BioC 2.11: CHECK report for GenomicRanges on perceval

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/GenomicRanges.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.10.7'
* 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 whether package 'GenomicRanges' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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:
  'makeSeqnameIds'
Undocumented S4 methods:
  generic 'splitAsListReturnedClass' and siglist 'GRanges'
All user-level objects in a package (including S4 classes and methods)
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 ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
findSpliceOverlaps-methods 21.378  4.629  26.846
summarizeOverlaps          11.167  1.743  14.439
Seqinfo-class               5.646  0.438   6.168
encodeOverlaps-methods      5.374  0.470   6.268
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'GenomicRanges_unit_tests.R'
 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-2.11-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/2.15/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/2.15/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/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function 'ref_locs_to_query_locs':
cigar_utils.c:1096: 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/2.15/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:119: warning: 'start' may be used uninitialized in this function
transcript_utils.c:119: note: 'start' was declared here
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
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-2.11-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
GRanges-class	0.616	0.011	0.627
GRangesList-class	1.630	0.021	1.652
GappedAlignmentPairs-class	4.631	0.098	4.764
GappedAlignments-class	2.078	0.035	2.116
GenomicRanges-comparison	1.351	0.005	1.356
Seqinfo-class	5.646	0.438	6.168
SummarizedExperiment-class	0.088	0.003	0.096
cigar-utils	0.495	0.022	0.526
constraint	0.672	0.013	0.700
countGenomicOverlaps	0.000	0.000	0.001
coverage-methods	1.942	0.037	1.994
encodeOverlaps-methods	5.374	0.470	6.268
findOverlaps-methods	3.862	0.084	4.084
findSpliceOverlaps-methods	21.378	4.629	26.846
inter-range-methods	0.697	0.004	0.703
intra-range-methods	0.130	0.002	0.132
nearest-methods	0.640	0.003	0.644
phicoef	0.002	0.001	0.003
seqinfo	0.009	0.001	0.010
seqlevels-utils	0.546	0.021	0.575
setops-methods	2.605	0.035	2.734
strand-utils	0.010	0.000	0.011
summarizeOverlaps	11.167	1.743	14.439

Summary

Command output