flowStats 1.5.4
Florian Hahne and Chao-Jen Wong
| Bioconductor Changelog | | Snapshot Date: 2009-12-07 11:32:00 -0800 (Mon, 07 Dec 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowStats | | Last Changed Rev: 43402 / Revision: 43434 | | Last Changed Date: 2009-12-04 16:56:30 -0800 (Fri, 04 Dec 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | [ WARNINGS ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/flowStats.Rcheck'
* using R version 2.11.0 Under development (unstable) (2009-11-10 r50388)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowStats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowStats' version '1.5.4'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'flowStats' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated 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
.plotGPAprocess: no visible binding for global variable 'whichS'
.plotGPAprocess: no visible binding for global variable 'cluster'
.plotWorkFlow: no visible binding for global variable 'cluster'
.plotWorkFlow: no visible binding for global variable 'bogus'
normQA: no visible binding for global variable 'group'
normQA: no visible binding for global variable 'hasPeak'
print.GPA: no visible binding for global variable 'x'
warpSet: no visible binding for global variable 'wfuns'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'idFeaturesByBackgating':
idFeaturesByBackgating
Code: function(bg, nDim, thres.sigma = 2.5, lambda = 0.1,
reference.method = "median", plot.workflow = FALSE,
ask = names(dev.cur()) != "pdf")
Docs: function(bg, nDim, thres.sigma = 2.5, lambda = 1/1.4,
reference.method = "median", plot.workflow = FALSE,
ask = names(dev.cur()) != "pdf")
Mismatches in argument default values:
Name: 'lambda' Code: 0.1 Docs: 1/1.4
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There was 1 warning, see
/loc/home/biocbuild/bbs-2.6-bioc/meat/flowStats.Rcheck/00check.log
for details
* install options are ' --no-html'
* installing *source* package 'flowStats' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: rrcov
Loading required package: robustbase
Loading required package: pcaPP
Loading required package: mvtnorm
pcaPP 0.1-1 loaded
Scalable Robust Estimators with High Breakdown Point (version 1.0-00)
Attaching package: 'flowCore'
The following object(s) are masked from package:stats :
alias,
filter
Loading required package: splines
Loading required package: zoo
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Warning in namespaceImportFrom(self, asNamespace(ns), allVars, allFuns, :
Found methods to import for function "addName" but not the generic itself
** help
*** installing help indices
** building package indices ...
* DONE (flowStats)