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BioC 3.0: CHECK report for VariantAnnotation on zin1

This page was generated on 2015-04-10 09:39:30 -0700 (Fri, 10 Apr 2015).

Package 912/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantAnnotation 1.12.9
Valerie Obenchain
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/VariantAnnotation
Last Changed Rev: 98524 / Revision: 102249
Last Changed Date: 2015-01-20 14:44:33 -0800 (Tue, 20 Jan 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: VariantAnnotation
Version: 1.12.9
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings VariantAnnotation_1.12.9.tar.gz
StartedAt: 2015-04-10 05:12:44 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 05:20:19 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 454.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: VariantAnnotation.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings VariantAnnotation_1.12.9.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/VariantAnnotation.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.12.9’
* 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 ... [27s/27s] 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
'library' or 'require' call to ‘snpStats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' 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:::.SummarizedExperiment.charbound’
  ‘GenomicRanges:::.bind.arrays’ ‘GenomicRanges:::.cbind.DataFrame’
  ‘GenomicRanges:::clone’ ‘IRanges:::.expandByColumnSet’
  ‘S4Vectors:::recycleVector’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.predictCoding: no visible global function definition for
  ‘transcriptsBy’
.predictCodingGRangesList: no visible binding for global variable
  ‘GENETIC_CODE’
.spliceSites: no visible global function definition for ‘togroup’
VCFHeader: no visible global function definition for ‘DataFrameList’
addTotalDepthRuns: no visible global function definition for ‘viewMins’
parseFilterStrings: no visible global function definition for ‘togroup’
probabilityToSnpMatrix: no visible global function definition for
  ‘post2g’
softFilter: no visible global function definition for ‘evalSeparately’
vranges2Vcf: no visible global function definition for ‘DataFrameList’
vranges2Vcf : genoArray: no visible global function definition for
  ‘togroup’
liftOver,VRanges-Chain: no visible global function definition for
  ‘togroup’
summarizeVariants,TxDb-VCF-IntronVariants: no visible global function
  definition for ‘intronsByTranscript’
summarizeVariants,TxDb-VCF-SpliceSiteVariants: no visible global
  function definition for ‘intronsByTranscript’
* 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 GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘VariantAnnotation/libs/VariantAnnotation.so’:
  Found non-API call to R: ‘getConnection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [85s/95s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
locateVariants-methods    25.178  0.360  25.579
predictCoding-methods     13.709  0.136  13.890
getTranscriptSeqs-methods  6.688  0.088   6.872
summarizeVariants-methods  5.701  0.072   5.784
SIFTDb-class               4.857  0.088   6.662
PolyPhenDb-class           1.208  0.160   8.929
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘VariantAnnotation_unit_tests.R’ [144s/145s]
 [145s/145s] 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

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/VariantAnnotation.Rcheck/00check.log’
for details.

VariantAnnotation.Rcheck/00install.out:

* installing *source* package ‘VariantAnnotation’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-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-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c dna_hash.c -o dna_hash.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c rle.c -o rle.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c strhash.c -o strhash.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c utilities.c -o utilities.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c vcffile.c -o vcffile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c vcftype.c -o vcftype.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c writevcf.c -o writevcf.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/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 writevcf.o /home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-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
GLtoGP0.6720.0880.762
PROVEANDb-class0.0000.0000.001
PolyPhenDb-class1.2080.1608.929
SIFTDb-class4.8570.0886.662
ScanVcfParam-class1.0720.0081.083
VCF-class1.1880.0201.210
VCFHeader-class0.0560.0000.055
VRanges-class0.2760.0000.279
VRangesList-class0.30.00.3
VariantType-class0.0080.0040.010
filterVcf-methods1.0800.0281.111
genotypeToSnpMatrix-methods3.0000.1123.169
getTranscriptSeqs-methods6.6880.0886.872
isSNV-methods0.6080.0160.623
locateVariants-methods25.178 0.36025.579
predictCoding-methods13.709 0.13613.890
probabilityToSnpMatrix0.0800.0000.082
readVcf-methods2.1640.0002.165
refLocsToLocalLocs-methods3.7560.0323.794
scanVcf-methods0.1520.0000.151
snpSummary0.1920.0000.193
summarizeVariants-methods5.7010.0725.784
writeVcf-methods1.1640.0081.177