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INSTALL report for DeMixT on tokay2

This page was generated on 2019-04-09 12:45:43 -0400 (Tue, 09 Apr 2019).

Package 408/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DeMixT 0.99.9
Zeya Wang , Fan Gao
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/DeMixT
Branch: master
Last Commit: cf860b0
Last Changed Date: 2019-04-02 15:33:18 -0400 (Tue, 02 Apr 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  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: DeMixT
Version: 0.99.9
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/DeMixT_0.99.9.tar.gz && rm -rf DeMixT.buildbin-libdir && mkdir DeMixT.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DeMixT.buildbin-libdir DeMixT_0.99.9.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DeMixT_0.99.9.zip && rm DeMixT_0.99.9.tar.gz DeMixT_0.99.9.zip
StartedAt: 2019-04-08 19:45:16 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 19:46:10 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 53.7 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/DeMixT_0.99.9.tar.gz && rm -rf DeMixT.buildbin-libdir && mkdir DeMixT.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DeMixT.buildbin-libdir DeMixT_0.99.9.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DeMixT_0.99.9.zip && rm DeMixT_0.99.9.tar.gz DeMixT_0.99.9.zip
###
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  % 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  547k  100  547k    0     0  8764k      0 --:--:-- --:--:-- --:--:-- 9776k

install for i386

* installing *source* package 'DeMixT' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c DeMixT.c -o DeMixT.o
DeMixT.c: In function 'Tdemix':
DeMixT.c:253:7: warning: implicit declaration of function 'Rprintf' [-Wimplicit-function-declaration]
       if (nHavepi != 1)  Rprintf("Iteration %d: updating purities\n", i+1);
       ^
DeMixT.c:43:9: warning: unused variable 'nthread' [-Wunused-variable]
     int nthread=*thread;
         ^
DeMixT.c:36:45: warning: variable 'st2_sig_2' set but not used [-Wunused-but-set-variable]
   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
                                             ^
DeMixT.c:36:33: warning: variable 'st1_sig_2' set but not used [-Wunused-but-set-variable]
   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
                                 ^
DeMixT.c:36:22: warning: variable 'st2_mu_2' set but not used [-Wunused-but-set-variable]
   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
                      ^
DeMixT.c:36:11: warning: variable 'st1_mu_2' set but not used [-Wunused-but-set-variable]
   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
           ^
DeMixT.c: In function 'gettumor':
DeMixT.c:540:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^
DeMixT.c:540:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^
DeMixT.c: In function 'getpi':
DeMixT.c:1229:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^
DeMixT.c:1229:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^
DeMixT.c: In function 'getpiT':
DeMixT.c:1259:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^
DeMixT.c:1259:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^
DeMixT.c: In function 'Tdemix':
DeMixT.c:188:11: warning: 'Tavgtmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
         if(Tavgtmp <= 0) Tavgtmp = exp(10*log(2.0) + p->Tsigma[j]/2.0*pow(log(2.0), 2.0));
           ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c registerDynamicSymbol.c -o registerDynamicSymbol.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o DeMixT.dll tmp.def DeMixT.o init.o registerDynamicSymbol.o -fopenmp -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/DeMixT.buildbin-libdir/00LOCK-DeMixT/00new/DeMixT/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DeMixT'
    finding HTML links ... done
    DeMixT                                  html  
    DeMixT_S1                               html  
    DeMixT_S2                               html  
    Optimum_KernelC                         html  
    test.data1.comp1                        html  
    test.data1.truth                        html  
    test.data1.y                            html  
    test.data2.comp1                        html  
    test.data2.comp2                        html  
    test.data2.truth                        html  
    test.data2.y                            html  
    test.data3.comp1                        html  
    test.data3.comp2                        html  
    test.data3.truth                        html  
    test.data3.y                            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 'DeMixT' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c DeMixT.c -o DeMixT.o
DeMixT.c: In function 'Tdemix':
DeMixT.c:253:7: warning: implicit declaration of function 'Rprintf' [-Wimplicit-function-declaration]
       if (nHavepi != 1)  Rprintf("Iteration %d: updating purities\n", i+1);
       ^
DeMixT.c:43:9: warning: unused variable 'nthread' [-Wunused-variable]
     int nthread=*thread;
         ^
DeMixT.c:36:45: warning: variable 'st2_sig_2' set but not used [-Wunused-but-set-variable]
   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
                                             ^
DeMixT.c:36:33: warning: variable 'st1_sig_2' set but not used [-Wunused-but-set-variable]
   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
                                 ^
DeMixT.c:36:22: warning: variable 'st2_mu_2' set but not used [-Wunused-but-set-variable]
   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
                      ^
DeMixT.c:36:11: warning: variable 'st1_mu_2' set but not used [-Wunused-but-set-variable]
   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
           ^
DeMixT.c: In function 'gettumor':
DeMixT.c:540:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^
DeMixT.c:540:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^
DeMixT.c: In function 'getpi':
DeMixT.c:1229:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^
DeMixT.c:1229:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^
DeMixT.c: In function 'getpiT':
DeMixT.c:1259:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^
DeMixT.c:1259:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^
DeMixT.c: In function 'Tdemix':
DeMixT.c:188:11: warning: 'Tavgtmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
         if(Tavgtmp <= 0) Tavgtmp = exp(10*log(2.0) + p->Tsigma[j]/2.0*pow(log(2.0), 2.0));
           ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c registerDynamicSymbol.c -o registerDynamicSymbol.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o DeMixT.dll tmp.def DeMixT.o init.o registerDynamicSymbol.o -fopenmp -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/DeMixT.buildbin-libdir/DeMixT/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DeMixT' as DeMixT_0.99.9.zip
* DONE (DeMixT)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'DeMixT' successfully unpacked and MD5 sums checked