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INSTALL report for mgsa on tokay1

This page was generated on 2020-04-15 12:19:37 -0400 (Wed, 15 Apr 2020).

Package 1037/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mgsa 1.34.0
Sebastian Bauer
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/mgsa
Branch: RELEASE_3_10
Last Commit: e9c9941
Last Changed Date: 2019-10-29 13:08:18 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 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: mgsa
Version: 1.34.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/mgsa_1.34.0.tar.gz && rm -rf mgsa.buildbin-libdir && mkdir mgsa.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mgsa.buildbin-libdir mgsa_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL mgsa_1.34.0.zip && rm mgsa_1.34.0.tar.gz mgsa_1.34.0.zip
StartedAt: 2020-04-14 19:01:48 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 19:02:24 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 36.8 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/mgsa_1.34.0.tar.gz && rm -rf mgsa.buildbin-libdir && mkdir mgsa.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mgsa.buildbin-libdir mgsa_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL mgsa_1.34.0.zip && rm mgsa_1.34.0.tar.gz mgsa_1.34.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  217k  100  217k    0     0  5373k      0 --:--:-- --:--:-- --:--:-- 6029k

install for i386

* installing *source* package 'mgsa' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c mgsa-core.c -o mgsa-core.o
mgsa-core.c: In function 'ts_R_alloc':
mgsa-core.c:56:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical
 ^
mgsa-core.c: At top level:
mgsa-core.c:796:13: warning: 'print_context' defined but not used [-Wunused-function]
 static void print_context(struct context *cn)
             ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c mgsa.c -o mgsa.o
mgsa.c: In function 'mgsa_mcmc':
mgsa.c:552:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
mgsa.c:558:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical
 ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c mt.c -o mt.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o mgsa.dll tmp.def mgsa-core.o mgsa.o mt.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/mgsa.buildbin-libdir/00LOCK-mgsa/00new/mgsa/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mgsa'
    finding HTML links ... done
    MgsaGoSets-class                        html  
    MgsaMcmcResults-class                   html  
    MgsaResults-class                       html  
    MgsaSets-class                          html  
    alphaMcmcPost-methods                   html  
    alphaPost-methods                       html  
    betaMcmcPost-methods                    html  
    betaPost-methods                        html  
    createMgsaGoSets                        html  
    example-go                              html  
    example-o                               html  
    itemAnnotations-methods                 html  
    itemIndices-methods                     html  
    length-methods                          html  
    mgsa-methods                            html  
    mgsa-package                            html  
    nsamples-methods                        html  
    pMcmcPost-methods                       html  
    pPost-methods                           html  
    plot-MgsaResults-method                 html  
    populationSize-methods                  html  
    readGAF                                 html  
    restarts-methods                        html  
    setAnnotations-methods                  html  
    setsMcmcPost-methods                    html  
    setsResults-methods                     html  
    show-MgsaResults-method                 html  
    show-MgsaSets-method                    html  
    steps-methods                           html  
    studySetSizeInPopulation-methods        html  
    subMgsaSets-methods                     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 'mgsa' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c mgsa-core.c -o mgsa-core.o
mgsa-core.c: In function 'ts_R_alloc':
mgsa-core.c:56:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical
 ^
mgsa-core.c: At top level:
mgsa-core.c:796:13: warning: 'print_context' defined but not used [-Wunused-function]
 static void print_context(struct context *cn)
             ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c mgsa.c -o mgsa.o
mgsa.c: In function 'mgsa_mcmc':
mgsa.c:552:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
mgsa.c:558:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical
 ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c mt.c -o mt.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o mgsa.dll tmp.def mgsa-core.o mgsa.o mt.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/mgsa.buildbin-libdir/mgsa/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mgsa' as mgsa_1.34.0.zip
* DONE (mgsa)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'mgsa' successfully unpacked and MD5 sums checked