BioC 2.12: CHECK report for GenomicRanges on george2

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/GenomicRanges.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [23s/23s] 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [130s/135s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
findSpliceOverlaps-methods 35.859  0.404  37.290
encodeOverlaps-methods     15.677  0.132  16.120
inter-range-methods        12.364  1.432  13.961
summarizeOverlaps          11.756  0.388  13.678
GAlignmentsList-class       7.688  0.236   7.960
Seqinfo-class               6.329  0.336   7.057
findOverlaps-methods        6.228  0.048   6.289
GappedAlignmentPairs-class  5.008  0.020   5.154
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘GenomicRanges_unit_tests.R’ [100s/104s]
 [100s/104s] 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
  ‘/home/biocbuild/bbs-2.12-bioc/meat/GenomicRanges.Rcheck/00check.log’
for details.

* installing *source* package ‘GenomicRanges’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function ‘cigar_to_width’:
cigar_utils.c:779:19: warning: ‘width’ may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function ‘ref_locs_to_query_locs’:
cigar_utils.c:1144:8: warning: ‘n’ may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function ‘query_locs_to_ref_locs’:
cigar_utils.c:1226:8: warning: ‘n’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function ‘tlocs2rlocs’:
transcript_utils.c:142:38: warning: ‘end’ may be used uninitialized in this function [-Wuninitialized]
transcript_utils.c:119:24: note: ‘end’ was declared here
transcript_utils.c:142:38: warning: ‘start’ may be used uninitialized in this function [-Wuninitialized]
transcript_utils.c:119:17: note: ‘start’ was declared here
transcript_utils.c:236:3: warning: ‘nlocs’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -shared -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o cigar_utils.o transcript_utils.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/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
   ‘GenomicRangesIntroduction.Rnw’ 
   ‘GenomicRangesUseCases.Rnw’ 
   ‘OverlapEncodings.Rnw’ 
   ‘summarizeOverlaps.Rnw’ 
** testing if installed package can be loaded
* DONE (GenomicRanges)

name	user	system	elapsed
GAlignmentsList-class	7.688	0.236	7.960
GRanges-class	0.936	0.012	1.254
GRangesList-class	2.113	0.012	2.261
GappedAlignmentPairs-class	5.008	0.020	5.154
GappedAlignments-class	2.716	0.028	2.746
GenomicRanges-comparison	1.672	0.000	1.674
Seqinfo-class	6.329	0.336	7.057
SummarizedExperiment-class	0.432	0.000	0.434
cigar-utils	1.308	0.020	1.339
constraint	0.916	0.008	0.944
coverage-methods	2.044	0.008	2.073
encodeOverlaps-methods	15.677	0.132	16.120
findOverlaps-methods	6.228	0.048	6.289
findSpliceOverlaps-methods	35.859	0.404	37.290
inter-range-methods	12.364	1.432	13.961
intra-range-methods	0.284	0.000	0.293
nearest-methods	1.648	0.012	1.791
phicoef	0.016	0.004	0.019
seqinfo	0.036	0.000	0.035
seqlevels-utils	0.572	0.032	0.607
setops-methods	3.425	0.012	3.671
strand-utils	0.028	0.000	0.024
summarizeOverlaps	11.756	0.388	13.678

Summary

Command output