BioC 3.2: CHECK report for GenomicRanges on linux1.bioconductor.org

Package: GenomicRanges

Version: 1.22.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GenomicRanges_1.22.0.tar.gz

StartedAt: 2015-10-27 03:56:25 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:00:31 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 245.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GenomicRanges.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GenomicRanges_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/GenomicRanges.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicRanges/DESCRIPTION’ ... OK
* this is package ‘GenomicRanges’ version ‘1.22.0’
* package encoding: UTF-8
* 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 ... [9s/9s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 ... WARNING
Undocumented S4 methods:
  generic 'seqinfo' and siglist 'List'
  generic 'seqinfo' and siglist 'RangedData'
  generic 'seqinfo' and siglist 'RangesList'
  generic 'seqinfo<-' and siglist 'List'
  generic 'seqinfo<-' and siglist 'RangedData'
  generic 'seqnames' and siglist 'RangedData'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [97s/112s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
genomicvars              71.353  2.657  75.846
absoluteRanges            7.880  0.156   8.043
makeGRangesFromDataFrame  1.177  0.009  14.368
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘GenomicRanges_unit_tests.R’ [48s/49s]
 [49s/49s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/GenomicRanges.Rcheck/00check.log’
for details.

* installing *source* package ‘GenomicRanges’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-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:143:38: warning: ‘end’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:24: note: ‘end’ was declared here
  int nexons, j, start, end, width;
                        ^
transcript_utils.c:143:38: warning: ‘start’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:17: note: ‘start’ was declared here
  int nexons, j, start, end, width;
                 ^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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
GIntervalTree-class	0.001	0.000	0.001
GNCList-class	0.279	0.000	0.279
GRanges-class	1.16	0.00	1.16
GRangesList-class	0.650	0.008	0.658
GenomicRanges-comparison	0.376	0.000	0.377
SummarizedExperiment-class	0.004	0.000	0.004
absoluteRanges	7.880	0.156	8.043
constraint	1.334	0.008	1.342
coverage-methods	0.333	0.000	0.333
findOverlaps-methods	1.251	0.008	1.259
genomicvars	71.353	2.657	75.846
inter-range-methods	2.968	0.012	2.982
intra-range-methods	0.349	0.004	0.354
makeGRangesFromDataFrame	1.177	0.009	14.368
mapCoords-methods	0.001	0.000	0.000
nearest-methods	0.775	0.004	0.778
phicoef	0.003	0.000	0.004
range-squeezers	0.001	0.000	0.000
setops-methods	1.411	0.000	1.411
strand-utils	0.062	0.000	0.065
tile-methods	0.07	0.00	0.07
tileGenome	0.431	0.000	0.434