Back to Multiple platform build/check report for BioC 3.14
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-01-24 13:06:15 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

INSTALL results for flowClust on tokay2


To the developers/maintainers of the flowClust package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowClust.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 656/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowClust 3.32.0  (landing page)
Greg Finak , Mike Jiang
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/flowClust
git_branch: RELEASE_3_14
git_last_commit: 2978117
git_last_commit_date: 2021-10-26 11:52:08 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    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: flowClust
Version: 3.32.0
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/flowClust_3.32.0.tar.gz && rm -rf flowClust.buildbin-libdir && mkdir flowClust.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowClust.buildbin-libdir flowClust_3.32.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL flowClust_3.32.0.zip && rm flowClust_3.32.0.tar.gz flowClust_3.32.0.zip
StartedAt: 2022-01-23 05:27:59 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 05:29:23 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 84.4 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/flowClust_3.32.0.tar.gz && rm -rf flowClust.buildbin-libdir && mkdir flowClust.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowClust.buildbin-libdir flowClust_3.32.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL flowClust_3.32.0.zip && rm flowClust_3.32.0.tar.gz flowClust_3.32.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1610k  100 1610k    0     0  2431k      0 --:--:-- --:--:-- --:--:-- 2436k

install for i386

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

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
rm -f BoxCox.o BoxCoxPriors.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.o flowClust.dll
"C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386/Rscript.exe" "../tools/winlibs.R" 2.4
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c BoxCox.c -o BoxCox.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Nu.c -o Nu.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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;
      ^
At top level:
flowClust.c:10:27: warning: 'CEntries' defined but not used [-Wunused-const-variable=]
 static const R_CMethodDef CEntries[] = { { "flowClust", (DL_FUNC) & flowClust,
                           ^~~~~~~~
flowClust.c: In function 'flowClust':
flowClust.c:702:13: warning: 's3' may be used uninitialized in this function [-Wmaybe-uninitialized]
    status = gsl_min_fminimizer_set(s3, &F3, *nu, *nuLow, *nuUp);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
flowClust.c:647:15: warning: 's2' may be used uninitialized in this function [-Wmaybe-uninitialized]
       nu_hi = gsl_root_fsolver_x_upper(s2);
               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
flowClust.c:348:14: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
       x_hi = gsl_root_fsolver_x_upper(s);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c flowClustGaussian.c -o flowClustGaussian.o
flowClustGaussian.c: In function 'flowClustGaussian':
flowClustGaussian.c:207:14: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
       x_hi = gsl_root_fsolver_x_upper(s);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ranMVNT.c -o ranMVNT.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o flowClust.dll tmp.def BoxCox.o BoxCoxPriors.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.o -L../windows/gsl-2.4/lib/i386 -lgsl -lgslcblas -lm -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-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  
** 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
rm -f BoxCox.o BoxCoxPriors.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.o flowClust.dll
"C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64/Rscript.exe" "../tools/winlibs.R" 2.4
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c BoxCox.c -o BoxCox.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Nu.c -o Nu.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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;
      ^
At top level:
flowClust.c:10:27: warning: 'CEntries' defined but not used [-Wunused-const-variable=]
 static const R_CMethodDef CEntries[] = { { "flowClust", (DL_FUNC) & flowClust,
                           ^~~~~~~~
flowClust.c: In function 'flowClust':
flowClust.c:702:13: warning: 's3' may be used uninitialized in this function [-Wmaybe-uninitialized]
    status = gsl_min_fminimizer_set(s3, &F3, *nu, *nuLow, *nuUp);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
flowClust.c:647:15: warning: 's2' may be used uninitialized in this function [-Wmaybe-uninitialized]
       nu_hi = gsl_root_fsolver_x_upper(s2);
               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
flowClust.c:348:14: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
       x_hi = gsl_root_fsolver_x_upper(s);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c flowClustGaussian.c -o flowClustGaussian.o
flowClustGaussian.c: In function 'flowClustGaussian':
flowClustGaussian.c:207:14: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
       x_hi = gsl_root_fsolver_x_upper(s);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ranMVNT.c -o ranMVNT.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o flowClust.dll tmp.def BoxCox.o BoxCoxPriors.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.o -L../windows/gsl-2.4/lib/x64 -lgsl -lgslcblas -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/flowClust.buildbin-libdir/flowClust/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowClust' as flowClust_3.32.0.zip
* DONE (flowClust)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'flowClust' successfully unpacked and MD5 sums checked