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This page was generated on 2021-06-17 02:39:18 -0400 (Thu, 17 Jun 2021).

CHECK results for piano on machv2

To the developers/maintainers of the piano package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/piano.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1391/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
piano 2.8.0  (landing page)
Leif Varemo Wigge
Snapshot Date: 2021-06-15 06:50:12 -0400 (Tue, 15 Jun 2021)
URL: https://git.bioconductor.org/packages/piano
Branch: RELEASE_3_13
Last Commit: f9697f5
Last Changed Date: 2021-05-19 11:58:37 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: piano
Version: 2.8.0
Command: _R_CHECK_FORCE_SUGGESTS_=0 /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:piano.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings piano_2.8.0.tar.gz
StartedAt: 2021-06-15 22:12:00 -0400 (Tue, 15 Jun 2021)
EndedAt: 2021-06-15 22:15:06 -0400 (Tue, 15 Jun 2021)
EllapsedTime: 185.8 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/Versions/Current/Resources/bin/R CMD check --install=check:piano.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings piano_2.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/piano.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘piano/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘piano’ version ‘2.8.0’
* 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
  .git_fetch_output.txt
  .git_merge_output.txt
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 ... NOTE
Unknown packages ‘HTSanalyzeR’, ‘PGSEA’ in Rd xrefs
* 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
networkPlot     5.844  0.100   5.946
GSAheatmap      5.661  0.276   5.939
diffExp         5.625  0.245   5.935
geneSetSummary  5.597  0.084   5.684
runGSA          5.594  0.074   5.669
exploreGSAres   5.460  0.094   5.558
GSAsummaryTable 4.950  0.068   5.019
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/piano.Rcheck/00check.log’
for details.



Installation output

piano.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL piano
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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
GSAheatmap5.6610.2765.939
GSAsummaryTable4.9500.0685.019
consensusHeatmap1.2130.1281.341
consensusScores0.2180.0150.237
diffExp5.6250.2455.935
exploreGSAres5.4600.0945.558
extractFactors0.2110.0040.215
geneSetSummary5.5970.0845.684
loadGSC0.0160.0010.016
loadMAdata0.2490.0060.254
networkPlot5.8440.1005.946
networkPlot24.6490.2174.868
polarPlot0.5120.0640.576
runGSA5.5940.0745.669
runGSAhyper0.3740.0080.381
runQC0.5070.0530.560
writeFilesForKiwi0.2850.0060.290