BioC 2.13: CHECK report for ReQON on perceval
This page was generated on 2014-04-05 09:52:45 -0700 (Sat, 05 Apr 2014).
ReQON 1.8.0 Christopher Cabanski
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/ReQON | Last Changed Rev: 81642 / Revision: 88450 | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ OK ] | OK |
Summary
Package: ReQON |
Version: 1.8.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ReQON_1.8.0.tar.gz |
StartedAt: 2014-04-05 03:50:20 -0700 (Sat, 05 Apr 2014) |
EndedAt: 2014-04-05 03:54:42 -0700 (Sat, 05 Apr 2014) |
EllapsedTime: 261.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ReQON.Rcheck |
Warnings: 0 |
Command output
* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/ReQON.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReQON/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ReQON’ version ‘1.8.0’
* 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 ‘ReQON’ can be installed ... [20s/20s] 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
Packages in Depends field not imported from:
‘Rsamtools’ ‘seqbias’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘ReQON.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [74s/80s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ReQON 58.774 5.106 68.129
* 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
NOTE: There were 3 notes.
See
‘/Users/biocbuild/bbs-2.13-bioc/meat/ReQON.Rcheck/00check.log’
for details.
ReQON.Rcheck/00install.out:
* installing *source* package ‘ReQON’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ReQON)
ReQON.Rcheck/ReQON-Ex.timings:
name | user | system | elapsed
|
FWSEplot | 0.375 | 0.006 | 0.417 |
|
QualFreqPlot | 0.021 | 0.006 | 0.028 |
|
ReQON | 58.774 | 5.106 | 68.129 |
|
ReadPosErrorPlot | 0.005 | 0.007 | 0.015 |
|