Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/MouseAgingData
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     ERROR     skipped     OK  
merida1 macOS 12.7.1 Monterey/x86_64   OK     ERROR     WARNINGS     OK  

nebbiolo1 Summary

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Package: MouseAgingData
Version: 0.99.1
RVersion: 4.4
BiocVersion: 3.19
BuildCommand: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MouseAgingData
BuildTime: 24 minutes 10.72 seconds
CheckCommand: BiocCheckGitClone('MouseAgingData') && /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3293/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3293/845d9af2d0ef8a864d34513913f4dd2208ca29d6/MouseAgingData.install-out.txt MouseAgingData_0.99.1.tar.gz && BiocCheck('MouseAgingData_0.99.1.tar.gz', `new-package`=TRUE)
CheckTime: 3 minutes 35.69 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 1458.13 KiB
BuildID:: MouseAgingData_20240212215124
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: MouseAgingData. Starting Build package. Starting Check package.
PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1.

nebbiolo1 BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘MouseAgingData/DESCRIPTION’ ... OK
* preparing ‘MouseAgingData’:
* 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 ‘MouseAgingData_0.99.1.tar.gz’


nebbiolo1 CHECK output

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

 BiocCheckGitClone('MouseAgingData')

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

─ BiocCheckVersion: 1.39.23
─ BiocVersion: 3.19
─ Package: MouseAgingData
─ PackageVersion: 0.99.1
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3293/845d9af2d0ef8a864d34513913f4dd2208ca29d6/MouseAgingData
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
    * WARNING: System files in '/inst' should not be Git tracked.
      inst/.DS_Store
    * ERROR: System files found that should not be Git tracked.
      MouseAgingData.Rproj
* 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 ──
1 ERRORS | 1 WARNINGS | 1 NOTES

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




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

 R CMD CHECK

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

* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3293/845d9af2d0ef8a864d34513913f4dd2208ca29d6/MouseAgingData.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 ‘MouseAgingData/DESCRIPTION’ ... OK
* this is package ‘MouseAgingData’ 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
WARNING: omitting pointless dependence on 'R' without a version requirement
* checking serialization versions ... OK
* checking whether package ‘MouseAgingData’ can be installed ... WARNING
Found the following significant warnings:
  WARNING: omitting pointless dependence on 'R' without a version requirement
See ‘/home/pkgbuild/packagebuilder/workers/jobs/3293/845d9af2d0ef8a864d34513913f4dd2208ca29d6/MouseAgingData.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ...WARNING: omitting pointless dependence on 'R' without a version requirement
 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 ... [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
Namespaces in Imports field not imported from:
  ‘BiocGenerics’ ‘S4Vectors’ ‘methods’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [30s/30s] NOTE
parabiosis10X: no visible global function definition for ‘query’
Undefined global functions or variables:
  query
* 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 ... [11s/11s] ERROR
Running examples in ‘MouseAgingData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: parabiosis10X
> ### Title: Load mouse aging parabiosis data
> ### Aliases: parabiosis10X
> 
> ### ** Examples
> 
> data <- parabiosis10X()
Error in query(eh, title) : could not find function "query"
Calls: parabiosis10X
Execution halted
* 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 ... [2s/2s] OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/3293/845d9af2d0ef8a864d34513913f4dd2208ca29d6/MouseAgingData.Rcheck/00check.log’
for details.





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

 BiocCheck('MouseAgingData_0.99.1.tar.gz')

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

─ BiocCheckVersion: 1.39.23
─ BiocVersion: 3.19
─ Package: MouseAgingData
─ PackageVersion: 0.99.1
─ sourceDir: /tmp/Rtmp5lHARn/file3f07db7f10c324/MouseAgingData
─ installDir: /tmp/Rtmp5lHARn/file3f07db74a090f6
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3293/845d9af2d0ef8a864d34513913f4dd2208ca29d6/MouseAgingData.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...
* 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 (80%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
    * WARNING: Import BiocGenerics, methods, S4Vectors in NAMESPACE as
      well as DESCRIPTION.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
    * ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
      'VignetteEngine' in any vignettes:
    * ERROR: 'VignetteEngine' specified but not in the DESCRIPTION.
    * WARNING: Package listed as VignetteEngine or VignetteBuilder but
      not currently Suggested.
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MouseAgingData...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* 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; 1 lines (0%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 10 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...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    Maintainer is registered at support site.
    * ERROR: Add package to Watched Tags in your Support Site profile;
      visit https://support.bioconductor.org/accounts/edit/profile

─ BiocCheck results ──
3 ERRORS | 2 WARNINGS | 4 NOTES

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

nebbiolo1 BUILD BIN output

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merida1 Summary

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Package: MouseAgingData
Version: 0.99.1
RVersion: 4.4
BiocVersion: 3.19
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MouseAgingData
BuildTime: 45 minutes 32.35 seconds
CheckCommand: BiocCheckGitClone('MouseAgingData') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3293/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3293/845d9af2d0ef8a864d34513913f4dd2208ca29d6/MouseAgingData.install-out.txt MouseAgingData_0.99.1.tar.gz && BiocCheck('MouseAgingData_0.99.1.tar.gz', `new-package`=TRUE)
CheckTime: 9 minutes 36.26 seconds
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh MouseAgingData_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir
BuildBinTime: 1 minutes 8.24 seconds
PackageFileSize: 1431.17 KiB
BuildID:: MouseAgingData_20240212215124
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: MouseAgingData. Starting Build package. Starting Check package. Starting Build package.
PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1. Build Package status: 0.

merida1 BUILD SRC output

[top]

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

 R CMD BUILD

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

* checking for file ‘MouseAgingData/DESCRIPTION’ ... OK
* preparing ‘MouseAgingData’:
* 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 ‘MouseAgingData_0.99.1.tar.gz’


merida1 CHECK output

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

 BiocCheckGitClone('MouseAgingData')

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

─ BiocCheckVersion: 1.39.23
─ BiocVersion: 3.19
─ Package: MouseAgingData
─ PackageVersion: 0.99.1
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3293/845d9af2d0ef8a864d34513913f4dd2208ca29d6/MouseAgingData
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
    * WARNING: System files in '/inst' should not be Git tracked.
      inst/.DS_Store
    * ERROR: System files found that should not be Git tracked.
      MouseAgingData.Rproj
* 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 ──
1 ERRORS | 1 WARNINGS | 1 NOTES

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




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

 R CMD CHECK

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

* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3293/845d9af2d0ef8a864d34513913f4dd2208ca29d6/MouseAgingData.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 ‘MouseAgingData/DESCRIPTION’ ... OK
* this is package ‘MouseAgingData’ 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
WARNING: omitting pointless dependence on 'R' without a version requirement
* checking serialization versions ... OK
* checking whether package ‘MouseAgingData’ can be installed ... WARNING
Found the following significant warnings:
  WARNING: omitting pointless dependence on 'R' without a version requirement
See ‘/Users/pkgbuild/packagebuilder/workers/jobs/3293/845d9af2d0ef8a864d34513913f4dd2208ca29d6/MouseAgingData.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ...WARNING: omitting pointless dependence on 'R' without a version requirement
 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 ... [21s/26s] OK
* checking whether the package can be loaded with stated dependencies ... [20s/26s] OK
* checking whether the package can be unloaded cleanly ... [21s/29s] OK
* checking whether the namespace can be loaded with stated dependencies ... [19s/26s] OK
* checking whether the namespace can be unloaded cleanly ... [21s/26s] OK
* checking loading without being on the library search path ... [21s/30s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘BiocGenerics’ ‘S4Vectors’ ‘methods’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [63s/80s] NOTE
parabiosis10X: no visible global function definition for ‘query’
Undefined global functions or variables:
  query
* 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 ... [22s/23s] ERROR
Running examples in ‘MouseAgingData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: parabiosis10X
> ### Title: Load mouse aging parabiosis data
> ### Aliases: parabiosis10X
> 
> ### ** Examples
> 
> data <- parabiosis10X()
Error in query(eh, title) : could not find function "query"
Calls: parabiosis10X
Execution halted
* 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 ... [11s/11s] OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3293/845d9af2d0ef8a864d34513913f4dd2208ca29d6/MouseAgingData.Rcheck/00check.log’
for details.





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

 BiocCheck('MouseAgingData_0.99.1.tar.gz')

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

─ BiocCheckVersion: 1.39.23
─ BiocVersion: 3.19
─ Package: MouseAgingData
─ PackageVersion: 0.99.1
─ sourceDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//Rtmp0L2gWB/file62267bd6f419/MouseAgingData
─ installDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//Rtmp0L2gWB/file622675d99872
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3293/845d9af2d0ef8a864d34513913f4dd2208ca29d6/MouseAgingData.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...
* 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 (80%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
    * WARNING: Import BiocGenerics, methods, S4Vectors in NAMESPACE as
      well as DESCRIPTION.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
    * ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
      'VignetteEngine' in any vignettes:
    * ERROR: 'VignetteEngine' specified but not in the DESCRIPTION.
    * WARNING: Package listed as VignetteEngine or VignetteBuilder but
      not currently Suggested.
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MouseAgingData...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* 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; 1 lines (0%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 10 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...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    Maintainer is registered at support site.
    * ERROR: Add package to Watched Tags in your Support Site profile;
      visit https://support.bioconductor.org/accounts/edit/profile

─ BiocCheck results ──
3 ERRORS | 2 WARNINGS | 4 NOTES

See the MouseAgingData.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 MouseAgingData_0.99.1.tar.gz'
>>>>>>> 

WARNING: omitting pointless dependence on 'R' without a version requirement
* installing *source* package ‘MouseAgingData’ ...
** 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 (MouseAgingData)