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BioC 2.13: CHECK report for VariantAnnotation on zin1

This page was generated on 2014-04-05 09:48:07 -0700 (Sat, 05 Apr 2014).

Package 731/750HostnameOS / ArchBUILDCHECKBUILD BIN
VariantAnnotation 1.8.13
Valerie Obenchain
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/VariantAnnotation
Last Changed Rev: 87381 / Revision: 88450
Last Changed Date: 2014-03-12 15:13:34 -0700 (Wed, 12 Mar 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: VariantAnnotation
Version: 1.8.13
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings VariantAnnotation_1.8.13.tar.gz
StartedAt: 2014-04-05 04:28:40 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:35:53 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 433.1 seconds
RetCode: 0
Status:  OK 
CheckDir: VariantAnnotation.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/VariantAnnotation.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.8.13’
* 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 ‘VariantAnnotation’ can be installed ... [21s/22s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘BiocGenerics’ ‘IRanges’ ‘XVector’ ‘Rsamtools’
A package should be listed in only one of these fields.
* 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 ... NOTE
Unexported objects imported by ‘:::’ calls:
  ‘BiocGenerics:::labeledLine’ ‘BiocGenerics:::selectSome’
  ‘BiocGenerics:::testPackage’
  ‘GenomicFeatures:::.makeUCSCTxListFromGRangesList’
  ‘GenomicRanges:::.SummarizedExperiment.charbound’
  ‘GenomicRanges:::.cbind.DataFrame’
  ‘GenomicRanges:::.cbind.SummarizedExperiment’
  ‘GenomicRanges:::.rbind.SummarizedExperiment’ ‘GenomicRanges:::clone’
  ‘IRanges:::.expandByColumnSet’ ‘IRanges:::recycleVector’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘VariantAnnotation.Rnw’, ‘filterVcf.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [98s/106s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
locateVariants-methods     25.033  0.244  25.326
predictCoding-methods      13.801  0.164  13.992
getTranscriptSeqs-methods  11.213  0.092  11.371
summarizeVariants-methods  11.096  0.072  11.187
SIFTDb-class                5.705  0.104   7.112
refLocsToLocalLocs-methods  5.089  0.060   5.160
PolyPhenDb-class            1.824  0.128   8.757
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘VariantAnnotation_unit_tests.R’ [153s/154s]
 [153s/154s] 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/VariantAnnotation.Rcheck/00check.log’
for details.

VariantAnnotation.Rcheck/00install.out:

* installing *source* package ‘VariantAnnotation’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c dna_hash.c -o dna_hash.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c rle.c -o rle.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c strhash.c -o strhash.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c utilities.c -o utilities.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c vcffile.c -o vcffile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c vcftype.c -o vcftype.o
gcc -std=gnu99 -shared -L/usr/local/lib -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o /home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/VariantAnnotation.Rcheck/VariantAnnotation/libs
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘tabulate’ in package ‘VariantAnnotation’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (VariantAnnotation)

VariantAnnotation.Rcheck/VariantAnnotation-Ex.timings:

nameusersystemelapsed
GLtoGP0.6000.0920.693
PolyPhenDb-class1.8240.1288.757
SIFTDb-class5.7050.1047.112
ScanVcfParam-class0.9840.0080.993
VCF-class1.5240.0161.574
VCFHeader-class0.080.000.08
VRanges-class0.4240.0000.437
VRangesList-class0.4040.0000.404
VariantType-class0.0320.0000.032
filterVcf-methods1.7080.0201.733
genotypeToSnpMatrix-methods2.7680.1242.910
getTranscriptSeqs-methods11.213 0.09211.371
locateVariants-methods25.033 0.24425.326
predictCoding-methods13.801 0.16413.992
probabilityToSnpMatrix0.0880.0000.087
readVcf-methods2.6120.0082.625
readVcfLongForm0.7920.0000.842
refLocsToLocalLocs-methods5.0890.0605.160
scanVcf-methods0.1840.0000.185
snpSummary0.2240.0000.227
summarizeVariants-methods11.096 0.07211.187
writeVcf-methods1.7970.0001.801