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CHECK report for piano on tokay2

This page was generated on 2019-04-09 12:03:34 -0400 (Tue, 09 Apr 2019).

Package 1187/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
piano 1.23.0
Leif Varemo
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/piano
Branch: master
Last Commit: 0d4493e
Last Changed Date: 2018-10-30 11:54:31 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: piano
Version: 1.23.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:piano.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings piano_1.23.0.tar.gz
StartedAt: 2019-04-09 04:55:53 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:58:40 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 166.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: piano.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:piano.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings piano_1.23.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/piano.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'piano/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'piano' version '1.23.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'piano' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2zGK7l/R.INSTALL4f42ed36fa3/piano/man/diffExp.Rd:75: file link 'limma' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2zGK7l/R.INSTALL4f42ed36fa3/piano/man/diffExp.Rd:143: file link 'limma' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2zGK7l/R.INSTALL4f42ed36fa3/piano/man/loadMAdata.Rd:129: file link 'yeast2.db' in package 'yeast2.db' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2zGK7l/R.INSTALL4f42ed36fa3/piano/man/piano-package.Rd:25: file link 'limma-package' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2zGK7l/R.INSTALL4f42ed36fa3/piano/man/runGSA.Rd:250: file link 'HTSanalyzeR-package' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2zGK7l/R.INSTALL4f42ed36fa3/piano/man/runGSA.Rd:252: file link 'limma' in package 'limma' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/piano.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Missing or unexported object: 'rsbml::species'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
loadMAdata: no visible global function definition for 'exprs<-'
Undefined global functions or variables:
  exprs<-
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
diffExp 3.39   0.44    5.92
** running examples for arch 'x64' ... OK
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/piano.Rcheck/00check.log'
for details.



Installation output

piano.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/piano_1.23.0.tar.gz && rm -rf piano.buildbin-libdir && mkdir piano.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=piano.buildbin-libdir piano_1.23.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL piano_1.23.0.zip && rm piano_1.23.0.tar.gz piano_1.23.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  908k  100  908k    0     0  6141k      0 --:--:-- --:--:-- --:--:-- 6398k

install for i386

* installing *source* package 'piano' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'piano'
    finding HTML links ... done
    GSAheatmap                              html  
    GSAsummaryTable                         html  
    consensusHeatmap                        html  
    consensusScores                         html  
    diffExp                                 html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2zGK7l/R.INSTALL4f42ed36fa3/piano/man/diffExp.Rd:75: file link 'limma' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2zGK7l/R.INSTALL4f42ed36fa3/piano/man/diffExp.Rd:143: file link 'limma' in package 'limma' does not exist and so has been treated as a topic
    extractFactors                          html  
    geneSetSummary                          html  
    gsa_input                               html  
    gsa_results                             html  
    loadGSC                                 html  
    loadMAdata                              html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2zGK7l/R.INSTALL4f42ed36fa3/piano/man/loadMAdata.Rd:129: file link 'yeast2.db' in package 'yeast2.db' does not exist and so has been treated as a topic
    networkPlot                             html  
    piano-package                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2zGK7l/R.INSTALL4f42ed36fa3/piano/man/piano-package.Rd:25: file link 'limma-package' in package 'limma' does not exist and so has been treated as a topic
    polarPlot                               html  
    runGSA                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2zGK7l/R.INSTALL4f42ed36fa3/piano/man/runGSA.Rd:250: file link 'HTSanalyzeR-package' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2zGK7l/R.INSTALL4f42ed36fa3/piano/man/runGSA.Rd:252: file link 'limma' in package 'limma' does not exist and so has been treated as a topic
    runGSAhyper                             html  
    runQC                                   html  
    writeFilesForKiwi                       html  
** 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

install for x64

* installing *source* package 'piano' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'piano' as piano_1.23.0.zip
* DONE (piano)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'piano' successfully unpacked and MD5 sums checked

Tests output


Example timings

piano.Rcheck/examples_i386/piano-Ex.timings

nameusersystemelapsed
GSAheatmap3.190.113.30
GSAsummaryTable2.640.002.64
consensusHeatmap1.810.202.03
consensusScores0.160.020.17
diffExp3.390.445.92
extractFactors0.250.010.27
geneSetSummary2.530.032.56
loadGSC000
loadMAdata0.170.000.17
networkPlot2.660.002.65
polarPlot0.400.080.49
runGSA2.490.002.48
runGSAhyper0.170.000.17
runQC0.890.121.02
writeFilesForKiwi0.130.020.14

piano.Rcheck/examples_x64/piano-Ex.timings

nameusersystemelapsed
GSAheatmap3.460.063.52
GSAsummaryTable2.840.002.84
consensusHeatmap1.220.091.31
consensusScores0.160.000.16
diffExp3.310.223.53
extractFactors0.190.000.19
geneSetSummary2.830.002.82
loadGSC0.010.000.02
loadMAdata0.180.000.17
networkPlot3.70.03.7
polarPlot0.480.110.60
runGSA3.230.033.27
runGSAhyper0.180.000.17
runQC0.960.061.03
writeFilesForKiwi0.240.020.25