Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/mspms
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     OK     skipped     OK  
lconway macOS 12.7.1 Monterey/x86_64   ERROR     skipped     skipped     skipped  

nebbiolo2 Summary

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Package: mspms
Version: 0.99.0
RVersion: 4.4
BiocVersion: 3.20
BuildCommand: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data mspms
BuildTime: 6 minutes 46.16 seconds
CheckCommand: BiocCheckGitClone('mspms') && /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3460/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3460/mspms_20240701143310/mspms.install-out.txt mspms_0.99.0.tar.gz && BiocCheck('mspms_0.99.0.tar.gz', `new-package`=TRUE)
CheckTime: 5 minutes 24.82 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 3538.26 KiB
BuildID:: mspms_20240701143310
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: mspms. 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.

nebbiolo2 BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘mspms/DESCRIPTION’ ... OK
* preparing ‘mspms’:
* 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 ‘mspms_0.99.0.tar.gz’


nebbiolo2 CHECK output

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

 BiocCheckGitClone('mspms')

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

─ BiocCheckVersion: 1.41.3
─ BiocVersion: 3.20
─ Package: mspms
─ PackageVersion: 0.99.0
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3460/mspms_20240701143310/mspms
─ 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/3460/mspms_20240701143310/mspms.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 ‘mspms/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mspms’ 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 whether package ‘mspms’ 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [5s/5s] NOTE
plot_cleavages_per_pos: no visible binding for global variable
  ‘condition’
plot_volcano: no visible binding for global variable ‘condition’
Undefined global functions or variables:
  condition
* 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 ... [1s/1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [263s/263s] OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
plot_all_icelogos 50.485  0.032  50.517
mspms_t_tests     49.828  0.028  49.856
log2fc_t_test     49.704  0.084  49.790
plot_volcano      49.536  0.036  49.572
mspms_anova       22.441  0.031  22.473
handle_outliers   16.439  0.120  16.559
log2fct_time       7.997  0.001   7.997
log2fct_condition  7.968  0.000   7.968
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [22s/22s]
 [23s/22s] 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: 1 NOTE
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/3460/mspms_20240701143310/mspms.Rcheck/00check.log’
for details.





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

 BiocCheck('mspms_0.99.0.tar.gz')

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

─ BiocCheckVersion: 1.41.3
─ BiocVersion: 3.20
─ Package: mspms
─ PackageVersion: 0.99.0
─ sourceDir: /tmp/RtmpaU4kuG/file35c4ad7bd6ab90/mspms
─ installDir: /tmp/RtmpaU4kuG/file35c4ad201ee01d
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3460/mspms_20240701143310/mspms.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...
    * NOTE: Update R version dependency from 4.1.0 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...
    * NOTE: The Description field in the DESCRIPTION is made up of less
      than 3 sentences. Provide a more detailed description of the
      package.
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (9%).
* 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 mspms...
* Checking coding practice...
    * NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 10 functions greater than 50 lines.
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
* 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; 43 lines (1%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 732 lines
      (24%) 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 | 9 NOTES

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

nebbiolo2 BUILD BIN output

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lconway Summary

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Package: mspms
Version: 0.99.0
RVersion: 4.4
BiocVersion: 3.20
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data mspms
BuildTime: 0 minutes 5.71 seconds
CheckCommand:
CheckTime:
BuildBinCommand:
BuildBinTime:
PackageFileSize: -1.00 KiB
BuildID:: mspms_20240701143310
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: mspms. 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: 1.

lconway BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘mspms/DESCRIPTION’ ... OK
* preparing ‘mspms’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘mspms_analysis.Rmd’ using rmarkdown

Quitting from lines 221-226 [unnamed-chunk-4] (mspms_analysis.Rmd)
Error: processing vignette 'mspms_analysis.Rmd' failed with diagnostics:
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/readxl/libs/readxl.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/readxl/libs/readxl.so, 0x0006): Symbol not found: (_iconv)
  Referenced from: '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/readxl/libs/readxl.so'
  Expected in: '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib'
--- failed re-building ‘mspms_analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘mspms_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted

lconway CHECK output

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lconway BUILD BIN output

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