maDB 1.12.0
Johannes Rainer
| Snapshot Date: 2008-08-08 00:12:03 -0700 (Fri, 08 Aug 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_2/madman/Rpacks/maDB | | Last Changed Rev: 31430 / Revision: 33132 | | Last Changed Date: 2008-04-29 16:50:18 -0700 (Tue, 29 Apr 2008) |
| 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 | N O T S U P P O R T E D |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory '/home/biocbuild/bbs-2.2-bioc/meat/maDB.Rcheck'
* using R version 2.7.1 (2008-06-23)
* using session charset: ISO8859-1
* checking for file 'maDB/DESCRIPTION' ... OK
* this is package 'maDB' version '1.12.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'maDB' 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 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
.calcRegulations: no visible binding for global variable 'con'
.calculateDBRegulations.old: no visible binding for global variable
'con'
dbGetGeneRegulationRanking: no visible global function definition for
'getDBAnnotation'
getAnnotation: possible error in dbGetAnnotation(con = con, id = id, v
= v, chip = chip, ...): unused argument(s) (con = con)
getAnnotation: possible error in getGene(mart = con, id = id, array =
.toMartChip(chip), ...): unused argument(s) (array =
.toMartChip(chip))
.resetAfterError: no visible binding for global variable
'ConnectionForErrors'
* 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 ... NOTE
S3 methods shown with full name in documentation object 'format.latex':
format.latex
S3 methods shown with full name in documentation object 'mean.center':
mean.center
The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking data for non-ASCII characters ... OK
* creating maDB-Ex.R ... OK
* checking examples ... OK
* creating maDB-manual.tex ... OK
* checking maDB-manual.tex using pdflatex ... OK
* Installing *source* package 'maDB' ...
** R
** data
** inst
** preparing package for lazy loading
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: pgUtils
Loading required package: Rdbi
Loading required package: RdbiPgSQL
Attaching package: 'RdbiPgSQL'
The following object(s) are masked from package:Rdbi :
dbAppendTable
Loading required package: limma
Creating a new generic function for "sort" in "maDB"
** help
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>>> Building/Updating help pages for package 'maDB'
Formats: text html latex example
EexprSet-class text html latex
Layout-class text html latex
MAtoG text html latex
MAtoR text html latex
MadbSet-class text html latex
Sample-class text html latex
SignalChannel-class text html latex
Similarity-class text html latex
arrowProgress text html latex example
average text html latex
calculateSimilarity text html latex example
checkForAnnotation text html latex
createDirs text html latex
createEexprSetFromLimma text html latex
createFile text html latex
createJOINQuery text html latex example
createSampleFromTable text html latex
dbCalculateRegulations text html latex
dbGetComparisons text html latex
dbGetGeneRegulationRanking text html latex
dbSearchSimilarPattern text html latex
deleteExperimentFromDB text html latex
distance.euclidian text html latex
distance.pearson text html latex
distance.pearson.uncentered text html latex
distance.spearman text html latex
drawMAPlot text html latex
drawVolcanoPlot text html latex
format.latex text html latex
getAnnotation text html latex
getDBAnnotation text html latex
getExpValue text html latex
getExperimentDBInfo text html latex
getMDB text html latex
getPK text html latex
getPathFromFile text html latex example
getSamplesFromDB text html latex
isDecimal text html latex example
loadFromDB text html latex
maDB-package text html latex
mapply text html latex example
mean.center text html latex example
meanWithoutNA text html latex example
medianWithoutNA text html latex example
multiGrep text html latex example
myGrep text html latex
newMadbSet text html latex
openMadbVignette text html latex
plotSimilarity text html latex
progress text html latex example
publishToDB text html latex
replaceAll text html latex example
replaces text html latex example
smallALL text html latex
toEexprSet text html latex
updateDBAnnotation text html latex
writeFigure text html latex
writeLatexTable text html latex
** building package indices ...
* DONE (maDB)