99.1
RVersion: 4.4
BiocVersion: 3.20
BuildCommand: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data PRONE
BuildTime: 1 minutes 49.67 seconds
CheckCommand: BiocCheckGitClone('PRONE') && /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3440/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3440/PRONE_20240701143232/PRONE.install-out.txt PRONE_0.99.1.tar.gz && BiocCheck('PRONE_0.99.1.tar.gz', `new-package`=TRUE)
CheckTime: 6 minutes 35.24 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 8532.44 KiB
BuildID:: PRONE_20240701143232
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: PRONE. 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: 1.

nebbiolo2 BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘PRONE/DESCRIPTION’ ... OK
* preparing ‘PRONE’:
* 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 ‘PRONE_0.99.1.tar.gz’


nebbiolo2 CHECK output

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

 BiocCheckGitClone('PRONE')

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

─ BiocCheckVersion: 1.41.3
─ BiocVersion: 3.20
─ Package: PRONE
─ PackageVersion: 0.99.1
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3440/PRONE_20240701143232/PRONE
─ 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/3440/PRONE_20240701143232/PRONE.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* 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 22.04.4 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PRONE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PRONE’ version ‘0.99.1’
* 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 ‘PRONE’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data      4.9Mb
    extdata   4.7Mb
    help      1.1Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [10s/10s] 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 ... [10s/10s] OK
* checking loading without being on the library search path ... [10s/10s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘NormalyzerDE:::calculateAvgMadMem’
  ‘NormalyzerDE:::calculateAvgReplicateVariation’
  ‘NormalyzerDE:::calculatePercentageAvgDiffInMat’
  ‘NormalyzerDE:::calculateReplicateCV’
  ‘NormalyzerDE:::calculateSummarizedCorrelationVector’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [38s/38s] NOTE
Found the following calls to attach():
File ‘PRONE/R/EigenMS.R’:
  attach(TREAT)
See section ‘Good practice’ in ‘?attach’.
* 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 ... [6s/6s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [148s/163s] OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
plot_pairs_panels            24.301  0.260  24.562
plot_intersection_enrichment  1.399  0.188  17.482
* 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 ... [4s/4s] OK
* DONE

Status: 4 NOTEs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/3440/PRONE_20240701143232/PRONE.Rcheck/00check.log’
for details.





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

 BiocCheck('PRONE_0.99.1.tar.gz')

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

─ BiocCheckVersion: 1.41.3
─ BiocVersion: 3.20
─ Package: PRONE
─ PackageVersion: 0.99.1
─ sourceDir: /tmp/Rtmpe6LihF/file3426bc5ea854ad/PRONE
─ installDir: /tmp/Rtmpe6LihF/file3426bc2ef860c1
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3440/PRONE_20240701143232/PRONE.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
    * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
      removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
    * ERROR: Package tarball exceeds the Bioconductor size requirement.
* 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (33%).
* 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 PRONE...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
    * NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
      times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 33 functions greater than 50 lines.
* Checking man page documentation...
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 1% 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; 1228 lines (16%) are > 80
      characters long.
    * NOTE: Consider 4 spaces instead of tabs; 37 lines (0%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 2720 lines
      (35%) 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 ──
1 ERRORS | 0 WARNINGS | 12 NOTES

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

nebbiolo2 BUILD BIN output

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lconway Summary

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Package: PRONE
Version: 0.99.1
RVersion: 4.4
BiocVersion: 3.20
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data PRONE
BuildTime: 1 minutes 23.04 seconds
CheckCommand: BiocCheckGitClone('PRONE') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3440/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3440/PRONE_20240701143232/PRONE.install-out.txt PRONE_0.99.1.tar.gz && BiocCheck('PRONE_0.99.1.tar.gz', `new-package`=TRUE)
CheckTime: 5 minutes 9.66 seconds
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh PRONE_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir
BuildBinTime: 0 minutes 42.65 seconds
PackageFileSize: 8954.72 KiB
BuildID:: PRONE_20240701143232
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: PRONE. 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.Checking Package status: 1. Build Package status: 0.

lconway BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘PRONE/DESCRIPTION’ ... OK
* preparing ‘PRONE’:
* 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 ‘PRONE_0.99.1.tar.gz’


lconway CHECK output

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

 BiocCheckGitClone('PRONE')

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

─ BiocCheckVersion: 1.41.3
─ BiocVersion: 3.20
─ Package: PRONE
─ PackageVersion: 0.99.1
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3440/PRONE_20240701143232/PRONE
─ 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/3440/PRONE_20240701143232/PRONE.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* 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 ‘PRONE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PRONE’ version ‘0.99.1’
* 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 ‘PRONE’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data      5.0Mb
    extdata   4.7Mb
    help      1.1Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘NormalyzerDE:::calculateAvgMadMem’
  ‘NormalyzerDE:::calculateAvgReplicateVariation’
  ‘NormalyzerDE:::calculatePercentageAvgDiffInMat’
  ‘NormalyzerDE:::calculateReplicateCV’
  ‘NormalyzerDE:::calculateSummarizedCorrelationVector’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [27s/28s] NOTE
Found the following calls to attach():
File ‘PRONE/R/EigenMS.R’:
  attach(TREAT)
See section ‘Good practice’ in ‘?attach’.
* checking Rd files ... [0s/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 ... [5s/5s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [112s/133s] OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
plot_pairs_panels            17.634  0.053  17.694
plot_intersection_enrichment  0.994  0.036  21.547
* 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 ... [7s/7s] OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3440/PRONE_20240701143232/PRONE.Rcheck/00check.log’
for details.





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

 BiocCheck('PRONE_0.99.1.tar.gz')

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

─ BiocCheckVersion: 1.41.3
─ BiocVersion: 3.20
─ Package: PRONE
─ PackageVersion: 0.99.1
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpMzuCGx/file15c2176ca823b/PRONE
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpMzuCGx/file15c2153181917
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3440/PRONE_20240701143232/PRONE.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
    * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
      removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
    * ERROR: Package tarball exceeds the Bioconductor size requirement.
* 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (33%).
* 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 PRONE...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
    * NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
      times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 33 functions greater than 50 lines.
* Checking man page documentation...
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 1% 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; 1228 lines (16%) are > 80
      characters long.
    * NOTE: Consider 4 spaces instead of tabs; 37 lines (0%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 2720 lines
      (35%) 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 ──
1 ERRORS | 0 WARNINGS | 12 NOTES

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

lconway BUILD BIN output

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

 R CMD BUILD

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

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir PRONE_0.99.1.tar.gz'
>>>>>>> 

* installing *source* package ‘PRONE’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (PRONE)