VariantTools 1.8.1
Michael Lawrence
| 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/VariantTools | | Last Changed Rev: 96066 / Revision: 102249 | | Last Changed Date: 2014-10-27 09:41:38 -0700 (Mon, 27 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
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### Running command:
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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings VariantTools_1.8.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/VariantTools.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 ‘VariantTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VariantTools’ version ‘1.8.1’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘VariantTools’ can be installed ... [28s/28s] 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
Unexported objects imported by ':::' calls:
‘BiocGenerics:::testPackage’ ‘S4Vectors:::mseq’
‘gmapR:::normalizeIndelAlleles’ ‘gmapR:::showSlots’
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
FisherStrandFilter : <anonymous>: no visible binding for global
variable ‘count.plus.ref’
FisherStrandFilter : <anonymous>: no visible binding for global
variable ‘count.minus.ref’
FisherStrandFilter : <anonymous>: no visible binding for global
variable ‘count.plus’
FisherStrandFilter : <anonymous>: no visible binding for global
variable ‘count.minus’
GenotypeRunVRanges: no visible global function definition for
‘seqlengths’
ReadPositionTTestFilter : <anonymous>: no visible binding for global
variable ‘read.pos.mean’
ReadPositionTTestFilter : <anonymous>: no visible binding for global
variable ‘read.pos.mean.ref’
ReadPositionTTestFilter : <anonymous>: no visible binding for global
variable ‘read.pos.var’
ReadPositionTTestFilter : <anonymous>: no visible binding for global
variable ‘read.pos.var.ref’
addGenotypeRuns: no visible global function definition for
‘keepSeqlevels’
callWildtype: no visible global function definition for ‘seqlevels<-’
extractCoverageForPositions: no visible global function definition for
‘seqlevels’
extractCoverageForPositions: no visible global function definition for
‘seqlevels<-’
loadAndComputeGenotypesForRegion: no visible global function definition
for ‘readVcfAsVRanges’
loadAndComputeGenotypesForRegion: no visible global function definition
for ‘sampleNames’
makeVRangesFromVariantGRanges: no visible binding for global variable
‘high.quality.total’
makeVRangesFromVariantGRanges: no visible binding for global variable
‘high.quality.ref’
makeVRangesFromVariantGRanges: no visible binding for global variable
‘high.quality’
pileupGRanges: no visible global function definition for ‘isIndel’
pileupGRanges: no visible binding for global variable ‘DNA_BASES’
pileupGRanges: no visible global function definition for ‘sampleNames’
pileupGRangesOverGenome: no visible global function definition for
‘isIndel’
pileupGRangesOverGenome: no visible binding for global variable
‘DNA_BASES’
pileupGRangesOverGenome: no visible global function definition for
‘sampleNames’
pileupVariants: no visible global function definition for
‘ApplyPileupsParam’
pileupVariants: no visible global function definition for ‘PileupFiles’
pileupVariants: no visible global function definition for ‘plpWhat<-’
pileupVariants: no visible global function definition for ‘plpWhat’
pileupVariants : pileupFun: no visible global function definition for
‘seqlevels’
pileupVariants: no visible global function definition for
‘applyPileups’
variantGR2Vcf: no visible global function definition for
‘sampleNames<-’
variantGR2Vcf: no visible global function definition for ‘genome<-’
variantGR2Vcf: no visible global function definition for ‘asVCF’
callableFraction,GRangesList: no visible global function definition for
‘seqlevels<-’
tallyVariants,BamFileList: no visible global function definition for
‘stackSamples’
tallyVariants,BamFileList: no visible global function definition for
‘VRangesList’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [76s/63s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
callGenotypes 43.083 1.748 31.522
postFilterVariants 5.661 0.376 6.069
callWildtype 5.684 0.260 5.959
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘VariantTools_unit_tests.R’ [0s/0s]
[0s/0s] 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
NOTE: There were 3 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/VariantTools.Rcheck/00check.log’
for details.