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INSTALL report for qpgraph on tokay2

This page was generated on 2018-10-17 08:34:08 -0400 (Wed, 17 Oct 2018).

Package 1158/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qpgraph 2.14.0
Robert Castelo
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/qpgraph
Branch: RELEASE_3_7
Last Commit: 96d71a2
Last Changed Date: 2018-04-30 10:35:10 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: qpgraph
Version: 2.14.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/qpgraph_2.14.0.tar.gz && rm -rf qpgraph.buildbin-libdir && mkdir qpgraph.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qpgraph.buildbin-libdir qpgraph_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL qpgraph_2.14.0.zip && rm qpgraph_2.14.0.tar.gz qpgraph_2.14.0.zip
StartedAt: 2018-10-16 19:59:52 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:01:51 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 118.6 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/qpgraph_2.14.0.tar.gz && rm -rf qpgraph.buildbin-libdir && mkdir qpgraph.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qpgraph.buildbin-libdir qpgraph_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL qpgraph_2.14.0.zip && rm qpgraph_2.14.0.tar.gz qpgraph_2.14.0.zip
###
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100 1855k  100 1855k    0     0  24.7M      0 --:--:-- --:--:-- --:--:-- 27.0M

install for i386

* installing *source* package 'qpgraph' ...

   **********************************************
   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˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c cliquer.c -o cliquer.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c graph.c -o graph.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c qpgraph.c -o qpgraph.o
qpgraph.c: In function 'qp_fast_path_weight':
qpgraph.c:5851:20: warning: left-hand operand of comma expression has no effect [-Wunused-value]
     int i = edges[k, 0];
                    ^
qpgraph.c:5852:20: warning: left-hand operand of comma expression has no effect [-Wunused-value]
     int j = edges[k, 1];
                    ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c reorder.c -o reorder.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o qpgraph.dll tmp.def cliquer.o graph.o qpgraph.o reorder.o -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lRblas -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/qpgraph.buildbin-libdir/qpgraph/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
Creating a generic function for 'det' from package 'Matrix' in package 'qpgraph'
** help
*** installing help indices
  converting help for package 'qpgraph'
    finding HTML links ... done
    EcoliOxygen                             html  
    HMgmm-class                             html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpIBO4ou/R.INSTALL1dec6d3066dd/qpgraph/man/HMgmm-class.Rd:65: file link 'dspMatrix-class' in package 'Matrix' does not exist and so has been treated as a topic
    SsdMatrix-class                         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpIBO4ou/R.INSTALL1dec6d3066dd/qpgraph/man/SsdMatrix-class.Rd:14: file link 'dspMatrix-class' in package 'Matrix' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpIBO4ou/R.INSTALL1dec6d3066dd/qpgraph/man/SsdMatrix-class.Rd:27: file link 'dspMatrix-class' in package 'Matrix' does not exist and so has been treated as a topic
    UGgmm-class                             html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpIBO4ou/R.INSTALL1dec6d3066dd/qpgraph/man/UGgmm-class.Rd:56: file link 'dspMatrix-class' in package 'Matrix' does not exist and so has been treated as a topic
    eQTLcross-class                         html  
    eQTLnetwork-class                       html  
    eQTLnetworkEstimate                     html  
    eQTLnetworkEstimationParam-class        html  
    graphParam-class                        html  
    qpAllCItests                            html  
    qpAnyGraph                              html  
    qpAvgNrr                                html  
    qpBoundary                              html  
    qpCItest                                html  
    qpClique                                html  
    qpCliqueNumber                          html  
    qpCov                                   html  
    qpEdgeNrr                               html  
    qpFunctionalCoherence                   html  
    qpG2Sigma                               html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpIBO4ou/R.INSTALL1dec6d3066dd/qpgraph/man/qpG2Sigma.Rd:51: file link 'rmvnorm' in package 'mvtnorm' does not exist and so has been treated as a topic
    qpGenNrr                                html  
    qpGetCliques                            html  
    qpGraph-class                           html  
    qpGraphDensity                          html  
    qpHTF                                   html  
    qpHist                                  html  
    qpIPF                                   html  
    qpImportNrr                             html  
    qpK2ParCor                              html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpIBO4ou/R.INSTALL1dec6d3066dd/qpgraph/man/qpK2ParCor.Rd:17: file link 'cov2cor' in package 'stats' does not exist and so has been treated as a topic
    qpNrr                                   html  
    qpPAC                                   html  
    qpPCC                                   html  
    qpPRscoreThreshold                      html  
    qpPathWeight                            html  
    qpPlotMap                               html  
    qpPlotNetwork                           html  
    qpPrecisionRecall                       html  
    qpRndGraph                              html  
    qpRndWishart                            html  
    qpTopPairs                              html  
    qpUnifRndAssociation                    html  
    qpUpdateCliquesRemoving                 html  
    qpgraph-package                         html  
** building package indices
** installing vignettes
   'eQTLnetworks.Rnw' 
   'qpTxRegNet.Rnw' 
   'qpgraphSimulate.Rnw' 
** testing if installed package can be loaded
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
In R CMD INSTALL

install for x64

* installing *source* package 'qpgraph' ...

   **********************************************
   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˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c cliquer.c -o cliquer.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c graph.c -o graph.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c qpgraph.c -o qpgraph.o
qpgraph.c: In function 'qp_fast_path_weight':
qpgraph.c:5851:20: warning: left-hand operand of comma expression has no effect [-Wunused-value]
     int i = edges[k, 0];
                    ^
qpgraph.c:5852:20: warning: left-hand operand of comma expression has no effect [-Wunused-value]
     int j = edges[k, 1];
                    ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c reorder.c -o reorder.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o qpgraph.dll tmp.def cliquer.o graph.o qpgraph.o reorder.o -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lRblas -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/qpgraph.buildbin-libdir/qpgraph/libs/x64
** testing if installed package can be loaded
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
* MD5 sums
packaged installation of 'qpgraph' as qpgraph_2.14.0.zip
* DONE (qpgraph)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'qpgraph' successfully unpacked and MD5 sums checked
In R CMD INSTALL