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This page was generated on 2023-10-20 09:38:08 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1518/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
piano 2.16.0  (landing page)
Leif Varemo Wigge
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/piano
git_branch: RELEASE_3_17
git_last_commit: 2185203
git_last_commit_date: 2023-04-25 10:26:52 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for piano on kjohnson2


To the developers/maintainers of the piano package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: piano
Version: 2.16.0
Command: _R_CHECK_FORCE_SUGGESTS_=0 /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:piano.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings piano_2.16.0.tar.gz
StartedAt: 2023-10-18 14:48:06 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 14:51:44 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 218.5 seconds
RetCode: 0
Status:   OK  
CheckDir: piano.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   _R_CHECK_FORCE_SUGGESTS_=0 /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:piano.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings piano_2.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/piano.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘piano/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘piano’ version ‘2.16.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: ‘rsbml’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘piano’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
diffExp        4.696  0.268   7.589
GSAheatmap     3.781  0.124   5.987
networkPlot2   3.631  0.148   5.802
networkPlot    3.706  0.062   5.779
geneSetSummary 3.684  0.072   5.778
exploreGSAres  3.605  0.056   5.637
runGSA         3.543  0.051   5.493
* 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 ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/piano.Rcheck/00check.log’
for details.



Installation output

piano.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL piano
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘piano’ ...
** using staged installation
** R
** data
** 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 (piano)

Tests output


Example timings

piano.Rcheck/piano-Ex.timings

nameusersystemelapsed
GSAheatmap3.7810.1245.987
GSAsummaryTable3.0740.0594.808
consensusHeatmap0.7410.1101.293
consensusScores0.1500.0130.255
diffExp4.6960.2687.589
exploreGSAres3.6050.0565.637
extractFactors0.2590.0090.409
geneSetSummary3.6840.0725.778
loadGSC0.0130.0000.019
loadMAdata0.1940.0070.305
networkPlot3.7060.0625.779
networkPlot23.6310.1485.802
polarPlot0.4100.0530.703
runGSA3.5430.0515.493
runGSAhyper0.2270.0060.357
runQC0.4150.0500.709
writeFilesForKiwi0.1380.0070.228