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This page was generated on 2021-07-30 15:05:48 -0400 (Fri, 30 Jul 2021).

INSTALL results for CellNOptR on tokay2

To the developers/maintainers of the CellNOptR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CellNOptR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 266/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellNOptR 1.38.0  (landing page)
A.Gabor
Snapshot Date: 2021-07-29 04:50:02 -0400 (Thu, 29 Jul 2021)
URL: https://git.bioconductor.org/packages/CellNOptR
Branch: RELEASE_3_13
Last Commit: 8e211e0
Last Changed Date: 2021-05-19 11:50:40 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: CellNOptR
Version: 1.38.0
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CellNOptR_1.38.0.tar.gz && rm -rf CellNOptR.buildbin-libdir && mkdir CellNOptR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CellNOptR.buildbin-libdir CellNOptR_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CellNOptR_1.38.0.zip && rm CellNOptR_1.38.0.tar.gz CellNOptR_1.38.0.zip
StartedAt: 2021-07-29 08:41:35 -0400 (Thu, 29 Jul 2021)
EndedAt: 2021-07-29 08:43:04 -0400 (Thu, 29 Jul 2021)
EllapsedTime: 89.3 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CellNOptR_1.38.0.tar.gz && rm -rf CellNOptR.buildbin-libdir && mkdir CellNOptR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CellNOptR.buildbin-libdir CellNOptR_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CellNOptR_1.38.0.zip && rm CellNOptR_1.38.0.tar.gz CellNOptR_1.38.0.zip
###
##############################################################################
##############################################################################


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100 1417k  100 1417k    0     0  3185k      0 --:--:-- --:--:-- --:--:-- 3185k

install for i386

* installing *source* package 'CellNOptR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-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  
REDIRECT:topic	 setSignals<-,CNOlist-method -> CNOlist-class.html [ FAIL ]
    CNOlist-methods                         html  
REDIRECT:topic	 setSignals<- -> CNOlist-methods.html [ FAIL ]
REDIRECT:topic	 setSignals<-,CNOlist -> CNOlist-methods.html [ FAIL ]
REDIRECT:topic	 setSignals<-,CNOlist,CNOlist-method -> CNOlist-methods.html [ FAIL ]
    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  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/CellNOptR.buildbin-libdir/00LOCK-CellNOptR/00new/CellNOptR/help/prep4Sim.html
    preprocessing                           html  
    randomizeCNOlist                        html  
    readBND                                 html  
    readBNET                                html  
    readMIDAS                               html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/CellNOptR.buildbin-libdir/00LOCK-CellNOptR/00new/CellNOptR/help/readMidas.html
    readSBMLQual                            html  
    readSIF                                 html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/CellNOptR.buildbin-libdir/00LOCK-CellNOptR/00new/CellNOptR/help/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  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/CellNOptR.buildbin-libdir/00LOCK-CellNOptR/00new/CellNOptR/help/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/CellNOptR.buildbin-libdir/CellNOptR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CellNOptR' as CellNOptR_1.38.0.zip
* DONE (CellNOptR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CellNOptR' successfully unpacked and MD5 sums checked