VariantTools 1.16.0
Michael Lawrence
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/VariantTools | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| morelia | 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-3.4-bioc/R/bin/R CMD check --no-vignettes --timings VariantTools_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/VariantTools.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-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 ‘1.16.0’
* 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 ... 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:::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
GenotypeRunVRanges: no visible global function definition for
‘setNames’
LowerFrequencyInOtherFilter : <anonymous>: no visible global function
definition for ‘pbinom’
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’
calculatePowerInOther: no visible global function definition for
‘pbinom’
caseControlFET: no visible binding for global variable
‘control.alt.depth’
caseControlFET: no visible binding for global variable
‘control.total.depth’
compute_GL: no visible global function definition for ‘dbinom’
fisher_p : <anonymous>: no visible global function definition for
‘dhyper’
fisher_p_List: no visible global function definition for ‘dhyper’
fisher_p_vectorized: no visible global function definition for ‘dhyper’
installed: no visible global function definition for
‘packageDescription’
minCallableCoverage: no visible global function definition for ‘pbinom’
t.test_welch: no visible global function definition for ‘pt’
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 dbinom dhyper makeVRangesFromVariantGRanges
packageDescription pbinom pt rawDepth read.pos.mean read.pos.mean.ref
read.pos.var read.pos.var.ref setNames variantGRangesIsDeprecated
variantGRangesToVRanges
Consider adding
importFrom("stats", "dbinom", "dhyper", "pbinom", "pt", "setNames")
importFrom("utils", "packageDescription")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
callGenotypes 22.536 4.968 37.824
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/VariantTools.Rcheck/00check.log’
for details.