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BioC 3.2: CHECK report for Rariant on zin1

This page was generated on 2016-04-23 10:13:44 -0700 (Sat, 23 Apr 2016).

Package 840/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rariant 1.6.2
Julian Gehring
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Rariant
Last Changed Rev: 116082 / Revision: 116712
Last Changed Date: 2016-04-10 09:51:21 -0700 (Sun, 10 Apr 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rariant
Version: 1.6.2
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Rariant_1.6.2.tar.gz
StartedAt: 2016-04-23 04:21:33 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 04:26:47 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 314.2 seconds
RetCode: 0
Status:  OK 
CheckDir: Rariant.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Rariant_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/Rariant.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rariant/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rariant’ version ‘1.6.2’
* package encoding: UTF-8
* 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 ‘Rariant’ can be installed ... [29s/29s] OK
* checking installed package size ... NOTE
  installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   5.2Mb
* 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
rariantFromBam: no visible global function definition for ‘metadata<-’
* 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’ ... NOTE
The following files should probably not be installed:
  ‘rariant-inspect-ci.png’, ‘rariant-inspect-shift.png’

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 ... [19s/19s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test_all.R’ [18s/18s]
 [19s/19s] 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-3.2-bioc/meat/Rariant.Rcheck/00check.log’
for details.


Rariant.Rcheck/00install.out:

* installing *source* package ‘Rariant’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
* DONE (Rariant)

Rariant.Rcheck/Rariant-Ex.timings:

nameusersystemelapsed
Rariant-package0.1400.0430.694
ci-adjust0.0050.0000.005
ci-assessment0.0180.0040.022
ci-utils0.0060.0000.006
convert-utils0.1330.0080.141
mismatch-plot3.4880.0643.563
plot-cis0.9750.0200.994
prop-cis0.0060.0000.006
prop-tests0.0080.0000.008
rariant0.1710.0000.184
shiny0.0010.0000.000
split-sample0.0010.0000.002