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BioC 3.4: CHECK report for intansv on malbec1

This page was generated on 2017-04-15 16:11:33 -0400 (Sat, 15 Apr 2017).

Package 635/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
intansv 1.12.0
Wen Yao
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/intansv
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  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: intansv
Version: 1.12.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings intansv_1.12.0.tar.gz
StartedAt: 2017-04-14 23:19:41 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:24:52 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 311.1 seconds
RetCode: 0
Status:  OK 
CheckDir: intansv.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings intansv_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/intansv.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 ‘intansv/DESCRIPTION’ ... OK
* this is package ‘intansv’ version ‘1.12.0’
* 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 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   20.428  0.008  20.453
geneAnnotation 17.844  0.076  17.933
svAnnotation    6.048  0.004   6.059
plotRegion      5.288  0.000   5.295
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/intansv.Rcheck/00check.log’
for details.


intansv.Rcheck/00install.out:

* installing *source* package ‘intansv’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (intansv)

intansv.Rcheck/intansv-Ex.timings:

nameusersystemelapsed
geneAnnotation17.844 0.07617.933
methodsMerge20.428 0.00820.453
plotChromosome4.8840.0044.894
plotRegion5.2880.0005.295
readBreakDancer3.4360.0003.442
readCnvnator0.5760.0000.573
readDelly3.8840.0003.890
readLumpy3.4560.0003.461
readPindel2.7800.0002.783
readSoftSearch0.2600.0000.261
readSvseq0.8280.0000.832
svAnnotation6.0480.0046.059