BeadExplorer 1.4.0
Gareth Elvidge
| Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/BeadExplorer | | Last Changed Rev: 27709 / Revision: 30966 | | Last Changed Date: 2007-10-02 17:41:09 -0700 (Tue, 02 Oct 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | OK | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | OK | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | [ OK ] | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/BeadExplorer.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'BeadExplorer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BeadExplorer' version '1.4.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'BeadExplorer' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... 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 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
batchAnalysis: no visible binding for global variable 'output'
beadAnalysis: no visible binding for global variable 'examplebeadData'
beadAnalysis: no visible binding for global variable 'examplebeadQC'
boxplotArrays: no visible binding for global variable 'oqc'
getQC2: no visible binding for global variable 'HumWG6'
getQC2: no visible binding for global variable 'HumRef8'
Found possibly global 'T' or 'F' in the following function:
boxplotQC
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* creating BeadExplorer-Ex.R ... OK
* checking examples ... OK
* creating BeadExplorer-manual.tex ... OK
* checking BeadExplorer-manual.tex ... OK
installing R.css in D:/biocbld/bbs-2.1-bioc/meat/BeadExplorer.Rcheck
---------- Making package BeadExplorer ------------
adding build stamp to DESCRIPTION
installing R files
installing inst files
installing data files
installing man source files
installing indices
not zipping data
installing help
Note: unmatched right brace in 'beadData-class' on or after line 61
Note: unmatched right brace in 'beadData-class.Rd' on or after line 61
Note: unmatched right brace in 'readQC' on or after line 23
Note: unmatched right brace in 'readQC.Rd' on or after line 23
Note: unmatched right brace in 'scatterPlot' on or after line 44
Note: unmatched right brace in 'scatterPlot.Rd' on or after line 44
>>> Building/Updating help pages for package 'BeadExplorer'
Formats: text html latex example chm
HumRef8v1 text html latex example chm
HumWG6v1 text html latex example chm
addManifest text html latex example chm
batchAnalysis text html latex example chm
beadAnalysis text html latex example chm
beadData-accessor text html latex chm
beadData-class text html latex example chm
beadQC-class text html latex example chm
boxplotArrays text html latex example chm
boxplotQC text html latex example chm
clusterplot text html latex example chm
cutoff text html latex example chm
detectionCalls text html latex example chm
dotplotArrays text html latex example chm
dotplotQC text html latex example chm
examplebeadData text html latex example chm
examplebeadQC text html latex example chm
extract text html latex example chm
filterData text html latex example chm
getAnnot text html latex example chm
getArrayStats text html latex example chm
getDet text html latex example chm
getExprs text html latex example chm
getID text html latex example chm
getQC text html latex example chm
getQC2 text html latex example chm
htmloutput text html latex example chm
multiDensity text html latex example chm
multiecdf text html latex example chm
normalise text html latex example chm
pc text html latex example chm
plotSamples text html latex example chm
readBead text html latex example chm
readManifest text html latex example chm
readQC text html latex example chm
scatterPlot text html latex example chm
write.beadData text html latex example chm
writeQC text html latex example chm
HHC5012: Error: Cannot create a temporary file in your TEMP path.
HHC4016: Warning: Cannot open "Intel\DMIX;c:\Program Files\Windows Resource Kits\Tools\;c:\Program Files\Affymetrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".
Microsoft HTML Help Compiler 4.74.8702
Compiling d:\biocbld\bbs-2.1-bioc\meat\BeadExplorer.Rcheck\00_pkg_src\BeadExplorer\chm\BeadExplorer.chm
HHC4016: Warning: Cannot open "Intel\DMIX;c:\Program Files\Windows Resource Kits\Tools\;c:\Program Files\Affymetrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".
The following files were not compiled:
preparing package BeadExplorer for lazy loading
Loading required package: widgetTools
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Loading required package: Biobase
Loading required package: tools
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: affy
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: R2HTML
Loading required package: tkWidgets
Loading required package: DynDoc
adding MD5 sums
* DONE (BeadExplorer)