Back to Multiple platform build/check report for BioC 3.8
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

CHECK report for immunoClust on tokay1

This page was generated on 2019-04-13 11:25:00 -0400 (Sat, 13 Apr 2019).

Package 770/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
immunoClust 1.14.1
Till Soerensen
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/immunoClust
Branch: RELEASE_3_8
Last Commit: c89a3c8
Last Changed Date: 2018-12-01 05:45:45 -0400 (Sat, 01 Dec 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: immunoClust
Version: 1.14.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:immunoClust.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings immunoClust_1.14.1.tar.gz
StartedAt: 2019-04-13 03:10:29 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:18:24 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 475.6 seconds
RetCode: 0
Status:  OK  
CheckDir: immunoClust.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:immunoClust.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings immunoClust_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/immunoClust.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'immunoClust/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'immunoClust' version '1.14.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'immunoClust' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/immunoClust/libs/i386/immunoClust.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
dat.fcs            74.43   0.06   74.50
cell.process       68.72   0.02   68.77
cell.SubClustering 16.88   0.04   16.92
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
dat.fcs            64.67   0.11   64.79
cell.process       63.43   0.06   63.50
cell.SubClustering 17.69   0.02   17.70
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/immunoClust.Rcheck/00check.log'
for details.



Installation output

immunoClust.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/immunoClust_1.14.1.tar.gz && rm -rf immunoClust.buildbin-libdir && mkdir immunoClust.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=immunoClust.buildbin-libdir immunoClust_1.14.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL immunoClust_1.14.1.zip && rm immunoClust_1.14.1.tar.gz immunoClust_1.14.1.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  430k  100  430k    0     0  3354k      0 --:--:-- --:--:-- --:--:-- 3445k

install for i386

* installing *source* package 'immunoClust' ...

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


** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_meta.cpp -o R_meta.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_model.cpp -o R_model.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c dist_mvn.cpp -o dist_mvn.o
dist_mvn.cpp: In member function 'int dist_mvn::hellinger(double*)':
dist_mvn.cpp:56:14: warning: variable 'det_k' set but not used [-Wunused-but-set-variable]
  double det, det_k, det_l, logD;
              ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c em_meta.cpp -o em_meta.o
em_meta.cpp: In member function 'double em_meta::bt_step()':
em_meta.cpp:704:10: warning: variable 'sndLike' set but not used [-Wunused-but-set-variable]
   double sndLike = 0.0;
          ^
em_meta.cpp: In member function 'int em_meta::wt_step()':
em_meta.cpp:1047:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
  double minNk = T_sum;
         ^
em_meta.cpp:1049:9: warning: variable 'minDelta' set but not used [-Wunused-but-set-variable]
  double minDelta = FLTMAX;
         ^
em_meta.cpp: In member function 'int em_meta::st_step()':
em_meta.cpp:1117:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
  double minNk = T_sum;
         ^
em_meta.cpp:1119:9: warning: variable 'minDelta' set but not used [-Wunused-but-set-variable]
  double minDelta = FLTMAX;
         ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c em_mvn.cpp -o em_mvn.o
em_mvn.cpp: In member function 'int em_gaussian::build(const int*, double*, int*)':
em_mvn.cpp:721:13: warning: variable 'maxClust' set but not used [-Wunused-but-set-variable]
         int maxClust = -1;
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c em_mvt.cpp -o em_mvt.o
em_mvt.cpp: In member function 'int em_mvt::t_step()':
em_mvt.cpp:521:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
  double minNk = T_sum;
         ^
em_mvt.cpp: In member function 'int em_mvt::build(const int*, double*, int*)':
em_mvt.cpp:771:13: warning: variable 'maxClust' set but not used [-Wunused-but-set-variable]
         int maxClust = -1;
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c em_mvt2.cpp -o em_mvt2.o
em_mvt2.cpp: In member function 'int em_mvt2::t_step()':
em_mvt2.cpp:508:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
  double minNk = T_sum;
         ^
em_mvt2.cpp: In member function 'int em_mvt2::build(const int*, double*, int*)':
em_mvt2.cpp:805:13: warning: variable 'maxClust' set but not used [-Wunused-but-set-variable]
         int maxClust = -1;
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c hc_meta.cpp -o hc_meta.o
hc_meta.cpp: In member function 'int mvn_dendro::mahalanobis_w(int*, int*, double*)':
hc_meta.cpp:814:16: warning: variable 'S_i' set but not used [-Wunused-but-set-variable]
  const double *S_i, *S_j;
                ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c hc_mvn.cpp -o hc_mvn.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c immunoClust.c -o immunoClust.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c meta_norm.cpp -o meta_norm.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c meta_scale.cpp -o meta_scale.o
meta_scale.cpp: In member function 'void meta_scale::quantile()':
meta_scale.cpp:846:10: warning: variable 'w' set but not used [-Wunused-but-set-variable]
  double *w, *m, *s;
          ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c normalize.cpp -o normalize.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c sub_mvn.cpp -o sub_mvn.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c util.cpp -o util.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c vs_htrans.cpp -o vs_htrans.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o immunoClust.dll tmp.def R_meta.o R_model.o dist_mvn.o em_meta.o em_mvn.o em_mvt.o em_mvt2.o hc_meta.o hc_mvn.o immunoClust.o meta_norm.o meta_scale.o normalize.o sub_mvn.o util.o vs_htrans.o -L/i386/lib -lgsl -lgslcblas -lm -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/immunoClust.buildbin-libdir/immunoClust/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'immunoClust'
    finding HTML links ... done
    cell.ClustData                          html  
    cell.EM                                 html  
    cell.FitModel                           html  
    cell.ME                                 html  
    cell.SubClustering                      html  
    cell.hclust                             html  
    cell.process                            html  
    cell.removed                            html  
    dat.exp                                 html  
    dat.fcs                                 html  
    dat.meta                                html  
    immunoClust-package                     html  
    immunoClust.object                      html  
    meta.ME                                 html  
    meta.SubClustering                      html  
    meta.clustering                         html  
    meta.export                             html  
    meta.exprs                              html  
    meta.hclust                             html  
    meta.normalize                          html  
    meta.plot                               html  
    meta.process                            html  
    meta.regnorm                            html  
    plot.immunoClust                        html  
    splom.immunoClust                       html  
    trans.ApplyToData                       html  
    trans.FitToData                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'immunoClust' ...

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


** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_meta.cpp -o R_meta.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_model.cpp -o R_model.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c dist_mvn.cpp -o dist_mvn.o
dist_mvn.cpp: In member function 'int dist_mvn::hellinger(double*)':
dist_mvn.cpp:56:14: warning: variable 'det_k' set but not used [-Wunused-but-set-variable]
  double det, det_k, det_l, logD;
              ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c em_meta.cpp -o em_meta.o
em_meta.cpp: In member function 'double em_meta::bt_step()':
em_meta.cpp:704:10: warning: variable 'sndLike' set but not used [-Wunused-but-set-variable]
   double sndLike = 0.0;
          ^
em_meta.cpp: In member function 'int em_meta::wt_step()':
em_meta.cpp:1047:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
  double minNk = T_sum;
         ^
em_meta.cpp:1049:9: warning: variable 'minDelta' set but not used [-Wunused-but-set-variable]
  double minDelta = FLTMAX;
         ^
em_meta.cpp: In member function 'int em_meta::st_step()':
em_meta.cpp:1117:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
  double minNk = T_sum;
         ^
em_meta.cpp:1119:9: warning: variable 'minDelta' set but not used [-Wunused-but-set-variable]
  double minDelta = FLTMAX;
         ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c em_mvn.cpp -o em_mvn.o
em_mvn.cpp: In member function 'int em_gaussian::build(const int*, double*, int*)':
em_mvn.cpp:721:13: warning: variable 'maxClust' set but not used [-Wunused-but-set-variable]
         int maxClust = -1;
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c em_mvt.cpp -o em_mvt.o
em_mvt.cpp: In member function 'int em_mvt::t_step()':
em_mvt.cpp:521:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
  double minNk = T_sum;
         ^
em_mvt.cpp: In member function 'int em_mvt::build(const int*, double*, int*)':
em_mvt.cpp:771:13: warning: variable 'maxClust' set but not used [-Wunused-but-set-variable]
         int maxClust = -1;
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c em_mvt2.cpp -o em_mvt2.o
em_mvt2.cpp: In member function 'int em_mvt2::t_step()':
em_mvt2.cpp:508:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
  double minNk = T_sum;
         ^
em_mvt2.cpp: In member function 'int em_mvt2::build(const int*, double*, int*)':
em_mvt2.cpp:805:13: warning: variable 'maxClust' set but not used [-Wunused-but-set-variable]
         int maxClust = -1;
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c hc_meta.cpp -o hc_meta.o
hc_meta.cpp: In member function 'int mvn_dendro::mahalanobis_w(int*, int*, double*)':
hc_meta.cpp:814:16: warning: variable 'S_i' set but not used [-Wunused-but-set-variable]
  const double *S_i, *S_j;
                ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c hc_mvn.cpp -o hc_mvn.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c immunoClust.c -o immunoClust.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c meta_norm.cpp -o meta_norm.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c meta_scale.cpp -o meta_scale.o
meta_scale.cpp: In member function 'void meta_scale::quantile()':
meta_scale.cpp:846:10: warning: variable 'w' set but not used [-Wunused-but-set-variable]
  double *w, *m, *s;
          ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c normalize.cpp -o normalize.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c sub_mvn.cpp -o sub_mvn.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c util.cpp -o util.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c vs_htrans.cpp -o vs_htrans.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o immunoClust.dll tmp.def R_meta.o R_model.o dist_mvn.o em_meta.o em_mvn.o em_mvt.o em_mvt2.o hc_meta.o hc_mvn.o immunoClust.o meta_norm.o meta_scale.o normalize.o sub_mvn.o util.o vs_htrans.o -L/x64/lib -lgsl -lgslcblas -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/immunoClust.buildbin-libdir/immunoClust/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'immunoClust' as immunoClust_1.14.1.zip
* DONE (immunoClust)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'immunoClust' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

immunoClust.Rcheck/examples_i386/immunoClust-Ex.timings

nameusersystemelapsed
cell.ClustData2.290.042.52
cell.EM1.300.041.33
cell.FitModel1.270.001.26
cell.ME0.870.000.88
cell.SubClustering16.88 0.0416.92
cell.hclust0.010.000.02
cell.process68.72 0.0268.77
cell.removed0.020.000.01
dat.exp1.030.001.03
dat.fcs74.43 0.0674.50
dat.meta000
immunoClust.object0.000.020.02
meta.ME0.020.010.03
meta.SubClustering0.20.00.2
meta.clustering1.710.001.71
meta.export1.090.001.09
meta.exprs0.020.000.02
meta.hclust000
meta.normalize0.000.020.01
meta.plot3.170.033.20
meta.process1.370.001.38
meta.regnorm0.020.000.01
plot.immunoClust0.830.010.85
splom.immunoClust1.210.021.23
trans.ApplyToData0.070.000.07
trans.FitToData0.260.000.26

immunoClust.Rcheck/examples_x64/immunoClust-Ex.timings

nameusersystemelapsed
cell.ClustData2.430.032.51
cell.EM1.370.021.39
cell.FitModel1.220.011.23
cell.ME0.820.020.85
cell.SubClustering17.69 0.0217.70
cell.hclust0.020.000.01
cell.process63.43 0.0663.50
cell.removed000
dat.exp0.990.011.00
dat.fcs64.67 0.1164.79
dat.meta0.000.020.01
immunoClust.object000
meta.ME0.020.000.02
meta.SubClustering0.120.000.12
meta.clustering1.110.001.11
meta.export1.060.001.06
meta.exprs000
meta.hclust000
meta.normalize000
meta.plot3.480.033.51
meta.process1.660.001.66
meta.regnorm0.010.000.02
plot.immunoClust0.880.020.89
splom.immunoClust0.920.010.93
trans.ApplyToData0.050.000.05
trans.FitToData0.230.030.28