GenomicAlignments 1.2.2
Bioconductor Package Maintainer
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/GenomicAlignments | | Last Changed Rev: 100079 / Revision: 102249 | | Last Changed Date: 2015-03-02 14:03:13 -0800 (Mon, 02 Mar 2015) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | [ OK ] | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.0/bioc/src/contrib/GenomicAlignments_1.2.2.tar.gz && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch GenomicAlignments_1.2.2.tar.gz && rm GenomicAlignments_1.2.2.tar.gz
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1359k 100 1359k 0 0 62.8M 0 --:--:-- --:--:-- --:--:-- 102M
install for i386
* installing to library 'D:/biocbld/bbs-3.0-bioc/R/library'
* installing *source* package 'GenomicAlignments' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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:671:9: warning: 'f_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:669:16: warning: 'breakpoint' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:534:2: warning: 'ans_breakpoints' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:580:12: note: 'ans_breakpoints' was declared here
cigar_utils.c:665:12: warning: 'flag_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:729:12: warning: 'flag_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'cigar_narrow':
cigar_utils.c:882:24: warning: 'OP' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:850:7: note: 'OP' was declared here
cigar_utils.c:874:8: warning: 'OPL' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:849:17: note: 'OPL' was declared here
cigar_utils.c: In function 'cigar_qnarrow':
cigar_utils.c:1066:24: warning: 'OP' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:1034:7: note: 'OP' was declared here
cigar_utils.c:1058:8: warning: 'OPL' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:1033:17: note: 'OPL' was declared here
cigar_utils.c: In function 'ref_locs_to_query_locs':
cigar_utils.c:1185:8: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'query_locs_to_ref_locs':
cigar_utils.c:1267:8: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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 encodeOverlaps_methods.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.0-bioc/R/library/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 to library 'D:/biocbld/bbs-3.0-bioc/R/library'
* installing *source* package 'GenomicAlignments' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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:671:9: warning: 'f_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:669:16: warning: 'breakpoint' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:534:2: warning: 'ans_breakpoints' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:580:12: note: 'ans_breakpoints' was declared here
cigar_utils.c:665:12: warning: 'flag_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:729:12: warning: 'flag_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'ref_locs_to_query_locs':
cigar_utils.c:1185:8: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'query_locs_to_ref_locs':
cigar_utils.c:1267:8: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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 encodeOverlaps_methods.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.0-bioc/R/library/GenomicAlignments/libs/x64
** testing if installed package can be loaded
* DONE (GenomicAlignments)