marray 1.17.0
Yee Hwa (Jean) Yang
| Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/marray | | Last Changed Rev: 28557 / Revision: 29143 | | Last Changed Date: 2007-11-07 23:00:31 -0800 (Wed, 07 Nov 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 |
* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/marray.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-09 r43632)
* checking for file 'marray/DESCRIPTION' ... OK
* this is package 'marray' version '1.17.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'marray' 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 name space 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
findID: no visible binding for global variable ‘gnames’
findID: no visible global function definition for ‘phenoData’
htmlPage: no visible binding for global variable ‘Gnames’
maTwoSamples: no visible global function definition for ‘gpTools’
scale.na: no visible global function definition for ‘applyy’
widget.mapGeneInfo: no visible global function definition for
‘widgetRender’
widget.TwoSamples: no visible global function definition for
‘widgetRender’
* 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 marray-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... NOTE
--- running texi2dvi on vignettes
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './marrayClasses.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './marrayClasses.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './marrayClasses.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './marrayClassesShort.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './marrayClassesShort.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './marrayInput.tex' ...
Package natbib Warning: Citation `Spot' on page 2 undefined on input line 103.
Package natbib Warning: Citation `Image' on page 2 undefined on input line 103.
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './marrayInput.tex' ...
Package natbib Warning: Citation `Spot' on page 2 undefined on input line 103.
Package natbib Warning: Citation `Image' on page 2 undefined on input line 103.
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './marrayInput.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './marrayNorm.tex' ...
LaTeX Warning: Citation `Dudoit&Yang02' on page 1 undefined on input line 52.
LaTeX Warning: Citation `Dudoitetal02' on page 1 undefined on input line 88.
LaTeX Warning: Citation `Cleveland79' on page 2 undefined on input line 100.
LaTeX Warning: Citation `Norm' on page 2 undefined on input line 100.
LaTeX Warning: Citation `NormNAR' on page 2 undefined on input line 100.
LaTeX Warning: Citation `Norm' on page 2 undefined on input line 117.
LaTeX Warning: Citation `NormNAR' on page 2 undefined on input line 117.
LaTeX Warning: Citation `NormNAR' on page 3 undefined on input line 211.
LaTeX Warning: Citation `NormNAR' on page 4 undefined on input line 273.
LaTeX Warning: Citation `Norm' on page 7 undefined on input line 417.
LaTeX Warning: Citation `NormNAR' on page 7 undefined on input line 417.
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './marrayNorm.tex' ...
LaTeX Warning: Citation `Dudoit&Yang02' on page 1 undefined on input line 52.
LaTeX Warning: Citation `Dudoitetal02' on page 2 undefined on input line 88.
LaTeX Warning: Citation `Cleveland79' on page 2 undefined on input line 100.
LaTeX Warning: Citation `Norm' on page 2 undefined on input line 100.
LaTeX Warning: Citation `NormNAR' on page 2 undefined on input line 100.
LaTeX Warning: Citation `Norm' on page 2 undefined on input line 117.
LaTeX Warning: Citation `NormNAR' on page 2 undefined on input line 117.
LaTeX Warning: Citation `NormNAR' on page 4 undefined on input line 211.
LaTeX Warning: Citation `NormNAR' on page 4 undefined on input line 273.
LaTeX Warning: Citation `Norm' on page 7 undefined on input line 417.
LaTeX Warning: Citation `NormNAR' on page 7 undefined on input line 417.
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './marrayNorm.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './marrayNorm.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './marrayPlots.tex' ...
Package natbib Warning: Citation `Dudoitetal02' on page 9 undefined on input li
Package natbib Warning: Citation `Norm' on page 9 undefined on input line 511.
Package natbib Warning: Citation `NormNAR' on page 9 undefined on input line 51
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './marrayPlots.tex' ...
Package natbib Warning: Citation `Dudoitetal02' on page 10 undefined on input l
Package natbib Warning: Citation `Norm' on page 10 undefined on input line 511.
Package natbib Warning: Citation `NormNAR' on page 10 undefined on input line 5
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './marrayPlots.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './marray.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './marray.tex' ...
* creating marray-manual.tex ... OK
* checking marray-manual.tex ... OK
/loc/home/biocbuild/bbs-2.2-bioc/meat/marray.Rcheck
* Installing *source* package 'marray' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: limma
** help
Note: removing empty section \value
Note: removing empty section \examples
Note: unmatched right brace in 'maColorBar' on or after line 10
Note: removing empty section \details
Note: unmatched right brace in 'maLoess' on or after line 33
Note: unmatched right brace in 'maPlot' on or after line 27
Note: unmatched right brace in 'maTop' on or after line 18
Note: unmatched right brace in 'plotMA' on or after line 59
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \note
Note: removing empty section \details
>>> Building/Updating help pages for package 'marray'
Formats: text html latex example
boxplot text html latex example
bracketMethods text html latex
cbind text html latex
checkTargetInfo text html latex example
coerce-methods text html latex
dim text html latex example
findID text html latex example
htmlPage text html latex example
image text html latex example
ma2D text html latex example
maBoxplot text html latex example
maColorBar text html latex example
maCompCoord text html latex example
maCompInd text html latex example
maCompLayout text html latex example
maCompNormA text html latex example
maCompPlate text html latex example
maCoord2Ind text html latex example
maDefaultPar text html latex example
maDotsDefaults text html latex example
maDotsMatch text html latex example
maGenControls text html latex example
maGeneTable text html latex example
maImage text html latex example
maImage.func text html latex example
maInd2Coord text html latex example
maLegendLines text html latex example
maLoess text html latex example
maLoessLines text html latex example
maMAD text html latex example
maMed text html latex example
maNA text html latex
maNorm text html latex example
maNorm2D text html latex example
maNormLoess text html latex example
maNormMAD text html latex example
maNormMain text html latex example
maNormMed text html latex example
maNormScale text html latex example
maNum2Logic text html latex example
maPalette text html latex example
maPlot text html latex example
maPlot.func text html latex example
maSelectGnames text html latex example
maText text html latex example
maTop text html latex example
maTwoSamples text html latex
mapGeneInfo text html latex example
marray-internal text html latex
marrayInfo-class text html latex example
marrayLayout-class text html latex example
marrayNorm-class text html latex example
marrayRaw-class text html latex example
opVersionID text html latex example
plotMA text html latex example
print-methods text html latex
read.Galfile text html latex example
read.marrayInfo text html latex example
read.marrayLayout text html latex example
read.marrayRaw text html latex Note: removing empty section \examples
example
rm.na text html latex example
showLargeObject text html latex
stat.confband.text text html latex example
stat.gnames text html latex example
swirl text html latex
write.list text html latex example
write.marray text html latex example
write.xls text html latex example
** building package indices ...
* DONE (marray)