BioC 2.11: CHECK report for GenomicRanges on lamb1

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/GenomicRanges.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.10.7’
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
findSpliceOverlaps-methods 24.593  0.288  25.925
summarizeOverlaps          10.257  0.080  10.810
encodeOverlaps-methods      6.904  0.068   7.171
Seqinfo-class               6.125  0.200   7.387
GappedAlignmentPairs-class  5.164  0.048   5.395
* 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
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/GenomicRanges.Rcheck/00check.log’
for details.

* installing *source* package ‘GenomicRanges’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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:1130:8: warning: ‘n’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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/lib64 -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o cigar_utils.o transcript_utils.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-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
GRanges-class	0.704	0.004	0.708
GRangesList-class	1.536	0.004	1.596
GappedAlignmentPairs-class	5.164	0.048	5.395
GappedAlignments-class	1.956	0.032	2.467
GenomicRanges-comparison	1.416	0.004	1.419
Seqinfo-class	6.125	0.200	7.387
SummarizedExperiment-class	0.080	0.000	0.079
cigar-utils	0.500	0.012	0.565
constraint	0.600	0.008	0.613
countGenomicOverlaps	0.000	0.000	0.001
coverage-methods	2.044	0.024	2.324
encodeOverlaps-methods	6.904	0.068	7.171
findOverlaps-methods	3.757	0.020	3.845
findSpliceOverlaps-methods	24.593	0.288	25.925
inter-range-methods	0.604	0.000	0.608
intra-range-methods	0.132	0.004	0.134
nearest-methods	0.612	0.000	0.613
phicoef	0.004	0.000	0.002
seqinfo	0.008	0.004	0.010
seqlevels-utils	0.492	0.016	0.509
setops-methods	2.524	0.016	2.719
strand-utils	0.008	0.000	0.010
summarizeOverlaps	10.257	0.080	10.810

Summary

Command output