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This page was generated on 2021-09-24 15:06:05 -0400 (Fri, 24 Sep 2021).

BUILD BIN results for cn.mops on tokay2

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raw results

Package 340/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.38.0  (landing page)
Gundula Povysil
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/cn.mops
git_branch: RELEASE_3_13
git_last_commit: c1ccf44
git_last_commit_date: 2021-05-19 11:50:48 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cn.mops
Version: 1.38.0
Command: rm -rf cn.mops.buildbin-libdir && mkdir cn.mops.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cn.mops.buildbin-libdir cn.mops_1.38.0.tar.gz
StartedAt: 2021-09-24 07:46:31 -0400 (Fri, 24 Sep 2021)
EndedAt: 2021-09-24 07:47:55 -0400 (Fri, 24 Sep 2021)
EllapsedTime: 84.6 seconds
RetCode: 0
Status:   OK  
PackageFile: cn.mops_1.38.0.zip
PackageFileSize: 1.982 MiB

Command output

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###
### Running command:
###
###   rm -rf cn.mops.buildbin-libdir && mkdir cn.mops.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cn.mops.buildbin-libdir cn.mops_1.38.0.tar.gz
###
##############################################################################
##############################################################################



install for i386

* installing *source* package 'cn.mops' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_cnmops.c -o R_init_cnmops.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cnmops.cpp -o cnmops.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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:
C:/Users/BIOCBU~1/BBS-3~1.13-/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:/rtools40/mingw32/bin/g++ -std=gnu++11 -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-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/cn.mops.buildbin-libdir/00LOCK-cn.mops/00new/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  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/cn.mops.buildbin-libdir/00LOCK-cn.mops/00new/cn.mops/help/cnvdetectionresult.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/cn.mops.buildbin-libdir/00LOCK-cn.mops/00new/cn.mops/help/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 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.mops' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_cnmops.c -o R_init_cnmops.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cnmops.cpp -o cnmops.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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:
C:/Users/BIOCBU~1/BBS-3~1.13-/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:/rtools40/mingw64/bin/g++ -std=gnu++11 -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-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-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_1.38.0.zip
* DONE (cn.mops)