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CHECK report for piano on tokay2

This page was generated on 2018-10-17 08:37:10 -0400 (Wed, 17 Oct 2018).

Package 1094/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
piano 1.20.1
Leif Varemo
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/piano
Branch: RELEASE_3_7
Last Commit: 97a8e33
Last Changed Date: 2018-09-04 06:23:39 -0400 (Tue, 04 Sep 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: piano
Version: 1.20.1
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:piano.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings piano_1.20.1.tar.gz
StartedAt: 2018-10-17 03:58:32 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:01:17 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 164.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: piano.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:piano.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings piano_1.20.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/piano.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.20.1'
* 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-3.7-bioc/tmpdir/Rtmpycai5l/R.INSTALL1b847d626dc8/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-3.7-bioc/tmpdir/Rtmpycai5l/R.INSTALL1b847d626dc8/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-3.7-bioc/tmpdir/Rtmpycai5l/R.INSTALL1b847d626dc8/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-3.7-bioc/tmpdir/Rtmpycai5l/R.INSTALL1b847d626dc8/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-3.7-bioc/tmpdir/Rtmpycai5l/R.INSTALL1b847d626dc8/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-3.7-bioc/tmpdir/Rtmpycai5l/R.INSTALL1b847d626dc8/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-3.7-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 ... OK
* 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
** 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-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/3.7/bioc/src/contrib/piano_1.20.1.tar.gz && rm -rf piano.buildbin-libdir && mkdir piano.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=piano.buildbin-libdir piano_1.20.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL piano_1.20.1.zip && rm piano_1.20.1.tar.gz piano_1.20.1.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  14.9M      0 --:--:-- --:--:-- --:--:-- 16.7M

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-3.7-bioc/tmpdir/Rtmpycai5l/R.INSTALL1b847d626dc8/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-3.7-bioc/tmpdir/Rtmpycai5l/R.INSTALL1b847d626dc8/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-3.7-bioc/tmpdir/Rtmpycai5l/R.INSTALL1b847d626dc8/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-3.7-bioc/tmpdir/Rtmpycai5l/R.INSTALL1b847d626dc8/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-3.7-bioc/tmpdir/Rtmpycai5l/R.INSTALL1b847d626dc8/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-3.7-bioc/tmpdir/Rtmpycai5l/R.INSTALL1b847d626dc8/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
In R CMD INSTALL

install for x64

* installing *source* package 'piano' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'piano' as piano_1.20.1.zip
* DONE (piano)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'piano' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

piano.Rcheck/examples_i386/piano-Ex.timings

nameusersystemelapsed
GSAheatmap4.590.114.70
GSAsummaryTable4.000.034.03
consensusHeatmap1.700.061.83
consensusScores0.240.020.25
diffExp3.700.444.89
extractFactors0.250.000.25
geneSetSummary2.720.002.72
loadGSC0.030.000.03
loadMAdata0.190.000.19
networkPlot2.870.002.88
polarPlot0.360.180.54
runGSA3.110.003.11
runGSAhyper0.170.000.17
runQC0.930.050.97
writeFilesForKiwi0.120.020.14

piano.Rcheck/examples_x64/piano-Ex.timings

nameusersystemelapsed
GSAheatmap3.500.033.55
GSAsummaryTable3.420.003.42
consensusHeatmap1.580.081.66
consensusScores0.240.030.26
diffExp4.030.224.38
extractFactors0.150.030.19
geneSetSummary3.890.003.89
loadGSC0.020.000.01
loadMAdata0.170.000.18
networkPlot4.500.014.51
polarPlot0.630.110.74
runGSA4.110.004.10
runGSAhyper0.310.000.32
runQC1.050.131.17
writeFilesForKiwi0.140.010.16