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INSTALL report for DESeq on tokay2

This page was generated on 2020-10-17 11:56:26 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE DESeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 459/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DESeq 1.40.0
Simon Anders
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/DESeq
Branch: RELEASE_3_11
Last Commit: 4819d95
Last Changed Date: 2020-04-27 14:20:51 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] ERROR  skipped  skipped 
machv2 macOS 10.14.6 Mojave / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: DESeq
Version: 1.40.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/DESeq_1.40.0.tar.gz && rm -rf DESeq.buildbin-libdir && mkdir DESeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DESeq.buildbin-libdir DESeq_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL DESeq_1.40.0.zip && rm DESeq_1.40.0.tar.gz DESeq_1.40.0.zip
StartedAt: 2020-10-16 17:31:19 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 17:32:39 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 79.7 seconds
RetCode: 0
Status:  OK  

Command output

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### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/DESeq_1.40.0.tar.gz && rm -rf DESeq.buildbin-libdir && mkdir DESeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DESeq.buildbin-libdir DESeq_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL DESeq_1.40.0.zip && rm DESeq_1.40.0.tar.gz DESeq_1.40.0.zip
###
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100  654k  100  654k    0     0  5439k      0 --:--:-- --:--:-- --:--:-- 5793k

install for i386

* installing *source* package 'DESeq' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pval.c -o pval.o
pval.c: In function 'add_from_both_sides':
pval.c:26:11: warning: unused variable 'esttotalperlength' [-Wunused-variable]
    double esttotalperlength = total/2;
           ^~~~~~~~~~~~~~~~~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o DESeq.dll tmp.def pval.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/DESeq.buildbin-libdir/00LOCK-DESeq/00new/DESeq/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DESeq'
    finding HTML links ... done
    CountDataSet-class                      html  
    adjustScvForBias                        html  
    conditions                              html  
    counts                                  html  
    dispTable                               html  
    estimateDispersions                     html  
    estimateSizeFactors                     html  
    estimateSizeFactorsForMatrix            html  
    estimateVarianceFunctions               html  
    fitInfo                                 html  
    fitNbinomGLMs                           html  
    fitNbinomGLMsForMatrix                  html  
    getBaseMeansAndVariances                html  
    getVarianceStabilizedData               html  
    makeExampleCountDataSet                 html  
    nbinomGLMTest                           html  
    nbinomTest                              html  
    nbinomTestForMatrices                   html  
    nbkd.sf                                 html  
    newCountDataSet                         html  
    newCountDataSetFromHTSeqCount           html  
    plotDispEsts                            html  
    plotMA                                  html  
    plotPCA                                 html  
    residualsEcdfPlot                       html  
    scvPlot                                 html  
    sizeFactors                             html  
    varianceFitDiagnostics                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2
** testing if installed package can be loaded from final location
Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'DESeq' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pval.c -o pval.o
pval.c: In function 'add_from_both_sides':
pval.c:26:11: warning: unused variable 'esttotalperlength' [-Wunused-variable]
    double esttotalperlength = total/2;
           ^~~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o DESeq.dll tmp.def pval.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/DESeq.buildbin-libdir/DESeq/libs/x64
** testing if installed package can be loaded
Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2
* MD5 sums
packaged installation of 'DESeq' as DESeq_1.40.0.zip
* DONE (DESeq)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'DESeq' successfully unpacked and MD5 sums checked