GenomicAlignments 1.12.2
Bioconductor Package Maintainer
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/GenomicAlignments | | Branch: RELEASE_3_5 | | Last Commit: b5d6f19 | | Last Changed Date: 2017-08-16 03:19:10 -0400 (Wed, 16 Aug 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/GenomicAlignments_1.12.2.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=GenomicAlignments.buildbin-libdir --merge-multiarch GenomicAlignments_1.12.2.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL GenomicAlignments_1.12.2.zip && rm GenomicAlignments_1.12.2.tar.gz GenomicAlignments_1.12.2.zip
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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
1 1372k 1 16139 0 0 419k 0 0:00:03 --:--:-- 0:00:03 425k
100 1372k 100 1372k 0 0 22.4M 0 --:--:-- --:--:-- --:--:-- 22.7M
install for i386
* installing *source* package 'GenomicAlignments' ...
** libs
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/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
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/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
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/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
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/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/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 [-Wmaybe-uninitialized]
f_elt++;
^
cigar_utils.c:658:27: warning: 'range_buf2' may be used uninitialized in this function [-Wmaybe-uninitialized]
range_buf1 = range_buf2->elts[*f_elt - 1];
^
cigar_utils.c:674:22: warning: 'range_buf1' may be used uninitialized in this function [-Wmaybe-uninitialized]
*(breakpoint++) = IntPairAE_get_nelt(range_buf1);
^
cigar_utils.c:674:16: warning: 'breakpoint' may be used uninitialized in this function [-Wmaybe-uninitialized]
*(breakpoint++) = IntPairAE_get_nelt(range_buf1);
^
cigar_utils.c:670:12: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
flag_elt++;
^
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:708:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (*flag_elt == NA_INTEGER) {
^
cigar_utils.c: In function 'cigar_narrow':
cigar_utils.c:887:17: warning: 'OP' may be used uninitialized in this function [-Wmaybe-uninitialized]
buf_offset += sprintf(cigar_buf + buf_offset,
^
cigar_utils.c:855:7: note: 'OP' was declared here
char OP /* Operation */;
^
cigar_utils.c:879:8: warning: 'OPL' may be used uninitialized in this function [-Wmaybe-uninitialized]
OPL -= Lwidth;
^
cigar_utils.c:854:17: note: 'OPL' was declared here
int offset, n, OPL /* Operation Length */;
^
cigar_utils.c: In function 'cigar_qnarrow':
cigar_utils.c:1071:17: warning: 'OP' may be used uninitialized in this function [-Wmaybe-uninitialized]
buf_offset += sprintf(cigar_buf + buf_offset,
^
cigar_utils.c:1039:7: note: 'OP' was declared here
char OP /* Operation */;
^
cigar_utils.c:1063:8: warning: 'OPL' may be used uninitialized in this function [-Wmaybe-uninitialized]
OPL -= Lqwidth;
^
cigar_utils.c:1038:17: note: 'OPL' was declared here
int offset, n, OPL /* Operation Length */;
^
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/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
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/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/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:182:2: warning: 'out_nelt0' may be used uninitialized in this function [-Wmaybe-uninitialized]
CharAE_delete_at(out, out_nelt0, j1 * nrow);
^
encodeOverlaps_methods.c:99:6: note: 'out_nelt0' was declared here
int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej,
^
C:/Rtools/mingw_32/bin/gcc -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 -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/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
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/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
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/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
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/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
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/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/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 [-Wmaybe-uninitialized]
f_elt++;
^
cigar_utils.c:658:27: warning: 'range_buf2' may be used uninitialized in this function [-Wmaybe-uninitialized]
range_buf1 = range_buf2->elts[*f_elt - 1];
^
cigar_utils.c:674:22: warning: 'range_buf1' may be used uninitialized in this function [-Wmaybe-uninitialized]
*(breakpoint++) = IntPairAE_get_nelt(range_buf1);
^
cigar_utils.c:674:16: warning: 'breakpoint' may be used uninitialized in this function [-Wmaybe-uninitialized]
*(breakpoint++) = IntPairAE_get_nelt(range_buf1);
^
cigar_utils.c:670:12: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
flag_elt++;
^
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:708:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (*flag_elt == NA_INTEGER) {
^
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/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
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/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
encodeOverlaps_methods.c: In function 'overlap_encoding':
encodeOverlaps_methods.c:182:2: warning: 'out_nelt0' may be used uninitialized in this function [-Wmaybe-uninitialized]
CharAE_delete_at(out, out_nelt0, j1 * nrow);
^
encodeOverlaps_methods.c:99:6: note: 'out_nelt0' was declared here
int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej,
^
C:/Rtools/mingw_64/bin/gcc -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 -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/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicAlignments' as GenomicAlignments_1.12.2.zip
* DONE (GenomicAlignments)
* installing to library 'C:/Users/biocbuild/bbs-3.5-bioc/R/library'
package 'GenomicAlignments' successfully unpacked and MD5 sums checked