Back to Multiple platform build/check report for BioC 3.9
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

INSTALL report for deepSNV on tokay2

This page was generated on 2019-10-16 12:26:08 -0400 (Wed, 16 Oct 2019).

Package 405/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deepSNV 1.30.0
Moritz Gerstung
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/deepSNV
Branch: RELEASE_3_9
Last Commit: f598bac
Last Changed Date: 2019-05-02 11:53:34 -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  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

Summary

Package: deepSNV
Version: 1.30.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/deepSNV_1.30.0.tar.gz && rm -rf deepSNV.buildbin-libdir && mkdir deepSNV.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=deepSNV.buildbin-libdir deepSNV_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL deepSNV_1.30.0.zip && rm deepSNV_1.30.0.tar.gz deepSNV_1.30.0.zip
StartedAt: 2019-10-15 20:31:31 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 20:33:14 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 102.6 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/deepSNV_1.30.0.tar.gz && rm -rf deepSNV.buildbin-libdir && mkdir deepSNV.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=deepSNV.buildbin-libdir deepSNV_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL deepSNV_1.30.0.zip && rm deepSNV_1.30.0.tar.gz deepSNV_1.30.0.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 1278k  100 1278k    0     0  17.8M      0 --:--:-- --:--:-- --:--:-- 20.1M

install for i386

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

   **********************************************
   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-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c bam2R.cpp -o bam2R.o
bam2R.cpp: In function 'int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*)':
bam2R.cpp:96:13: warning: unused variable 'iter' [-Wunused-variable]
  hts_itr_t *iter = NULL;
             ^
bam2R.cpp:99:6: warning: unused variable 'c' [-Wunused-variable]
  int c = 0;
      ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c betabinom.c -o betabinom.o
betabinom.c: In function 'pbb':
betabinom.c:27:9: warning: unused variable 'log' [-Wunused-variable]
  int i, log=0;
         ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o deepSNV.dll tmp.def bam2R.o betabinom.o -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib/i386 -lhts -lz -lm -lws2_32 -lpthread -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/deepSNV.buildbin-libdir/00LOCK-deepSNV/00new/deepSNV/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'deepSNV'
    finding HTML links ... done
    Extract-methods                         html  
    RCC                                     html  
    RF                                      html  
    bam2R                                   html  
    betabinLRT                              html  
    bf2Vcf                                  html  
    finding level-2 HTML links ... done

    consensusSequence-methods               html  
    control-methods                         html  
    coordinates-methods                     html  
    counts                                  html  
    dbetabinom                              html  
    deepSNV-class                           html  
    deepSNV-methods                         html  
    deepSNV-package                         html  
    estimateDirichlet-methods               html  
    estimateDispersion-methods              html  
    estimateRho                             html  
    loadAllData                             html  
    makePrior                               html  
    manhattanPlot                           html  
    mcChunk                                 html  
    normalize-methods                       html  
    p.combine                               html  
    p.val-methods                           html  
    pbetabinom                              html  
    phiX                                    html  
    pi                                      html  
    plot.deepSNV                            html  
    qvals2Vcf                               html  
    repeatMask-methods                      html  
    shearwater                              html  
    show-deepSNV-method                     html  
    summary-methods                         html  
    test-methods                            html  
    trueSNVs                                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 'deepSNV' ...

   **********************************************
   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-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c bam2R.cpp -o bam2R.o
bam2R.cpp: In function 'int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*)':
bam2R.cpp:96:13: warning: unused variable 'iter' [-Wunused-variable]
  hts_itr_t *iter = NULL;
             ^
bam2R.cpp:99:6: warning: unused variable 'c' [-Wunused-variable]
  int c = 0;
      ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c betabinom.c -o betabinom.o
betabinom.c: In function 'pbb':
betabinom.c:27:9: warning: unused variable 'log' [-Wunused-variable]
  int i, log=0;
         ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o deepSNV.dll tmp.def bam2R.o betabinom.o -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib/x64 -lhts -lz -lm -lws2_32 -lpthread -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/deepSNV.buildbin-libdir/deepSNV/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'deepSNV' as deepSNV_1.30.0.zip
* DONE (deepSNV)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'deepSNV' successfully unpacked and MD5 sums checked