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INSTALL report for cn.mops on tokay1

This page was generated on 2019-04-13 11:21:57 -0400 (Sat, 13 Apr 2019).

Package 285/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.28.0
Guenter Klambauer
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/cn.mops
Branch: RELEASE_3_8
Last Commit: f953d10
Last Changed Date: 2018-10-30 11:41:48 -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  OK  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: cn.mops
Version: 1.28.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/cn.mops_1.28.0.tar.gz && rm -rf cn.mops.buildbin-libdir && mkdir cn.mops.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cn.mops.buildbin-libdir cn.mops_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL cn.mops_1.28.0.zip && rm cn.mops_1.28.0.tar.gz cn.mops_1.28.0.zip
StartedAt: 2019-04-12 19:40:30 -0400 (Fri, 12 Apr 2019)
EndedAt: 2019-04-12 19:41:31 -0400 (Fri, 12 Apr 2019)
EllapsedTime: 61.3 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/cn.mops_1.28.0.tar.gz && rm -rf cn.mops.buildbin-libdir && mkdir cn.mops.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cn.mops.buildbin-libdir cn.mops_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL cn.mops_1.28.0.zip && rm cn.mops_1.28.0.tar.gz cn.mops_1.28.0.zip
###
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install for i386

* installing *source* package 'cn.mops' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_cnmops.c -o R_init_cnmops.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cnmops.cpp -o cnmops.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c segment.cpp -o segment.o
segment.cpp: In function 'SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
segment.cpp:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable]
  double globalMean,globalSd,diff,M2,globalVariance;
                    ^
segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable]
  double oldStatistic, meanLeft,meanRight,varLeft,varRight;
         ^
segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable]
  double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1;
                               ^
segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable]
  double newPValue, maxPValue,oldPValue,maxIdx;
                                        ^
In file included from segment.cpp:10:0:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rmath.h:212:15: warning: unused variable 'Rf_beta' [-Wunused-variable]
 #define beta  Rf_beta
               ^
segment.cpp:64:9: note: in expansion of macro 'beta'
  double beta,nn;
         ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o cn.mops.dll tmp.def R_init_cnmops.o cnmops.o segment.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/cn.mops.buildbin-libdir/cn.mops/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cn.mops'
    finding HTML links ... done
    CNVDetectionResult                      html  
    CNVRanges                               html  
    X                                       html  
    XRanges                                 html  
    calcFractionalCopyNumbers-CNVDetectionResult-method
                                            html  
    calcFractionalCopyNumbers               html  
    calcIntegerCopyNumbers-CNVDetectionResult-method
                                            html  
    calcIntegerCopyNumbers                  html  
    cn.mops                                 html  
    cnvr-CNVDetectionResult-method          html  
    cnvr                                    html  
    cnvs-CNVDetectionResult-method          html  
    cnvs                                    html  
    exomeCounts                             html  
    exomecn.mops                            html  
    getReadCountsFromBAM                    html  
    getSegmentReadCountsFromBAM             html  
    gr-CNVDetectionResult-method            html  
    gr                                      html  
    haplocn.mops                            html  
    individualCall-CNVDetectionResult-method
                                            html  
    individualCall                          html  
    iniCall-CNVDetectionResult-method       html  
    iniCall                                 html  
    integerCopyNumber-CNVDetectionResult-method
                                            html  
    integerCopyNumber                       html  
    localAssessments-CNVDetectionResult-method
                                            html  
    localAssessments                        html  
    makeRobustCNVR                          html  
    normalizeChromosomes                    html  
    normalizeGenome                         html  
    normalizedData-CNVDetectionResult-method
                                            html  
    normalizedData                          html  
    params-CNVDetectionResult-method        html  
    params                                  html  
    plot                                    html  
    posteriorProbs-CNVDetectionResult-method
                                            html  
    posteriorProbs                          html  
    referencecn.mops                        html  
    sampleNames-CNVDetectionResult-method   html  
    sampleNames                             html  
    segment                                 html  
    segmentation-CNVDetectionResult-method
                                            html  
    segmentation                            html  
    segplot-CNVDetectionResult-method       html  
    segplot                                 html  
    show                                    html  
    singlecn.mops                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'cn.mops' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_cnmops.c -o R_init_cnmops.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cnmops.cpp -o cnmops.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c segment.cpp -o segment.o
segment.cpp: In function 'SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
segment.cpp:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable]
  double globalMean,globalSd,diff,M2,globalVariance;
                    ^
segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable]
  double oldStatistic, meanLeft,meanRight,varLeft,varRight;
         ^
segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable]
  double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1;
                               ^
segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable]
  double newPValue, maxPValue,oldPValue,maxIdx;
                                        ^
In file included from segment.cpp:10:0:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rmath.h:212:15: warning: unused variable 'Rf_beta' [-Wunused-variable]
 #define beta  Rf_beta
               ^
segment.cpp:64:9: note: in expansion of macro 'beta'
  double beta,nn;
         ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o cn.mops.dll tmp.def R_init_cnmops.o cnmops.o segment.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/cn.mops.buildbin-libdir/cn.mops/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cn.mops' as cn.mops_1.28.0.zip
* DONE (cn.mops)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'cn.mops' successfully unpacked and MD5 sums checked
In R CMD INSTALL