GenomicAlignments 1.4.2
Bioconductor Package Maintainer
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/GenomicAlignments | | Last Changed Rev: 109036 / Revision: 109384 | | Last Changed Date: 2015-09-30 17:42:34 -0700 (Wed, 30 Sep 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | [ OK ] | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD INSTALL GenomicAlignments
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* installing to library ‘/home/biocbuild/bbs-3.1-bioc/R/library’
* installing *source* package ‘GenomicAlignments’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function ‘cigar_ranges’:
cigar_utils.c:678:9: warning: ‘f_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
f_elt++;
^
cigar_utils.c:676:20: warning: ‘breakpoint’ may be used uninitialized in this function [-Wmaybe-uninitialized]
*(breakpoint++) = IntPairAE_get_nelt(range_buf_p);
^
cigar_utils.c:672:12: warning: ‘flag_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
flag_elt++;
^
cigar_utils.c: In function ‘cigar_width’:
cigar_utils.c:736:12: warning: ‘flag_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
flag_elt++;
^
cigar_utils.c: In function ‘cigar_narrow’:
cigar_utils.c:882:6: warning: ‘Roffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (offset == Roffset)
^
cigar_utils.c:854:15: note: ‘Roffset’ was declared here
int Loffset, Roffset, buf_offset;
^
cigar_utils.c:880:6: warning: ‘Loffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (offset == Loffset)
^
cigar_utils.c:854:6: note: ‘Loffset’ was declared here
int Loffset, Roffset, buf_offset;
^
cigar_utils.c: In function ‘cigar_qnarrow’:
cigar_utils.c:1066:6: warning: ‘Roffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (offset == Roffset)
^
cigar_utils.c:1038:15: note: ‘Roffset’ was declared here
int Loffset, Roffset, buf_offset;
^
cigar_utils.c:1064:6: warning: ‘Loffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (offset == Loffset)
^
cigar_utils.c:1038:6: note: ‘Loffset’ was declared here
int Loffset, Roffset, buf_offset;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -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 [-Wmaybe-uninitialized]
CharAE_set_nelt(out, out_nelt0 + j2 * nrow);
^
encodeOverlaps_methods.c:99:6: note: ‘out_nelt0’ was declared here
int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej,
^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/R/library/GenomicAlignments/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (GenomicAlignments)