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BioC 3.4: INSTALL report for deepSNV on moscato1

This page was generated on 2016-09-21 03:44:03 -0700 (Wed, 21 Sep 2016).

Package 300/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deepSNV 1.19.4
Moritz Gerstung
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/deepSNV
Last Changed Rev: 117893 / Revision: 121152
Last Changed Date: 2016-05-26 11:46:10 -0700 (Thu, 26 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: deepSNV
Version: 1.19.4
Command: rm -rf deepSNV.buildbin-libdir && mkdir deepSNV.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/deepSNV_1.19.4.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=deepSNV.buildbin-libdir --merge-multiarch deepSNV_1.19.4.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL deepSNV_1.19.4.zip && rm deepSNV_1.19.4.tar.gz deepSNV_1.19.4.zip
StartedAt: 2016-09-19 21:03:44 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 21:04:33 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 49.7 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf deepSNV.buildbin-libdir && mkdir deepSNV.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/deepSNV_1.19.4.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=deepSNV.buildbin-libdir --merge-multiarch deepSNV_1.19.4.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL deepSNV_1.19.4.zip  && rm deepSNV_1.19.4.tar.gz deepSNV_1.19.4.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 1277k  100 1277k    0     0  40.6M      0 --:--:-- --:--:-- --:--:-- 46.2M

install for i386

* installing *source* package 'deepSNV' ...

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


** libs
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c bam2R.cpp -o bam2R.o
bam2R.cpp: In function 'int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*)':
bam2R.cpp:43:13: warning: unused variable 'iter' [-Wunused-variable]
  hts_itr_t *iter = NULL;
             ^
bam2R.cpp:46:6: warning: unused variable 'c' [-Wunused-variable]
  int c = 0;
      ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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 -LD:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/lib/i386 -lhts -lz -pthread -lws2_32 -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/deepSNV.buildbin-libdir/deepSNV/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c bam2R.cpp -o bam2R.o
bam2R.cpp: In function 'int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*)':
bam2R.cpp:43:13: warning: unused variable 'iter' [-Wunused-variable]
  hts_itr_t *iter = NULL;
             ^
bam2R.cpp:46:6: warning: unused variable 'c' [-Wunused-variable]
  int c = 0;
      ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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 -LD:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/lib/x64 -lhts -lz -pthread -lws2_32 -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/deepSNV.buildbin-libdir/deepSNV/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'deepSNV' as deepSNV_1.19.4.zip
* DONE (deepSNV)
* installing to library 'D:/biocbld/bbs-3.4-bioc/R/library'
package 'deepSNV' successfully unpacked and MD5 sums checked