deepSNV 1.23.0
Moritz Gerstung
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/deepSNV | | Last Changed Rev: 129129 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf deepSNV.buildbin-libdir && mkdir deepSNV.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/deepSNV_1.23.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=deepSNV.buildbin-libdir --merge-multiarch deepSNV_1.23.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL deepSNV_1.23.0.zip && rm deepSNV_1.23.0.tar.gz deepSNV_1.23.0.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 1275k 100 1275k 0 0 22.9M 0 --:--:-- --:--:-- --:--:-- 24.4M
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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/Rhtslib/lib/i386 -lhts -lz -pthread -lws2_32 -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/Rhtslib/lib/x64 -lhts -lz -pthread -lws2_32 -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/deepSNV.buildbin-libdir/deepSNV/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'deepSNV' as deepSNV_1.23.0.zip
* DONE (deepSNV)
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'deepSNV' successfully unpacked and MD5 sums checked