intansv 1.13.0
Wen Yao
| Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/intansv | | Last Changed Rev: 122712 / Revision: 129046 | | Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| 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 intansv_1.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/intansv.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 ‘intansv/DESCRIPTION’ ... OK
* this is package ‘intansv’ 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘intansv’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.9Mb
sub-directories of 1Mb or more:
extdata 5.5Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
LumpyCluster: no visible global function definition for 'subjectHits'
PindelCluster: no visible global function definition for 'subjectHits'
breakDancerCluster: no visible global function definition for
'subjectHits'
dellyCluster: no visible global function definition for 'subjectHits'
geneAnnotation: no visible global function definition for 'queryHits'
geneAnnotation: no visible global function definition for 'subjectHits'
methodsCluster: no visible global function definition for 'hclust'
methodsCluster: no visible global function definition for 'as.dist'
methodsCluster: no visible global function definition for 'cutree'
methodsMerge: no visible global function definition for 'subjectHits'
plotChromosome: no visible global function definition for 'queryHits'
plotChromosome: no visible global function definition for 'subjectHits'
plotChromosome: no visible global function definition for
'seqlengths<-'
plotChromosome: no visible global function definition for 'seqlengths'
plotChromosome: no visible global function definition for 'ggplot'
plotChromosome: no visible global function definition for 'aes'
plotRegion: no visible global function definition for 'seqlengths<-'
plotRegion: no visible global function definition for 'ggplot'
plotRegion: no visible global function definition for 'subjectHits'
plotRegion: no visible global function definition for 'aes_string'
readBreakDancer: no visible global function definition for 'read.table'
readBreakDancer: no visible global function definition for
'subjectHits'
readCnvnator : <anonymous>: no visible global function definition for
'read.table'
readCnvnator: no visible global function definition for 'subjectHits'
readDelly : <anonymous>: no visible global function definition for
'read.table'
readDelly: no visible global function definition for 'subjectHits'
readLumpy: no visible global function definition for 'read.table'
readLumpy: no visible global function definition for 'subjectHits'
readPindel : <anonymous>: no visible global function definition for
'read.table'
readPindel: no visible global function definition for 'subjectHits'
readSoftSearch: no visible global function definition for 'read.table'
readSoftSearch: no visible global function definition for 'subjectHits'
readSvseq : <anonymous>: no visible global function definition for
'read.table'
readSvseq: no visible global function definition for 'subjectHits'
readSvseq : <anonymous>: no visible global function definition for
'subjectHits'
softSearchCluster: no visible global function definition for
'subjectHits'
svAnnotation: no visible global function definition for '.hasSlot'
svAnnotation: no visible global function definition for 'queryHits'
svAnnotation: no visible global function definition for 'subjectHits'
Undefined global functions or variables:
.hasSlot aes aes_string as.dist cutree ggplot hclust queryHits
read.table seqlengths seqlengths<- subjectHits
Consider adding
importFrom("methods", ".hasSlot")
importFrom("stats", "as.dist", "cutree", "hclust")
importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 sizes of PDF files under ‘inst/doc’ ... 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
methodsMerge 31.456 0.077 31.797
geneAnnotation 25.894 0.699 26.881
plotChromosome 9.474 0.021 9.569
plotRegion 7.600 0.029 7.703
svAnnotation 7.303 0.199 7.568
readDelly 5.673 0.011 5.719
readLumpy 5.095 0.011 5.203
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘rtracklayer’
* 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
‘/Users/biocbuild/bbs-3.5-bioc/meat/intansv.Rcheck/00check.log’
for details.