Bioconductor Single Package Builder - Build History

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

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
lconway macOS 12.5.1 Monterey/x86_64   OK     ERROR     OK     OK  
nebbiolo2 Linux (Ubuntu 22.04.2 LTS)/x86_64   OK     ERROR     skipped     OK  

lconway Summary

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Package: orthosData
Version: 0.99.0
RVersion: 4.3
BiocVersion: 3.18
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data orthosData
BuildTime: 0 minutes 27.34 seconds
CheckCommand: BiocCheckGitClone('orthosData') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3042/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3042/orthosData_20230530135609/orthosData.install-out.txt orthosData_0.99.0.tar.gz && BiocCheck('orthosData_0.99.0.tar.gz', `new-package`=TRUE)
CheckTime: 15 minutes 0.82 seconds
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh orthosData_0.99.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir
BuildBinTime: 0 minutes 19.87 seconds
PackageFileSize: 295.76 KiB
BuildID:: orthosData_20230530135609
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: orthosData. Starting Build package. Starting Check package. Starting Build package.
PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. Build Package status: 0.

lconway BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘orthosData/DESCRIPTION’ ... OK
* preparing ‘orthosData’:
* 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 ‘orthosData_0.99.0.tar.gz’


lconway CHECK output

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

 BiocCheckGitClone('orthosData')

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

─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: orthosData
─ PackageVersion: 0.99.0
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3042/orthosData_20230530135609/orthosData
─ 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...

─ 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/3042/orthosData_20230530135609/orthosData.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84266)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘orthosData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘orthosData’ version ‘0.99.0’
* 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 ‘orthosData’ 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 ... WARNING
Invalid license file pointers: LICENSE
* 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
':::' call which should be '::': ‘AnnotationHub:::getInfoOnIds’
  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 ... [19s/20s] 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 ... WARNING
Undocumented arguments in documentation object 'GetorthosContrastDB'
  ‘ARCHS4v’
Documented arguments not in \usage in documentation object 'GetorthosContrastDB':
  ‘ARCH4v’

Undocumented arguments in documentation object 'GetorthosModels'
  ‘ARCHS4v’
Documented arguments not in \usage in documentation object 'GetorthosModels':
  ‘ARCH4v’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [0m/13m] OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
GetorthosContrastDB 2.656  3.262 460.649
GetorthosModels     2.088  2.557 296.128
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3042/orthosData_20230530135609/orthosData.Rcheck/00check.log’
for details.






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

 BiocCheck('orthosData_0.99.0.tar.gz')

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

─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: orthosData
─ PackageVersion: 0.99.0
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpYLQsK5/filecb0a1bc7b9f9/orthosData
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpYLQsK5/filecb0a70f5f35d
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3042/orthosData_20230530135609/orthosData.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...
    ExperimentData
* 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:
      ExpressionData
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...
    * NOTE: The Description field in the DESCRIPTION is made up by less
      than 3 sentences. Please consider expanding this field, and
      structure it as a full paragraph
* 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 pinned package versions...
* 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 orthosData...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
      times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      is 1 function greater than 50 lines.
* Checking man page documentation...
* 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; 52 lines (8%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 18 lines
      (3%) 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...
    * ERROR: Maintainer must subscribe to the bioc-devel mailing list.
      Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 7 NOTES

See the orthosData.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 orthosData_0.99.0.tar.gz'
>>>>>>> 

* installing *source* package ‘orthosData’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (orthosData)



nebbiolo2 Summary

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Package: orthosData
Version: 0.99.0
RVersion: 4.3
BiocVersion: 3.18
BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data orthosData
BuildTime: 0 minutes 38.56 seconds
CheckCommand: BiocCheckGitClone('orthosData') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3042/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3042/orthosData_20230530135609/orthosData.install-out.txt orthosData_0.99.0.tar.gz && BiocCheck('orthosData_0.99.0.tar.gz', `new-package`=TRUE)
CheckTime: 15 minutes 2.11 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 295.88 KiB
BuildID:: orthosData_20230530135609
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: orthosData. Starting Build package. Starting Check package.
PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1.

nebbiolo2 BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘orthosData/DESCRIPTION’ ... OK
* preparing ‘orthosData’:
* 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 ‘orthosData_0.99.0.tar.gz’


nebbiolo2 CHECK output

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

 BiocCheckGitClone('orthosData')

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

─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: orthosData
─ PackageVersion: 0.99.0
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3042/orthosData_20230530135609/orthosData
─ 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...

─ 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/3042/orthosData_20230530135609/orthosData.Rcheck’
* using R version 4.3.0 RC (2023-04-18 r84287)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘orthosData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘orthosData’ version ‘0.99.0’
* 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 ‘orthosData’ 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 ... WARNING
Invalid license file pointers: LICENSE
* 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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
':::' call which should be '::': ‘AnnotationHub:::getInfoOnIds’
  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 ... [28s/28s] 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 ... WARNING
Undocumented arguments in documentation object 'GetorthosContrastDB'
  ‘ARCHS4v’
Documented arguments not in \usage in documentation object 'GetorthosContrastDB':
  ‘ARCH4v’

Undocumented arguments in documentation object 'GetorthosModels'
  ‘ARCHS4v’
Documented arguments not in \usage in documentation object 'GetorthosModels':
  ‘ARCH4v’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [0m/12m] OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
GetorthosContrastDB 3.903  2.368 407.137
GetorthosModels     3.058  2.157 297.600
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [2s/2s] OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/3042/orthosData_20230530135609/orthosData.Rcheck/00check.log’
for details.






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

 BiocCheck('orthosData_0.99.0.tar.gz')

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

─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: orthosData
─ PackageVersion: 0.99.0
─ sourceDir: /tmp/Rtmpp9CA5m/file12073260311aee/orthosData
─ installDir: /tmp/Rtmpp9CA5m/file1207326e9507a8
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3042/orthosData_20230530135609/orthosData.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...
    ExperimentData
* 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:
      ExpressionData
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...
    * NOTE: The Description field in the DESCRIPTION is made up by less
      than 3 sentences. Please consider expanding this field, and
      structure it as a full paragraph
* 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 pinned package versions...
* 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 orthosData...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
      times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      is 1 function greater than 50 lines.
* Checking man page documentation...
* 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; 52 lines (8%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 18 lines
      (3%) 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...
    * ERROR: Maintainer must subscribe to the bioc-devel mailing list.
      Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 7 NOTES

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

nebbiolo2 BUILD BIN output

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