Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2023-02-01 11:06:04 -0500 (Wed, 01 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4511
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4289
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4318
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 nebbiolo2


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? 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 1483/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
piano 2.14.0  (landing page)
Leif Varemo Wigge
Snapshot Date: 2023-01-31 14:00:04 -0500 (Tue, 31 Jan 2023)
git_url: https://git.bioconductor.org/packages/piano
git_branch: RELEASE_3_16
git_last_commit: 11f1964
git_last_commit_date: 2022-11-01 11:08:10 -0500 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: piano
Version: 2.14.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:piano.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings piano_2.14.0.tar.gz
StartedAt: 2023-01-31 22:48:10 -0500 (Tue, 31 Jan 2023)
EndedAt: 2023-01-31 22:53:04 -0500 (Tue, 31 Jan 2023)
EllapsedTime: 293.9 seconds
RetCode: 0
Status:   OK  
CheckDir: piano.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:piano.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings piano_2.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/piano.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘piano/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘piano’ version ‘2.14.0’
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
diffExp         7.365  0.367   8.666
GSAheatmap      6.205  0.180   9.634
networkPlot2    5.847  0.072   6.384
networkPlot     5.800  0.028   5.833
exploreGSAres   5.617  0.048   6.292
GSAsummaryTable 4.907  0.088   9.787
runGSA          4.727  0.008   5.331
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Running_gene-set_analysis_with_piano.Rmd’ using ‘UTF-8’... OK
  ‘piano-vignette.Rnw’ using ‘latin1’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/piano.Rcheck/00check.log’
for details.



Installation output

piano.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL piano
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/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
GSAheatmap6.2050.1809.634
GSAsummaryTable4.9070.0889.787
consensusHeatmap1.5250.0483.017
consensusScores0.1980.0200.274
diffExp7.3650.3678.666
exploreGSAres5.6170.0486.292
extractFactors0.1880.0040.191
geneSetSummary3.5550.0363.596
loadGSC0.0220.0000.023
loadMAdata0.3190.0000.319
networkPlot5.8000.0285.833
networkPlot25.8470.0726.384
polarPlot0.6520.0280.918
runGSA4.7270.0085.331
runGSAhyper0.2330.0000.233
runQC0.3190.0120.331
writeFilesForKiwi0.1110.0040.115