Bioconductor Single Package Builder - Build History

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

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo1 Linux (Ubuntu 20.04.4 LTS)/x86_64   WARNINGS     WARNINGS     skipped     OK  
merida1 macOS 10.14.6 Mojave/x86_64   TIMEOUT     skipped     skipped     skipped  

nebbiolo1 Summary

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Package: protlocassign
Version: 0.99.2
RVersion: 4.2
BiocVersion: 3.15
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data protlocassign
BuildTime: 8 minutes 27.54 seconds
CheckCommand: BiocCheckGitClone('protlocassign') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings protlocassign_0.99.2.tar.gz && BiocCheck('protlocassign_0.99.2.tar.gz', `new-package`=TRUE)
CheckTime: 5 minutes 1.44 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 4720.61 KiB
BuildID:: protlocassign_20220415203955
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: protlocassign. 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. Checking Package status: 0.

nebbiolo1 BUILD SRC output

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 R CMD BUILD

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

* checking for file ‘protlocassign/DESCRIPTION’ ... OK
* preparing ‘protlocassign’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
Warning: ‘inst/doc’ file
    ‘protlocassignTutorials.html’
  ignored as vignettes have been rebuilt.
  Run R CMD build with --no-build-vignettes to prevent rebuilding.
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘protlocassign_0.99.2.tar.gz’

nebbiolo1 CHECK output

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

 BiocCheckGitClone('protlocassign')

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

─ BiocCheckVersion: 1.31.37
─ BiocVersion: 3.15
─ Package: protlocassign
─ PackageVersion: 0.99.2
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2541/8e7534f8f8816ff9fd3a8b917600b988749b12c1/protlocassign
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output 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/2541/8e7534f8f8816ff9fd3a8b917600b988749b12c1/protlocassign.Rcheck’
* using R version 4.2.0 beta (2022-04-12 r82161)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘protlocassign/DESCRIPTION’ ... OK
* this is package ‘protlocassign’ 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 whether package ‘protlocassign’ can be installed ... [7s/7s] OK
* checking installed package size ... NOTE
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [11s/11s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [227s/231s] OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
mixtureHeatMap   174.476  0.520 174.998
protPepProfile_i  11.377  0.012  11.389
protPepProfile    11.150  0.056  11.206
mixturePlotPanel   6.535  0.008   6.543
profileSummarize   6.169  0.012   6.438
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [2s/2s]
 [3s/3s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKI SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2541/8e7534f8f8816ff9fd3a8b917600b988749b12c1/protlocassign.Rcheck/00check.log’
for details.






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

 BiocCheck('protlocassign_0.99.2.tar.gz')

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

─ BiocCheckVersion: 1.31.37
─ BiocVersion: 3.15
─ Package: protlocassign
─ PackageVersion: 0.99.2
─ sourceDir: /tmp/RtmpbHtMlQ/filedd9a22630325/protlocassign
─ installDir: /tmp/RtmpbHtMlQ/filedd9a47fec7c5
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2541/8e7534f8f8816ff9fd3a8b917600b988749b12c1/protlocassign.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking package dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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...
    * NOTE: Update R version dependency from 4.1.0 to 4.2.0.
* Checking package size...
* Checking individual file sizes...
    * WARNING: The following files are over 5MB in size:
      'inst/doc/protlocassignTutorials.html'
* 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:
      RNASeq
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 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 protlocassign...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.There are 13
      functions > 50 lines.
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to the following man
      pages which document exported objects:
      protPepPlotfun.Rd
* 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; 234 lines (3%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 1163 lines
      (15%) are not.
    See http://bioconductor.org/developers/how-to/coding-style/
    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 name is in support site watched tags.

─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 6 NOTES

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

nebbiolo1 BUILD BIN output

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merida1 Summary
 
                			
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Package: protlocassign
 
                					
Version: 0.99.2
 
                					
RVersion: 4.2
                
 
                					
BiocVersion: 3.15
                
 

                					
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data protlocassign
 
                					
BuildTime: 14 minutes 59.96 seconds
 
                					
CheckCommand: 

   							
CheckTime: 

                 					
BuildBinCommand: 

 							
BuildBinTime: 

                					
PackageFileSize: -1.00 KiB
 
                					
BuildID:: protlocassign_20220415203955
 
                					
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: protlocassign. 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: -9. 
        				
                				
 
                			
 
                			
 
                			    
                				
merida1 BUILD SRC output
 
                    			
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===============================

 R CMD BUILD

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

* checking for file ‘protlocassign/DESCRIPTION’ ... OK
* preparing ‘protlocassign’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
TIMEOUT: R CMD build exceeded 15 mins




                				
 

                			
 
                			    
                				
merida1 CHECK output
 
                    			
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merida1 BUILD BIN output
 
                    			
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