BioC 2.12: CHECK report for GenomicRanges on pelham

* 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)

name	user	system	elapsed
GAlignmentsList-class	8.357	0.307	9.122
GRanges-class	0.730	0.020	0.774
GRangesList-class	1.687	0.029	1.873
GappedAlignmentPairs-class	4.322	0.075	4.643
GappedAlignments-class	2.030	0.053	2.144
GenomicRanges-comparison	1.031	0.018	1.074
Seqinfo-class	6.212	0.429	6.808
SummarizedExperiment-class	0.301	0.025	0.327
cigar-utils	0.686	0.040	0.744
constraint	1.027	0.036	1.081
coverage-methods	1.821	0.062	1.928
encodeOverlaps-methods	10.837	0.422	12.518
findOverlaps-methods	5.264	0.164	5.673
findSpliceOverlaps-methods	30.777	3.669	35.578
inter-range-methods	11.090	2.058	13.477
intra-range-methods	0.206	0.018	0.225
makeSeqnameIds	0.190	0.021	0.261
nearest-methods	1.360	0.044	1.433
phicoef	0.008	0.010	0.022
seqinfo	0.021	0.011	0.033
seqlevels-utils	0.524	0.054	0.594
setops-methods	3.099	0.130	3.336
strand-utils	0.019	0.008	0.026
summarizeOverlaps	13.545	1.822	17.787

Summary

Command output