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INSTALL report for cn.farms on tokay2

This page was generated on 2019-04-09 11:59:09 -0400 (Tue, 09 Apr 2019).

Package 294/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.farms 1.31.0
Andreas Mitterecker
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/cn.farms
Branch: master
Last Commit: 1797438
Last Changed Date: 2018-10-30 11:54:29 -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: cn.farms
Version: 1.31.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/cn.farms_1.31.0.tar.gz && rm -rf cn.farms.buildbin-libdir && mkdir cn.farms.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cn.farms.buildbin-libdir cn.farms_1.31.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL cn.farms_1.31.0.zip && rm cn.farms_1.31.0.tar.gz cn.farms_1.31.0.zip
StartedAt: 2019-04-08 20:08:26 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 20:09:55 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 88.9 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/cn.farms_1.31.0.tar.gz && rm -rf cn.farms.buildbin-libdir && mkdir cn.farms.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cn.farms.buildbin-libdir cn.farms_1.31.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL cn.farms_1.31.0.zip && rm cn.farms_1.31.0.tar.gz cn.farms_1.31.0.zip
###
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install for i386

* installing *source* package 'cn.farms' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_cnfarms.c -o R_init_cnfarms.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c laplace.cpp -o laplace.o
laplace.cpp: In function 'SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
laplace.cpp:442:6: warning: unused variable 'method' [-Wunused-variable]
  int method=0;
      ^
laplace.cpp: In function 'void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)':
laplace.cpp:368:56: warning: 'I1right' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double rightMoment1=1.0*rightMy*I0right+1.0*rightSigma*I1right;
                                                        ^
laplace.cpp:393:86: warning: 'I1left' may be used uninitialized in this function [-Wmaybe-uninitialized]
  moment2 = (-0.5*a+0.25*(b-1/sigmaZ)*(b-1/sigmaZ)+(b*leftWeight)/(sigmaZ)+(leftWeight*I1left*sqrtMa)/(sqrt(2.0)*sigmaZ))/(a*a);
                                                                                      ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c sparse_farms.c -o sparse_farms.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o cn.farms.dll tmp.def R_init_cnfarms.o laplace.o sparse_farms.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/cn.farms.buildbin-libdir/00LOCK-cn.farms/00new/cn.farms/libs/i386
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cn.farms'
    finding HTML links ... done
    callSummarize                           html  
    cn.farms                                html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/cn.farms.Rd:16: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    cnLibrary                               html  
    combineData                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/combineData.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/combineData.Rd:13: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/combineData.Rd:29: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    createAnnotation                        html  
    createMatrix                            html  
    distributionDistance                    html  
    dnaCopySf                               html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/dnaCopySf.Rd:22: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    doCnFarmsSingle                         html  
    flcSnp6Std                              html  
    flcStd                                  html  
    fragLengCorr                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/fragLengCorr.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/fragLengCorr.Rd:20: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    getFragmentSet                          html  
    getSingleProbeSetSize                   html  
    mlSummarization                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/mlSummarization.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/mlSummarization.Rd:36: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    normAdd                                 html  
    normalizeAverage                        html  
    normalizeCels                           html  
    normalizeNone                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/normalizeNone.Rd:29: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    normalizeNpData                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/normalizeNpData.Rd:25: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    normalizeQuantiles                      html  
    normalizeSequenceEffect                 html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/normalizeSequenceEffect.Rd:11: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    normalizeSor                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/normalizeSor.Rd:29: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    plotDendrogram                          html  
    plotDensity                             html  
    plotEvalIc                              html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/plotEvalIc.Rd:12: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    plotRegions                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/plotRegions.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/plotRegions.Rd:12: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    plotSmoothScatter                       html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/plotSmoothScatter.Rd:9: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    plotViolines                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/plotViolines.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    slSummarization                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/slSummarization.Rd:12: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/slSummarization.Rd:35: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    sparseFarmsC                            html  
    summarizeFarmsExact                     html  
    summarizeFarmsExact2                    html  
    summarizeFarmsExact3                    html  
    summarizeFarmsGaussian                  html  
    summarizeFarmsMethods                   html  
    summarizeFarmsStatistics                html  
    summarizeFarmsVariational               html  
    summarizeWindowBps                      html  
    summarizeWindowMethods                  html  
    summarizeWindowStd                      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 'cn.farms' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_cnfarms.c -o R_init_cnfarms.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c laplace.cpp -o laplace.o
laplace.cpp: In function 'SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
laplace.cpp:442:6: warning: unused variable 'method' [-Wunused-variable]
  int method=0;
      ^
laplace.cpp: In function 'void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)':
laplace.cpp:368:56: warning: 'I1right' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double rightMoment1=1.0*rightMy*I0right+1.0*rightSigma*I1right;
                                                        ^
laplace.cpp:367:52: warning: 'I1left' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double leftMoment1=1.0*leftMy*I0left+1.0*leftSigma*I1left;
                                                    ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c sparse_farms.c -o sparse_farms.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o cn.farms.dll tmp.def R_init_cnfarms.o laplace.o sparse_farms.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/cn.farms.buildbin-libdir/cn.farms/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cn.farms' as cn.farms_1.31.0.zip
* DONE (cn.farms)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'cn.farms' successfully unpacked and MD5 sums checked