plateCore 1.22.1
Errol Strain
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/plateCore | | Last Changed Rev: 93458 / Revision: 95116 | | Last Changed Date: 2014-08-18 14:08:56 -0700 (Mon, 18 Aug 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | 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 --no-multiarch plateCore_1.22.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/plateCore.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.22.1’
* 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 ... [32s/34s] 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 loading without being on the library search path ... 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 ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'flowPlate,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [172s/174s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mfiPlot-methods 20.229 0.049 20.495
summaryStats-methods 20.205 0.045 20.343
applyControlGates-methods 19.690 0.071 19.964
on-methods 13.355 0.065 13.530
fpbind-methods 9.885 0.037 10.048
compensate-methods 8.094 0.034 8.209
fixAutoFl-methods 7.756 0.034 7.847
Subset-methods 5.656 0.097 5.771
plotPlate-methods 5.564 0.028 5.621
* 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
WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
‘/Users/biocbuild/bbs-2.14-bioc/meat/plateCore.Rcheck/00check.log’
for details.
* 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
No methods found in "flowStats" for requests: %on%
** 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
No methods found in "flowStats" for requests: %on%
* DONE (plateCore)