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BUILD BIN report for flowClust on tokay2

This page was generated on 2019-10-16 12:21:45 -0400 (Wed, 16 Oct 2019).

Package 562/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowClust 3.22.0
Greg Finak , Mike Jiang
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/flowClust
Branch: RELEASE_3_9
Last Commit: 4eb453c
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  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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowClust
Version: 3.22.0
Command: rm -rf flowClust.buildbin-libdir && mkdir flowClust.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowClust.buildbin-libdir flowClust_3.22.0.tar.gz
StartedAt: 2019-10-16 09:12:46 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 09:13:38 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 51.5 seconds
RetCode: 0
Status:  OK  
PackageFile: flowClust_3.22.0.zip
PackageFileSize: 1.014 MiB

Command output

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###
### Running command:
###
###   rm -rf flowClust.buildbin-libdir && mkdir flowClust.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowClust.buildbin-libdir flowClust_3.22.0.tar.gz
###
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install for i386

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

   **********************************************
   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-3~1.9-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c BoxCox.c -o BoxCox.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c BoxCoxPriors.c -o BoxCoxPriors.o
BoxCoxPriors.c: In function 'BoxCoxGradientPriors':
BoxCoxPriors.c:57:16: warning: unused variable 'rowZ' [-Wunused-variable]
  rowPrecision, rowZ, rowLambda0;
                ^
BoxCoxPriors.c:33:24: warning: unused variable 'kappa0' [-Wunused-variable]
  double *nu0 = p->nu0, kappa0 = p->kappa0;
                        ^
BoxCoxPriors.c:32:7: warning: unused variable 'itersolve' [-Wunused-variable]
  int *itersolve = p->itersolve;
       ^
BoxCoxPriors.c:31:6: warning: unused variable 'iter' [-Wunused-variable]
  int iter = p->iter;
      ^
BoxCoxPriors.c:28:6: warning: unused variable 'model' [-Wunused-variable]
  int model = *p->model;
      ^
BoxCoxPriors.c:23:14: warning: unused variable 'SumZlogY' [-Wunused-variable]
  gsl_vector *SumZlogY = p->SumZlogY;
              ^
BoxCoxPriors.c:15:14: warning: unused variable 'Precision' [-Wunused-variable]
  gsl_matrix *Precision = p->Precision; // will be updated
              ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Nu.c -o Nu.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c flowClust.c -o flowClust.o
flowClust.c: In function 'flowClust':
flowClust.c:48:2: warning: unused variable 'matrixZUY2' [-Wunused-variable]
  matrixZUY2;
  ^
flowClust.c:46:48: warning: unused variable 'subRowZUY2' [-Wunused-variable]
  rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
                                                ^
flowClust.c:46:39: warning: unused variable 'rowZUY2' [-Wunused-variable]
  rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
                                       ^
flowClust.c: In function 'ECMUpdateSigmaG2':
flowClust.c:1111:6: warning: unused variable 'i' [-Wunused-variable]
  int i=0;
      ^
flowClust.c: In function 'flowClust':
flowClust.c:383:13: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
        x_hi = gsl_root_fsolver_x_upper(s);
             ^
flowClust.c:713:12: warning: 's3' may be used uninitialized in this function [-Wmaybe-uninitialized]
      nu_hi = gsl_min_fminimizer_x_upper(s3);
            ^
flowClust.c:675:14: warning: 's2' may be used uninitialized in this function [-Wmaybe-uninitialized]
        nu_hi = gsl_root_fsolver_x_upper(s2);
              ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c flowClustGaussian.c -o flowClustGaussian.o
flowClustGaussian.c: In function 'flowClustGaussian':
flowClustGaussian.c:242:13: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
        x_hi = gsl_root_fsolver_x_upper(s);
             ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ranMVNT.c -o ranMVNT.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o flowClust.dll tmp.def BoxCox.o BoxCoxPriors.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.o -L/i386/lib -lgsl -lgslcblas -lm -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/flowClust.buildbin-libdir/00LOCK-flowClust/00new/flowClust/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'Map' in package 'flowClust'
** help
*** installing help indices
  converting help for package 'flowClust'
    finding HTML links ... done
    BIC                                     html  
    Map                                     html  
    SimulateMixture                         html  
    Subset                                  html  
    box                                     html  
    density                                 html  
    dmvt                                    html  
    dmvtmix                                 html  
    flowClust-package                       html  
    flowClust                               html  
    flowClust.den                           html  
    flowClust2Prior                         html  
    hist                                    html  
    miscellaneous                           html  
    mkPrior                                 html  
    peakMatch                               html  
    plot.flowClust                          html  
    plot.flowCore                           html  
    plot.flowDens                           html  
    plotPrior                               html  
    rbox                                    html  
    rituximab                               html  
    ruleOutliers                            html  
    show.flowClust                          html  
    split                                   html  
    summary                                 html  
    tmixFilter                              html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuo3E8K/R.INSTALL15a448584c84/flowClust/man/tmixFilter.Rd:63: file link 'filter' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuo3E8K/R.INSTALL15a448584c84/flowClust/man/tmixFilter.Rd:75: file link 'filter' in package 'flowCore' does not exist and so has been treated as a topic
** 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 'flowClust' ...

   **********************************************
   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-3~1.9-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c BoxCox.c -o BoxCox.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c BoxCoxPriors.c -o BoxCoxPriors.o
BoxCoxPriors.c: In function 'BoxCoxGradientPriors':
BoxCoxPriors.c:57:16: warning: unused variable 'rowZ' [-Wunused-variable]
  rowPrecision, rowZ, rowLambda0;
                ^
BoxCoxPriors.c:33:24: warning: unused variable 'kappa0' [-Wunused-variable]
  double *nu0 = p->nu0, kappa0 = p->kappa0;
                        ^
BoxCoxPriors.c:32:7: warning: unused variable 'itersolve' [-Wunused-variable]
  int *itersolve = p->itersolve;
       ^
BoxCoxPriors.c:31:6: warning: unused variable 'iter' [-Wunused-variable]
  int iter = p->iter;
      ^
BoxCoxPriors.c:28:6: warning: unused variable 'model' [-Wunused-variable]
  int model = *p->model;
      ^
BoxCoxPriors.c:23:14: warning: unused variable 'SumZlogY' [-Wunused-variable]
  gsl_vector *SumZlogY = p->SumZlogY;
              ^
BoxCoxPriors.c:15:14: warning: unused variable 'Precision' [-Wunused-variable]
  gsl_matrix *Precision = p->Precision; // will be updated
              ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Nu.c -o Nu.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c flowClust.c -o flowClust.o
flowClust.c: In function 'flowClust':
flowClust.c:48:2: warning: unused variable 'matrixZUY2' [-Wunused-variable]
  matrixZUY2;
  ^
flowClust.c:46:48: warning: unused variable 'subRowZUY2' [-Wunused-variable]
  rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
                                                ^
flowClust.c:46:39: warning: unused variable 'rowZUY2' [-Wunused-variable]
  rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
                                       ^
flowClust.c: In function 'ECMUpdateSigmaG2':
flowClust.c:1111:6: warning: unused variable 'i' [-Wunused-variable]
  int i=0;
      ^
flowClust.c: In function 'flowClust':
flowClust.c:383:13: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
        x_hi = gsl_root_fsolver_x_upper(s);
             ^
flowClust.c:713:12: warning: 's3' may be used uninitialized in this function [-Wmaybe-uninitialized]
      nu_hi = gsl_min_fminimizer_x_upper(s3);
            ^
flowClust.c:675:14: warning: 's2' may be used uninitialized in this function [-Wmaybe-uninitialized]
        nu_hi = gsl_root_fsolver_x_upper(s2);
              ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c flowClustGaussian.c -o flowClustGaussian.o
flowClustGaussian.c: In function 'flowClustGaussian':
flowClustGaussian.c:242:13: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
        x_hi = gsl_root_fsolver_x_upper(s);
             ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ranMVNT.c -o ranMVNT.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o flowClust.dll tmp.def BoxCox.o BoxCoxPriors.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.o -L/x64/lib -lgsl -lgslcblas -lm -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/flowClust.buildbin-libdir/flowClust/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowClust' as flowClust_3.22.0.zip
* DONE (flowClust)