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INSTALL report for CellNOptR on tokay2

This page was generated on 2020-10-17 11:56:13 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CellNOptR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 253/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellNOptR 1.34.0
A.Gabor
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/CellNOptR
Branch: RELEASE_3_11
Last Commit: bc86474
Last Changed Date: 2020-04-27 14:27:42 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CellNOptR
Version: 1.34.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/CellNOptR_1.34.0.tar.gz && rm -rf CellNOptR.buildbin-libdir && mkdir CellNOptR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CellNOptR.buildbin-libdir CellNOptR_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL CellNOptR_1.34.0.zip && rm CellNOptR_1.34.0.tar.gz CellNOptR_1.34.0.zip
StartedAt: 2020-10-16 18:10:27 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 18:12:26 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 119.7 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/CellNOptR_1.34.0.tar.gz && rm -rf CellNOptR.buildbin-libdir && mkdir CellNOptR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CellNOptR.buildbin-libdir CellNOptR_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL CellNOptR_1.34.0.zip && rm CellNOptR_1.34.0.tar.gz CellNOptR_1.34.0.zip
###
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100 1412k  100 1412k    0     0  14.7M      0 --:--:-- --:--:-- --:--:-- 16.0M

install for i386

* installing *source* package 'CellNOptR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getFit.c -o getFit.o
getFit.c: In function 'getFit':
getFit.c:47:6: warning: unused variable 'nReacs' [-Wunused-variable]
  int nReacs = INTEGER(nReacs_in)[0];
      ^~~~~~
getFit.c:42:6: warning: unused variable 'selCounter' [-Wunused-variable]
  int selCounter = 0;
      ^~~~~~~~~~
getFit.c:41:6: warning: unused variable 'selection' [-Wunused-variable]
  int selection[40];
      ^~~~~~~~~
getFit.c:40:6: warning: unused variable 'or_max' [-Wunused-variable]
  int or_max = 0;
      ^~~~~~
getFit.c:39:6: warning: unused variable 'curr_max' [-Wunused-variable]
  int curr_max = 0;
      ^~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c simulatorT1.c -o simulatorT1.o
simulatorT1.c: In function 'simulatorT1':
simulatorT1.c:502:20: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
        if (MA[i][j]<0.95 & MA[i][j]>0.05)  // actually we could check if they are exatly 0 or 1
            ~~~~~~~~^~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c simulatorTN.c -o simulatorTN.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o CellNOptR.dll tmp.def getFit.o simulatorT1.o simulatorTN.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/CellNOptR.buildbin-libdir/00LOCK-CellNOptR/00new/CellNOptR/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CellNOptR'
    finding HTML links ... done
    CNORbool                                html  
    CNORwrap                                html  
    CNOdata                                 html  
    CNOlist-class                           html  
    CNOlist-methods                         html  
    CNOlistDREAM                            html  
    CNOlistToy                              html  
    CNOlistToy2                             html  
    CNOlistToyMMB                           html  
    CellNOptR-package                       html  
    DreamModel                              html  
    ToyModel                                html  
    ToyModel2                               html  
    buildBitString                          html  
    build_sif_table_from_rule               html  
    cSimulator                              html  
    checkSignals                            html  
    compressModel                           html  
    computeScoreT1                          html  
    computeScoreTN                          html  
    createAndRunILP                         html  
    createILPBitstringAll                   html  
    create_binaries                         html  
    crossInhibitedData                      html  
    crossvalidateBoolean                    html  
    cutAndPlot                              html  
    cutAndPlotResultsT1                     html  
    cutAndPlotResultsTN                     html  
    cutCNOlist                              html  
    cutModel                                html  
    cutNONC                                 html  
    cutSimList                              html  
    defaultParameters                       html  
    exhaustive                              html  
    expandGates                             html  
    findNONC                                html  
    gaBinaryT1                              html  
    gaBinaryT2                              html  
    gaBinaryTN                              html  
    getFit                                  html  
    graph2sif                               html  
    ilpBinaryT1                             html  
    ilpBinaryT2                             html  
    ilpBinaryTN                             html  
    indexFinder                             html  
    internals                               html  
    invokeCPLEX                             html  
    makeCNOlist                             html  
    mapBack                                 html  
    model2igraph                            html  
    model2sif                               html  
    normaliseCNOlist                        html  
    plot-methods                            html  
    plotCNOlist                             html  
    plotCNOlist2                            html  
    plotCNOlistLarge                        html  
    plotCNOlistLargePDF                     html  
    plotCNOlistPDF                          html  
    plotFit                                 html  
    plotModel                               html  
    plotOptimResults                        html  
    plotOptimResultsPDF                     html  
    plotOptimResultsPan                     html  
    prep4sim                                html  
    preprocessing                           html  
    randomizeCNOlist                        html  
    readBND                                 html  
    readBNET                                html  
    readMIDAS                               html  
    readSBMLQual                            html  
    readSIF                                 html  
    residualError                           html  
    sif2graph                               html  
    simulateT1                              html  
    simulateTN                              html  
    simulatorT0                             html  
    simulatorT1                             html  
    simulatorT2                             html  
    simulatorTN                             html  
    toSBML                                  html  
    writeDot                                html  
    writeFile                               html  
    writeMIDAS                              html  
    writeNetwork                            html  
    writeObjectiveFunction                  html  
    writeReport                             html  
    writeSIF                                html  
    writeScaffold                           html  
    write_bounds                            html  
    write_constraints                       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 'CellNOptR' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getFit.c -o getFit.o
getFit.c: In function 'getFit':
getFit.c:47:6: warning: unused variable 'nReacs' [-Wunused-variable]
  int nReacs = INTEGER(nReacs_in)[0];
      ^~~~~~
getFit.c:42:6: warning: unused variable 'selCounter' [-Wunused-variable]
  int selCounter = 0;
      ^~~~~~~~~~
getFit.c:41:6: warning: unused variable 'selection' [-Wunused-variable]
  int selection[40];
      ^~~~~~~~~
getFit.c:40:6: warning: unused variable 'or_max' [-Wunused-variable]
  int or_max = 0;
      ^~~~~~
getFit.c:39:6: warning: unused variable 'curr_max' [-Wunused-variable]
  int curr_max = 0;
      ^~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c simulatorT1.c -o simulatorT1.o
simulatorT1.c: In function 'simulatorT1':
simulatorT1.c:502:20: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
        if (MA[i][j]<0.95 & MA[i][j]>0.05)  // actually we could check if they are exatly 0 or 1
            ~~~~~~~~^~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c simulatorTN.c -o simulatorTN.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o CellNOptR.dll tmp.def getFit.o simulatorT1.o simulatorTN.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/CellNOptR.buildbin-libdir/CellNOptR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CellNOptR' as CellNOptR_1.34.0.zip
* DONE (CellNOptR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'CellNOptR' successfully unpacked and MD5 sums checked