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INSTALL report for GraphAlignment on tokay2

This page was generated on 2019-10-16 12:21:41 -0400 (Wed, 16 Oct 2019).

Package 713/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GraphAlignment 1.48.0
Joern P. Meier
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/GraphAlignment
Branch: RELEASE_3_9
Last Commit: ce9d1e4
Last Changed Date: 2019-05-02 11:53:09 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GraphAlignment
Version: 1.48.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GraphAlignment_1.48.0.tar.gz && rm -rf GraphAlignment.buildbin-libdir && mkdir GraphAlignment.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GraphAlignment.buildbin-libdir GraphAlignment_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GraphAlignment_1.48.0.zip && rm GraphAlignment_1.48.0.tar.gz GraphAlignment_1.48.0.zip
StartedAt: 2019-10-15 18:41:03 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 18:41:41 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 38.3 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/GraphAlignment_1.48.0.tar.gz && rm -rf GraphAlignment.buildbin-libdir && mkdir GraphAlignment.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GraphAlignment.buildbin-libdir GraphAlignment_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GraphAlignment_1.48.0.zip && rm GraphAlignment_1.48.0.tar.gz GraphAlignment_1.48.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100  103k  100  103k    0     0  1272k      0 --:--:-- --:--:-- --:--:-- 1392k

install for i386

* installing *source* package 'GraphAlignment' ...
** using staged installation
** 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 GA_alloc.c -o GA_alloc.o
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 GA_matrix.c -o GA_matrix.o
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 GA_matrix_R.c -o GA_matrix_R.o
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 GA_message.c -o GA_message.o
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 GA_vector.c -o GA_vector.o
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 GA_vector_R.c -o GA_vector_R.o
GA_vector_R.c: In function 'GA_clamp_mode_from_R':
GA_vector_R.c:139:9: warning: unused variable 'size' [-Wunused-variable]
     int size = LENGTH(robj);
         ^
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 GraphAlignment.c -o GraphAlignment.o
GraphAlignment.c: In function 'GA_encode_directed_graph':
GraphAlignment.c:138:20: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
                 if (matrix->elts[i][j] == 1)
                    ^
GraphAlignment.c:159:20: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
                 if (matrix->elts[i][j] == 1)
                    ^
GraphAlignment.c: In function 'GA_directed_mode_from_R':
GraphAlignment.c:264:9: warning: unused variable 'size' [-Wunused-variable]
     int size = LENGTH(robj);
         ^
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 lap.c -o lap.o
lap.c: In function 'LAP_lap':
lap.c:64:30: warning: 'last' may be used uninitialized in this function [-Wmaybe-uninitialized]
   col  j, j1, j2, endofpath, last, low, up, *collist, *matches;
                              ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o GraphAlignment.dll tmp.def GA_alloc.o GA_matrix.o GA_matrix_R.o GA_message.o GA_vector.o GA_vector_R.o GraphAlignment.o lap.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/GraphAlignment.buildbin-libdir/00LOCK-GraphAlignment/00new/GraphAlignment/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GraphAlignment'
    finding HTML links ... done
    AlignNetworks                           html  
    AlignedPairs                            html  
    AnalyzeAlignment                        html  
    ComputeLinkParameters                   html  
    ComputeM                                html  
    ComputeNodeParameters                   html  
    ComputeScores                           html  
    CreateScoreMatrix                       html  
    EncodeDirectedGraph                     html  
    GenerateExample                         html  
    GetBinNumber                            html  
    InitialAlignment                        html  
    InvertPermutation                       html  
    LinearAssignment                        html  
    MatrixToBin                             html  
    Permute                                 html  
    Trace                                   html  
    VectorToBin                             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 'GraphAlignment' ...
** 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 GA_alloc.c -o GA_alloc.o
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 GA_matrix.c -o GA_matrix.o
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 GA_matrix_R.c -o GA_matrix_R.o
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 GA_message.c -o GA_message.o
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 GA_vector.c -o GA_vector.o
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 GA_vector_R.c -o GA_vector_R.o
GA_vector_R.c: In function 'GA_clamp_mode_from_R':
GA_vector_R.c:139:9: warning: unused variable 'size' [-Wunused-variable]
     int size = LENGTH(robj);
         ^
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 GraphAlignment.c -o GraphAlignment.o
GraphAlignment.c: In function 'GA_encode_directed_graph':
GraphAlignment.c:138:20: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
                 if (matrix->elts[i][j] == 1)
                    ^
GraphAlignment.c:159:20: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
                 if (matrix->elts[i][j] == 1)
                    ^
GraphAlignment.c: In function 'GA_directed_mode_from_R':
GraphAlignment.c:264:9: warning: unused variable 'size' [-Wunused-variable]
     int size = LENGTH(robj);
         ^
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 lap.c -o lap.o
lap.c: In function 'LAP_lap':
lap.c:64:30: warning: 'last' may be used uninitialized in this function [-Wmaybe-uninitialized]
   col  j, j1, j2, endofpath, last, low, up, *collist, *matches;
                              ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o GraphAlignment.dll tmp.def GA_alloc.o GA_matrix.o GA_matrix_R.o GA_message.o GA_vector.o GA_vector_R.o GraphAlignment.o lap.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/GraphAlignment.buildbin-libdir/GraphAlignment/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GraphAlignment' as GraphAlignment_1.48.0.zip
* DONE (GraphAlignment)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GraphAlignment' successfully unpacked and MD5 sums checked