BioC 2.12: CHECK report for GenomicRanges on petty

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GenomicRanges.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GenomicRanges/DESCRIPTION' ... OK
* this is package 'GenomicRanges' version '1.11.40'
* 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/19s] 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 ... NOTE
coerce,RangesMapping-GenomicRanges: no visible global function
  definition for 'matching'
restrict,GenomicRanges: no visible binding for global variable 'orig'
restrict,GenomicRanges: no visible binding for global variable 'final'
restrict,GenomicRanges: no visible binding for global variable
  'posIndx'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'duplicated.GenomicRanges' 'makeSeqnameIds'
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... [108s/111s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
findSpliceOverlaps-methods 22.417  3.572  29.166
summarizeOverlaps          14.912  1.993  17.968
inter-range-methods         7.018  1.933   9.014
encodeOverlaps-methods      7.974  0.541   9.039
GAlignmentsList-class       6.968  0.453   7.466
Seqinfo-class               4.783  0.684   5.519
GappedAlignmentPairs-class  4.887  0.099   5.038
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'GenomicRanges_unit_tests.R' [67s/67s]
 [68s/68s] 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/GenomicRanges.Rcheck/00check.log'
for details.

* installing *source* package 'GenomicRanges' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function 'query_locs_to_ref_locs':
cigar_utils.c:1179: warning: 'n' may be used uninitialized in this function
cigar_utils.c: In function 'ref_locs_to_query_locs':
cigar_utils.c:1099: warning: 'n' may be used uninitialized in this function
cigar_utils.c: In function 'cigar_to_width':
cigar_utils.c:763: warning: 'width' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function 'tlocs2rlocs':
transcript_utils.c:208: warning: 'nlocs' may be used uninitialized in this function
transcript_utils.c:119: warning: 'end' may be used uninitialized in this function
transcript_utils.c:119: note: 'end' was declared here
transcript_utils.c:119: warning: 'start' may be used uninitialized in this function
transcript_utils.c:119: note: 'start' was declared here
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'GenomicRangesIntroduction.Rnw' 
   'GenomicRangesUseCases.Rnw' 
   'OverlapEncodings.Rnw' 
   'summarizeOverlaps.Rnw' 
** testing if installed package can be loaded
* DONE (GenomicRanges)

name	user	system	elapsed
GAlignmentsList-class	6.968	0.453	7.466
GRanges-class	0.491	0.046	0.537
GRangesList-class	2.107	0.064	2.175
GappedAlignmentPairs-class	4.887	0.099	5.038
GappedAlignments-class	1.736	0.105	1.847
GenomicRanges-comparison	0.731	0.042	0.774
Seqinfo-class	4.783	0.684	5.519
SummarizedExperiment-class	0.362	0.077	0.450
cigar-utils	0.718	0.098	0.819
constraint	0.967	0.138	1.111
coverage-methods	1.567	0.062	1.633
encodeOverlaps-methods	7.974	0.541	9.039
findOverlaps-methods	4.416	0.164	4.586
findSpliceOverlaps-methods	22.417	3.572	29.166
inter-range-methods	7.018	1.933	9.014
intra-range-methods	0.291	0.025	0.316
nearest-methods	1.732	0.054	1.787
phicoef	0.009	0.011	0.021
seqinfo	0.026	0.014	0.039
seqlevels-utils	0.701	0.076	0.777
setops-methods	3.870	0.111	3.998
strand-utils	0.022	0.009	0.033
summarizeOverlaps	14.912	1.993	17.968

Summary

Command output