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BioC 3.5: INSTALL report for deepSNV on tokay2

This page was generated on 2017-10-18 14:21:41 -0400 (Wed, 18 Oct 2017).

Package 327/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deepSNV 1.22.0
Moritz Gerstung
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/deepSNV
Branch: RELEASE_3_5
Last Commit: c7ce3a8
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: deepSNV
Version: 1.22.0
Command: rm -rf deepSNV.buildbin-libdir && mkdir deepSNV.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/deepSNV_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=deepSNV.buildbin-libdir --merge-multiarch deepSNV_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL deepSNV_1.22.0.zip && rm deepSNV_1.22.0.tar.gz deepSNV_1.22.0.zip
StartedAt: 2017-10-17 18:40:31 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 18:41:19 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 47.9 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://172.29.0.4/BBS/3.5/bioc/src/contrib/deepSNV_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=deepSNV.buildbin-libdir --merge-multiarch deepSNV_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL deepSNV_1.22.0.zip  && rm deepSNV_1.22.0.tar.gz deepSNV_1.22.0.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 1277k  100 1277k    0     0  19.2M      0 --:--:-- --:--:-- --:--:-- 19.8M

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"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-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_pileup_function(const bam_pileup1_t*, int, int, nttable_t)':
bam2R.cpp:69:1: warning: no return statement in function returning non-void [-Wreturn-type]
 }
 ^
bam2R.cpp: In function 'int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*)':
bam2R.cpp:76:13: warning: unused variable 'iter' [-Wunused-variable]
  hts_itr_t *iter = NULL;
             ^
bam2R.cpp:79:6: warning: unused variable 'c' [-Wunused-variable]
  int c = 0;
      ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-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 -LC:/Users/biocbuild/bbs-3.5-bioc/R/library/Rhtslib/lib/i386 -lhts -lz -pthread -lws2_32 -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-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"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-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_pileup_function(const bam_pileup1_t*, int, int, nttable_t)':
bam2R.cpp:69:1: warning: no return statement in function returning non-void [-Wreturn-type]
 }
 ^
bam2R.cpp: In function 'int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*)':
bam2R.cpp:76:13: warning: unused variable 'iter' [-Wunused-variable]
  hts_itr_t *iter = NULL;
             ^
bam2R.cpp:79:6: warning: unused variable 'c' [-Wunused-variable]
  int c = 0;
      ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-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 -LC:/Users/biocbuild/bbs-3.5-bioc/R/library/Rhtslib/lib/x64 -lhts -lz -pthread -lws2_32 -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/deepSNV.buildbin-libdir/deepSNV/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'deepSNV' as deepSNV_1.22.0.zip
* DONE (deepSNV)
* installing to library 'C:/Users/biocbuild/bbs-3.5-bioc/R/library'
package 'deepSNV' successfully unpacked and MD5 sums checked