VariantTools 1.13.0
Michael Lawrence
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VariantTools | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings VariantTools_1.13.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/VariantTools.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.13.0’
* 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 ... [15s/15s] 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
LowerFrequencyInOtherFilter : <anonymous>: no visible binding for
global variable ‘control.alt.depth’
LowerFrequencyInOtherFilter : <anonymous>: no visible binding for
global variable ‘control.total.depth’
LowerFrequencyInOtherFilter : <anonymous>: no visible binding for
global variable ‘raw.count’
LowerFrequencyInOtherFilter : <anonymous>: no visible binding for
global variable ‘raw.count.total’
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’
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’
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’
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 high.quality high.quality.ref
high.quality.total raw.count raw.count.total read.pos.mean
read.pos.mean.ref read.pos.var read.pos.var.ref
variantGRangesToVRanges
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'callVariants.Rd':
‘[IRanges]{FilterRules}’
Missing link or links in documentation object 'postFilterVariants.Rd':
‘[IRanges]{FilterRules}’
Missing link or links in documentation object 'qaVariants.Rd':
‘[IRanges]{FilterRules}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'annotateWithControlDepth':
annotateWithControlDepth
Code: function(case, control, control.cov, raw = FALSE)
Docs: function(case, control, control.cov)
Argument names in code not in docs:
raw
* 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 ... [90s/65s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
callGenotypes 56.813 10.106 42.128
* 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
Status: 2 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/VariantTools.Rcheck/00check.log’
for details.