BioC 3.3: CHECK report for GenomicRanges on oaxaca

Package: GenomicRanges

Version: 1.24.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicRanges_1.24.3.tar.gz

StartedAt: 2016-10-13 01:58:33 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 02:04:55 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 381.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GenomicRanges.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicRanges_1.24.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/GenomicRanges.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicRanges/DESCRIPTION’ ... OK
* this is package ‘GenomicRanges’ version ‘1.24.3’
* 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
genomicvars              65.482 21.720  96.139
GPos-class               62.229  8.092  87.849
makeGRangesFromDataFrame  1.409  0.047  18.496
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/GenomicRanges.Rcheck/00check.log’
for details.

* installing *source* package ‘GenomicRanges’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c transcript_utils.c -o transcript_utils.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.3-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
GNCList-class	0.527	0.009	0.559
GPos-class	62.229	8.092	87.849
GRanges-class	1.355	0.082	1.817
GRangesList-class	0.540	0.007	0.674
GenomicRanges-comparison	0.301	0.004	0.360
absoluteRanges	1.156	0.198	3.662
constraint	1.443	0.035	1.850
coverage-methods	0.305	0.001	0.341
findOverlaps-methods	1.542	0.008	1.829
genomicvars	65.482	21.720	96.139
inter-range-methods	2.737	0.831	3.594
intra-range-methods	0.452	0.005	0.457
makeGRangesFromDataFrame	1.409	0.047	18.496
nearest-methods	0.679	0.008	0.688
phicoef	0.003	0.000	0.003
range-squeezers	0.000	0.000	0.001
setops-methods	2.819	0.009	2.831
strand-utils	0.127	0.002	0.130
tile-methods	0.072	0.000	0.073
tileGenome	0.319	0.005	0.324