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This page was generated on 2022-01-24 13:08:08 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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

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 1417/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
piano 2.10.0  (landing page)
Leif Varemo Wigge
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/piano
git_branch: RELEASE_3_14
git_last_commit: 60ac74a
git_last_commit_date: 2021-10-26 12:07:50 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 2.10.0
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_2.10.0.tar.gz
StartedAt: 2022-01-23 16:27:17 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 16:30:40 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 203.5 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_2.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/piano.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘2.10.0’
* 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 ... 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    6.304  0.067   6.378
geneSetSummary 6.078  0.080   6.162
networkPlot2   5.894  0.186   6.089
GSAheatmap     5.718  0.257   5.982
exploreGSAres  5.671  0.123   5.797
diffExp        5.530  0.233   5.827
runGSA         5.504  0.075   5.582
* 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-3.14-bioc/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/4.1/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
GSAheatmap5.7180.2575.982
GSAsummaryTable4.8740.0924.971
consensusHeatmap1.2180.1501.374
consensusScores0.2110.0160.232
diffExp5.5300.2335.827
exploreGSAres5.6710.1235.797
extractFactors0.2970.0080.305
geneSetSummary6.0780.0806.162
loadGSC0.0200.0010.021
loadMAdata0.1780.0040.182
networkPlot6.3040.0676.378
networkPlot25.8940.1866.089
polarPlot0.3950.0590.455
runGSA5.5040.0755.582
runGSAhyper0.3410.0070.349
runQC0.5400.0550.596
writeFilesForKiwi0.2130.0030.216