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INSTALL report for mgsa on tokay2

This page was generated on 2020-10-17 11:57:05 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE mgsa PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1074/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mgsa 1.36.0
Sebastian Bauer
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/mgsa
Branch: RELEASE_3_11
Last Commit: 5bd0954
Last Changed Date: 2020-04-27 14:24:02 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: mgsa
Version: 1.36.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/mgsa_1.36.0.tar.gz && rm -rf mgsa.buildbin-libdir && mkdir mgsa.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mgsa.buildbin-libdir mgsa_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL mgsa_1.36.0.zip && rm mgsa_1.36.0.tar.gz mgsa_1.36.0.zip
StartedAt: 2020-10-16 17:10:46 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 17:11:32 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 46.0 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/mgsa_1.36.0.tar.gz && rm -rf mgsa.buildbin-libdir && mkdir mgsa.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mgsa.buildbin-libdir mgsa_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL mgsa_1.36.0.zip && rm mgsa_1.36.0.tar.gz mgsa_1.36.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  216k  100  216k    0     0  3407k      0 --:--:-- --:--:-- --:--:-- 3861k

install for i386

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

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


** 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 mgsa-core.c -o mgsa-core.o
mgsa-core.c: In function 'ts_R_alloc':
mgsa-core.c:56: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical
 
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:/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 mgsa.c -o mgsa.o
mgsa.c: In function 'mgsa_mcmc':
mgsa.c:552: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 
mgsa.c:558: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical
 
"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 mt.c -o mt.o
C:/rtools40/mingw32/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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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:/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 mgsa-core.c -o mgsa-core.o
mgsa-core.c: In function 'ts_R_alloc':
mgsa-core.c:56: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical
 
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:/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 mgsa.c -o mgsa.o
mgsa.c: In function 'mgsa_mcmc':
mgsa.c:552: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 
mgsa.c:558: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical
 
"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 mt.c -o mt.o
C:/rtools40/mingw64/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-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/mgsa.buildbin-libdir/mgsa/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mgsa' as mgsa_1.36.0.zip
* DONE (mgsa)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'mgsa' successfully unpacked and MD5 sums checked