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BioC 2.14: CHECK report for VariantAnnotation on petty

This page was generated on 2014-10-08 08:59:41 -0700 (Wed, 08 Oct 2014).

Package 803/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantAnnotation 1.10.5
Valerie Obenchain
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/VariantAnnotation
Last Changed Rev: 91895 / Revision: 95116
Last Changed Date: 2014-06-26 05:58:14 -0700 (Thu, 26 Jun 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: VariantAnnotation
Version: 1.10.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch VariantAnnotation_1.10.5.tar.gz
StartedAt: 2014-10-08 00:33:34 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 00:48:11 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 877.3 seconds
RetCode: 0
Status:  OK 
CheckDir: VariantAnnotation.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch VariantAnnotation_1.10.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/VariantAnnotation.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.10.5’
* 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 ... [51s/53s] 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 ... NOTE
':::' call which should be '::': ‘DBI:::dbListFields’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::labeledLine’ ‘BiocGenerics:::selectSome’
  ‘BiocGenerics:::testPackage’
  ‘GenomicFeatures:::.makeUCSCTxListFromGRangesList’
  ‘GenomicRanges:::.cbind.DataFrame’
  ‘GenomicRanges:::.cbind.SummarizedExperiment’
  ‘GenomicRanges:::.rbind.SummarizedExperiment’
  ‘GenomicRanges:::.SummarizedExperiment.charbound’
  ‘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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [173s/208s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
locateVariants-methods      41.412  2.645  44.211
predictCoding-methods       19.135  1.390  20.553
getTranscriptSeqs-methods   15.971  0.618  16.625
summarizeVariants-methods   14.732  1.067  15.810
SIFTDb-class                10.356  0.476  13.821
refLocsToLocalLocs-methods   5.981  0.435   6.418
readVcf-methods              6.072  0.048   6.125
genotypeToSnpMatrix-methods  5.549  0.314   5.876
PolyPhenDb-class             3.243  0.495  34.465
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘VariantAnnotation_unit_tests.R’ [232s/232s]
 [232s/232s] 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/VariantAnnotation.Rcheck/00check.log’
for details.

VariantAnnotation.Rcheck/00install.out:

* installing *source* package ‘VariantAnnotation’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c Biostrings_stubs.c -o Biostrings_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c IRanges_stubs.c -o IRanges_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c XVector_stubs.c -o XVector_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c dna_hash.c -o dna_hash.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c rle.c -o rle.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c strhash.c -o strhash.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c utilities.c -o utilities.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c vcffile.c -o vcffile.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c vcftype.c -o vcftype.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -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 /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-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
GLtoGP1.5240.2681.795
PROVEANDb-class0.0020.0010.002
PolyPhenDb-class 3.243 0.49534.465
SIFTDb-class10.356 0.47613.821
ScanVcfParam-class2.3130.0872.411
VCF-class4.7750.0604.839
VCFHeader-class0.1590.0020.162
VRanges-class0.8200.0030.826
VRangesList-class0.9330.0080.943
VariantType-class0.0260.0010.028
filterVcf-methods3.7650.0953.866
genotypeToSnpMatrix-methods5.5490.3145.876
getTranscriptSeqs-methods15.971 0.61816.625
isSNV-methods2.2590.0342.294
locateVariants-methods41.412 2.64544.211
predictCoding-methods19.135 1.39020.553
probabilityToSnpMatrix0.2180.0040.221
readVcf-methods6.0720.0486.125
refLocsToLocalLocs-methods5.9810.4356.418
scanVcf-methods0.4110.0190.430
snpSummary0.4630.0170.480
summarizeVariants-methods14.732 1.06715.810
writeVcf-methods3.9690.0364.004