BioC 2.13: CHECK report for plateCore on perceval
This page was generated on 2014-04-05 09:52:19 -0700 (Sat, 05 Apr 2014).
plateCore 1.20.0 Errol Strain
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/plateCore | 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: plateCore |
Version: 1.20.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch plateCore_1.20.0.tar.gz |
StartedAt: 2014-04-05 03:24:16 -0700 (Sat, 05 Apr 2014) |
EndedAt: 2014-04-05 03:28:26 -0700 (Sat, 05 Apr 2014) |
EllapsedTime: 250.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: plateCore.Rcheck |
Warnings: 0 |
Command output
* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/plateCore.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 ‘plateCore/DESCRIPTION’ ... OK
* this is package ‘plateCore’ version ‘1.20.0’
* 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 ‘plateCore’ can be installed ... [13s/16s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘flowCore’ ‘lattice’
A package should be listed in only one of these fields.
* 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:
‘flowViz’ ‘latticeExtra’
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 ... NOTE
panel.xyplot.flowPlate: warning in filterBoundary(filter =
filter[[nm]], parameters = c(channel.x.name, channel.y.name), frame =
frames[[nm]]): partial argument match of 'filter' to 'filter.object'
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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’:
‘plateCoreVig.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [114s/121s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
summaryStats-methods 13.032 0.099 13.359
mfiPlot-methods 12.934 0.116 13.536
applyControlGates-methods 11.826 0.087 12.015
on-methods 8.881 0.126 11.773
fpbind-methods 8.892 0.100 9.420
Subset-methods 6.279 0.132 6.648
fixAutoFl-methods 6.085 0.069 6.441
compensate-methods 5.327 0.044 5.492
* 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 4 notes.
See
‘/Users/biocbuild/bbs-2.13-bioc/meat/plateCore.Rcheck/00check.log’
for details.
plateCore.Rcheck/00install.out:
* installing *source* package ‘plateCore’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (plateCore)
plateCore.Rcheck/plateCore-Ex.timings:
name | user | system | elapsed
|
Subset-methods | 6.279 | 0.132 | 6.648 |
|
applyControlGates-methods | 11.826 | 0.087 | 12.015 |
|
compensate-methods | 5.327 | 0.044 | 5.492 |
|
compensationSet | 0.168 | 0.025 | 0.198 |
|
densityplot-methods | 1.447 | 0.038 | 1.556 |
|
fixAutoFl-methods | 6.085 | 0.069 | 6.441 |
|
flowPlate-class | 3.137 | 0.052 | 3.295 |
|
flowPlate-method | 3.456 | 0.048 | 3.653 |
|
fpbind-methods | 8.892 | 0.100 | 9.420 |
|
getGroups-methods | 1.562 | 0.051 | 1.706 |
|
gutterPlot-methods | 1.277 | 0.041 | 1.376 |
|
mfiPlot-methods | 12.934 | 0.116 | 13.536 |
|
on-methods | 8.881 | 0.126 | 11.773 |
|
panel.densityplot.flowPlate | 1.718 | 0.045 | 1.849 |
|
panel.xyplot.flowPlate | 1.640 | 0.037 | 1.716 |
|
plateCore-package | 3.264 | 0.060 | 3.467 |
|
plateSet-methods | 2.847 | 0.053 | 2.996 |
|
plotPlate-methods | 3.886 | 0.078 | 4.125 |
|
prepanel.densityplot.flowPlate | 1.696 | 0.037 | 1.820 |
|
prepanel.xyplot.flowPlate | 1.394 | 0.033 | 1.501 |
|
setControlGates-methods | 3.064 | 0.043 | 3.237 |
|
summaryStats-methods | 13.032 | 0.099 | 13.359 |
|
wellAnnotation-methods | 1.301 | 0.036 | 1.486 |
|
xyplot-methods | 1.417 | 0.032 | 1.460 |
|