GenomicAlignments 1.6.3
Bioconductor Package Maintainer
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/GenomicAlignments | | Last Changed Rev: 112191 / Revision: 116712 | | Last Changed Date: 2016-01-05 12:51:48 -0800 (Tue, 05 Jan 2016) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | [ OK ] | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.2/bioc/src/contrib/GenomicAlignments_1.6.3.tar.gz && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --library=GenomicAlignments.buildbin-libdir --merge-multiarch GenomicAlignments_1.6.3.tar.gz && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL GenomicAlignments_1.6.3.zip && rm GenomicAlignments_1.6.3.tar.gz GenomicAlignments_1.6.3.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 1369k 100 1369k 0 0 44.4M 0 --:--:-- --:--:-- --:--:-- 49.5M
install for i386
* installing *source* package 'GenomicAlignments' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:676:9: warning: 'f_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:658:27: warning: 'range_buf2' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:533:2: warning: 'range_buf1' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:590:13: note: 'range_buf1' was declared here
cigar_utils.c:674:16: warning: 'breakpoint' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:670:12: warning: 'flag_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:734:12: warning: 'flag_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'cigar_narrow':
cigar_utils.c:887:24: warning: 'OP' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:855:7: note: 'OP' was declared here
cigar_utils.c:879:8: warning: 'OPL' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:854:17: note: 'OPL' was declared here
cigar_utils.c: In function 'cigar_qnarrow':
cigar_utils.c:1071:24: warning: 'OP' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:1039:7: note: 'OP' was declared here
cigar_utils.c:1063:8: warning: 'OPL' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:1038:17: note: 'OPL' was declared here
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
coordinate_mapping_methods.c: In function 'to_query':
coordinate_mapping_methods.c:64:26: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
coordinate_mapping_methods.c: In function 'to_ref':
coordinate_mapping_methods.c:219:6: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
encodeOverlaps_methods.c: In function 'overlap_encoding':
encodeOverlaps_methods.c:180:17: warning: 'out_nelt0' may be used uninitialized in this function [-Wuninitialized]
encodeOverlaps_methods.c:99:6: note: 'out_nelt0' was declared here
gcc -m32 -shared -s -static-libgcc -o GenomicAlignments.dll tmp.def IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/i386
** R
** 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 'GenomicAlignments' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:676:9: warning: 'f_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:658:27: warning: 'range_buf2' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:533:2: warning: 'range_buf1' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:590:13: note: 'range_buf1' was declared here
cigar_utils.c:674:16: warning: 'breakpoint' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:670:12: warning: 'flag_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:734:12: warning: 'flag_elt' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
coordinate_mapping_methods.c: In function 'to_query':
coordinate_mapping_methods.c:64:26: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
coordinate_mapping_methods.c: In function 'to_ref':
coordinate_mapping_methods.c:219:6: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
gcc -m64 -shared -s -static-libgcc -o GenomicAlignments.dll tmp.def IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicAlignments' as GenomicAlignments_1.6.3.zip
* DONE (GenomicAlignments)
* installing to library 'D:/biocbld/bbs-3.2-bioc/R/library'
package 'GenomicAlignments' successfully unpacked and MD5 sums checked