GenomicRanges 1.12.2 Bioconductor Package Maintainer
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/GenomicRanges | Last Changed Rev: 75712 / Revision: 76155 | Last Changed Date: 2013-04-16 14:58:27 -0700 (Tue, 16 Apr 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ OK ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GenomicRanges.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GenomicRanges/DESCRIPTION' ... OK
* this is package 'GenomicRanges' version '1.12.2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'GenomicRanges' can be installed ... [19s/21s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [123s/128s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
findSpliceOverlaps-methods 30.777 3.669 35.578
summarizeOverlaps 13.545 1.822 17.787
inter-range-methods 11.090 2.058 13.477
encodeOverlaps-methods 10.837 0.422 12.518
GAlignmentsList-class 8.357 0.307 9.122
Seqinfo-class 6.212 0.429 6.808
findOverlaps-methods 5.264 0.164 5.673
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'GenomicRanges_unit_tests.R' [77s/79s]
[77s/80s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
* installing *source* package 'GenomicRanges' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c IRanges_stubs.c -o IRanges_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cigar_utils.c -o cigar_utils.o
cigar_utils.c:682:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(INTEGER(ans), 0, LENGTH(ans) * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
cigar_utils.c:682:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(INTEGER(ans), 0, LENGTH(ans) * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
cigar_utils.c:680:18: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
allOPs_length = strlen(allOPs);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
cigar_utils.c:1092:27: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
Rboolean _narrow_left = asLogical(narrow_left);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:946:20: note: expanded from macro 'asLogical'
#define asLogical Rf_asLogical
^
cigar_utils.c:1171:27: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
Rboolean _narrow_left = asLogical(narrow_left);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:946:20: note: expanded from macro 'asLogical'
#define asLogical Rf_asLogical
^
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c transcript_utils.c -o transcript_utils.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o cigar_utils.o transcript_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/GenomicRanges.Rcheck/GenomicRanges/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomicRanges)