VariantTools 1.17.4
Michael Lawrence
| Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VariantTools | | Last Changed Rev: 129015 / Revision: 129046 | | Last Changed Date: 2017-04-21 16:04:38 -0400 (Fri, 21 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | ERROR | skipped | skipped | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings VariantTools_1.17.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/VariantTools.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.17.4’
* 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 ... OK
* checking installed package size ... NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
doc 5.6Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘BiocGenerics:::testPackage’ ‘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
LowerFrequencyInOtherFilter : <anonymous>: no visible binding for
global variable ‘control.alt.depth’
LowerFrequencyInOtherFilter : <anonymous>: no visible binding for
global variable ‘control.total.depth’
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’
ReadPositionTTestFilter : <anonymous>: no visible global function
definition for ‘rawDepth’
StrandFETFilter : <anonymous>: no visible binding for global variable
‘count.plus.ref’
StrandFETFilter : <anonymous>: no visible binding for global variable
‘count.minus.ref’
StrandFETFilter : <anonymous>: no visible binding for global variable
‘count.plus’
StrandFETFilter : <anonymous>: no visible binding for global variable
‘count.minus’
caseControlFET: no visible binding for global variable
‘control.alt.depth’
caseControlFET: no visible binding for global variable
‘control.total.depth’
variantGR2Vcf: no visible global function definition for
‘variantGRangesIsDeprecated’
variantGR2Vcf: no visible global function definition for
‘makeVRangesFromVariantGRanges’
callVariants,GenomicRanges: no visible global function definition for
‘variantGRangesIsDeprecated’
callVariants,GenomicRanges: no visible global function definition for
‘variantGRangesToVRanges’
Undefined global functions or variables:
control.alt.depth control.total.depth count.minus count.minus.ref
count.plus count.plus.ref makeVRangesFromVariantGRanges rawDepth
read.pos.mean read.pos.mean.ref read.pos.var read.pos.var.ref
variantGRangesIsDeprecated variantGRangesToVRanges
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following directories should probably not be installed:
‘fig’
Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
callGenotypes 28.364 1.282 44.326
callSampleSpecificVariants 1.434 0.478 13.226
callVariants 0.676 0.251 6.673
tallyVariants 0.244 0.165 6.005
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘VariantTools_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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/VariantTools.Rcheck/00check.log’
for details.