BioC 2.12: CHECK report for GenomicRanges on petty

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GenomicRanges.Rcheck'
* using R version 3.0.1 (2013-05-16)
* 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 '1.12.5'
* 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 ... [24s/32s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [129s/130s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
findSpliceOverlaps-methods 27.629  2.916  31.375
summarizeOverlaps          14.856  1.919  18.372
encodeOverlaps-methods     11.321  0.340  12.012
inter-range-methods         9.962  1.539  11.550
GAlignmentsList-class       8.310  0.268   8.768
Seqinfo-class               7.351  0.444   7.976
findOverlaps-methods        6.809  0.100   6.941
GappedAlignmentPairs-class  5.332  0.071   5.456
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'GenomicRanges_unit_tests.R' [95s/96s]
 [96s/97s] 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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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=core2 -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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=core2 -g -O2  -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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=core2 -g -O2  -c cigar_utils.c -o cigar_utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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=core2 -g -O2  -c transcript_utils.c -o transcript_utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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)

name	user	system	elapsed
GAlignmentsList-class	8.310	0.268	8.768
GRanges-class	1.034	0.014	1.057
GRangesList-class	2.254	0.018	2.285
GappedAlignmentPairs-class	5.332	0.071	5.456
GappedAlignments-class	2.568	0.040	2.647
GenomicRanges-comparison	1.677	0.010	1.726
Seqinfo-class	7.351	0.444	7.976
SummarizedExperiment-class	0.732	0.007	0.740
cigar-utils	0.900	0.039	0.944
constraint	1.286	0.015	1.308
coverage-methods	2.774	0.048	2.825
encodeOverlaps-methods	11.321	0.340	12.012
findOverlaps-methods	6.809	0.100	6.941
findSpliceOverlaps-methods	27.629	2.916	31.375
inter-range-methods	9.962	1.539	11.550
intra-range-methods	0.297	0.017	0.318
makeSeqnameIds	0.225	0.024	0.260
nearest-methods	1.811	0.034	1.865
phicoef	0.009	0.007	0.016
seqinfo	0.025	0.009	0.033
seqlevels-utils	0.705	0.056	0.764
setops-methods	3.940	0.060	4.018
strand-utils	0.023	0.007	0.030
summarizeOverlaps	14.856	1.919	18.372

BioC 2.12: CHECK report for GenomicRanges on petty

Summary

Command output