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CHECK report for piano on tokay1

This page was generated on 2019-04-13 11:22:49 -0400 (Sat, 13 Apr 2019).

Package 1157/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
piano 1.22.0
Leif Varemo
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/piano
Branch: RELEASE_3_8
Last Commit: 5041f48
Last Changed Date: 2018-10-30 11:41:51 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: piano
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:piano.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings piano_1.22.0.tar.gz
StartedAt: 2019-04-13 04:33:12 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:36:35 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 203.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: piano.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:piano.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings piano_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/piano.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.22.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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-3.8-bioc/tmpdir/RtmpwzmoM5/R.INSTALL17e44f40498b/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-3.8-bioc/tmpdir/RtmpwzmoM5/R.INSTALL17e44f40498b/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-3.8-bioc/tmpdir/RtmpwzmoM5/R.INSTALL17e44f40498b/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-3.8-bioc/tmpdir/RtmpwzmoM5/R.INSTALL17e44f40498b/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-3.8-bioc/tmpdir/RtmpwzmoM5/R.INSTALL17e44f40498b/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-3.8-bioc/tmpdir/RtmpwzmoM5/R.INSTALL17e44f40498b/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-3.8-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-3.8-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://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/piano_1.22.0.tar.gz && rm -rf piano.buildbin-libdir && mkdir piano.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=piano.buildbin-libdir piano_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL piano_1.22.0.zip && rm piano_1.22.0.tar.gz piano_1.22.0.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  906k  100  906k    0     0  18.4M      0 --:--:-- --:--:-- --:--:-- 20.1M

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-3.8-bioc/tmpdir/RtmpwzmoM5/R.INSTALL17e44f40498b/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-3.8-bioc/tmpdir/RtmpwzmoM5/R.INSTALL17e44f40498b/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-3.8-bioc/tmpdir/RtmpwzmoM5/R.INSTALL17e44f40498b/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-3.8-bioc/tmpdir/RtmpwzmoM5/R.INSTALL17e44f40498b/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-3.8-bioc/tmpdir/RtmpwzmoM5/R.INSTALL17e44f40498b/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-3.8-bioc/tmpdir/RtmpwzmoM5/R.INSTALL17e44f40498b/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_1.22.0.zip
* DONE (piano)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-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
GSAheatmap3.380.163.53
GSAsummaryTable3.220.013.23
consensusHeatmap1.320.081.44
consensusScores0.140.020.15
diffExp2.540.403.39
extractFactors0.170.000.18
geneSetSummary2.640.002.64
loadGSC0.030.000.03
loadMAdata0.140.020.15
networkPlot2.840.002.85
polarPlot0.490.130.61
runGSA2.970.002.97
runGSAhyper0.180.000.18
runQC0.960.041.00
writeFilesForKiwi0.250.000.25

piano.Rcheck/examples_x64/piano-Ex.timings

nameusersystemelapsed
GSAheatmap3.410.033.43
GSAsummaryTable2.980.023.00
consensusHeatmap1.160.091.25
consensusScores0.190.020.21
diffExp3.200.193.39
extractFactors0.200.010.22
geneSetSummary3.270.003.26
loadGSC0.020.000.02
loadMAdata0.150.000.15
networkPlot3.300.033.33
polarPlot0.420.050.47
runGSA3.610.003.61
runGSAhyper0.200.010.22
runQC0.990.111.09
writeFilesForKiwi0.230.000.24