BioC 2.11: CHECK report for VariantAnnotation on lamb1

Package: VariantAnnotation

Version: 1.4.12

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings VariantAnnotation_1.4.12.tar.gz

StartedAt: 2013-03-25 05:27:43 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 05:35:50 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 487.0 seconds

RetCode: 0

Status: OK

CheckDir: VariantAnnotation.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/VariantAnnotation.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 ‘VariantAnnotation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VariantAnnotation’ version ‘1.4.12’
* 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 ‘VariantAnnotation’ 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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 compilation flags in Makevars ... 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
locateVariants-methods    33.286  0.836  34.442
getTranscriptSeqs-methods 20.734  0.472  21.510
predictCoding-methods      8.420  0.872   9.499
MatrixToSnpMatrix-methods  7.137  0.116   7.302
SIFTDb-class               5.584  0.184   6.330
summarizeVariants-methods  5.160  0.144   5.353
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘VariantAnnotation_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

* installing *source* package ‘VariantAnnotation’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c dna_hash.c -o dna_hash.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c rle.c -o rle.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c utilities.c -o utilities.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c vcffile.c -o vcffile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c vcftype.c -o vcftype.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c writevcf.c -o writevcf.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o dna_hash.o rle.o utilities.o vcffile.o vcftype.o writevcf.o /loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/usrlib//libbam.a /loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/usrlib//libbcf.a /loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -lz -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/VariantAnnotation.Rcheck/VariantAnnotation/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘VariantAnnotation.Rnw’ 
** testing if installed package can be loaded

* DONE (VariantAnnotation)

name	user	system	elapsed
MatrixToSnpMatrix-methods	7.137	0.116	7.302
PolyPhenDb-class	1.180	0.116	1.638
SIFTDb-class	5.584	0.184	6.330
ScanVcfParam-class	0.036	0.000	0.035
VAFilter-class	0	0	0
VAFilterResult-class	0	0	0
VAUtil-class	0.000	0.000	0.001
VCF-class	2.168	0.036	2.240
VCFHeader-class	0.080	0.036	0.121
VariantType-class	0.004	0.004	0.006
getTranscriptSeqs-methods	20.734	0.472	21.510
locateVariants-methods	33.286	0.836	34.442
predictCoding-methods	8.420	0.872	9.499
readVcf-methods	2.764	0.016	2.940
readVcfLongForm	1.004	0.004	1.068
refLocsToLocalLocs-methods	2.021	0.076	2.127
scanVcf-methods	0.252	0.012	0.264
summarizeVariants-methods	5.160	0.144	5.353
writeVcf-methods	1.252	0.000	1.291

Summary

Command output