tigre 1.5.2
Antti Honkela
| Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/tigre | | Last Changed Rev: 52644 / Revision: 53825 | | Last Changed Date: 2011-02-14 00:29:56 -0800 (Mon, 14 Feb 2011) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.6) / i386 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/tigre.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'tigre/DESCRIPTION' ... OK
* this is package 'tigre' version '1.5.2'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'tigre' can be installed ... OK
* checking installed package size ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Assignments in \usage in documentation object 'GPLearn':
model <- GPLearn(preprocData, TF = NULL, targets = NULL, useGpdisim = !is.null(TF),
randomize = FALSE, addPriors = FALSE, fixedParams = FALSE,
initParams = NULL, initialZero = TRUE, fixComps = NULL, dontOptimise = FALSE,
allowNegativeSensitivities = FALSE, quiet = FALSE, gpsimOptions = NULL,
allArgs = NULL)
Assignments in \usage in documentation object 'GPRankTargets':
scores <- GPRankTargets(preprocData, TF = NULL, knownTargets = NULL,
testTargets = NULL, filterLimit = 1.8, returnModels = FALSE,
options = NULL, scoreSaveFile = NULL)
scores <- GPRankTFs(preprocData, TFs, targets, filterLimit = 1.8,
returnModels = FALSE, options = NULL, scoreSaveFile = NULL)
Assignments in \usage in documentation object 'SCGoptim':
options <- optimiDefaultOptions()
newParams <- SCGoptim(x, fn, grad, options, ...)
newParams <- CGoptim(x, fn, grad, options, ...)
model <- modelOptimise(model, options, ...)
Assignments in \usage in documentation object 'generateModels':
models <- generateModels(preprocData, scores)
Assignments in \usage in documentation object 'gpsimCreate':
model <- gpsimCreate(numGenes, numProteins, times, geneVals,
geneVars, options, genes, annotation)
model <- gpdisimCreate(numGenes, numProteins, times, geneVals,
geneVars, options, genes, annotation)
Assignments in \usage in documentation object 'kernCompute':
K <- kernCompute(kern, X)
K <- kernCompute(kern, X1, X2)
Kd <- kernDiagCompute(kern, X)
Assignments in \usage in documentation object 'kernCreate':
kern <- kernCreate(X, type)
kern <- kernCreate(dim, type)
Assignments in \usage in documentation object 'kernDiagGradX':
gX <- kernDiagGradX(kern, X)
gX2 <- kernGradX(kern, X)
gX2 <- kernGradX(kern, X1, X2)
Assignments in \usage in documentation object 'kernGradient':
g <- kernGradient(kern, x, partial)
g <- kernGradient(kern, x1, x2, partial_)
Assignments in \usage in documentation object 'lnDiffErfs':
v <- lnDiffErfs(x1, x2)
Assignments in \usage in documentation object 'modelDisplay':
model <- modelDisplay(model)
Assignments in \usage in documentation object 'modelExpandParam':
model <- modelExpandParam(model, param, untransformed.values = FALSE)
model <- modelUpdateProcesses(model)
Assignments in \usage in documentation object 'modelExtractParam':
param <- modelExtractParam(model, only.values = TRUE, untransformed.values = FALSE)
Assignments in \usage in documentation object 'modelGradient':
v <- modelObjective(model)
ll <- modelLogLikelihood(model)
g <- modelGradient(params, model, ...)
Assignments in \usage in documentation object 'modelTieParam':
model <- modelTieParam(model, paramsList)
Assignments in \usage in documentation object 'optimiDefaultConstraint':
val <- optimiDefaultConstraint(constraint)
Assignments in \usage in documentation object 'processData':
preprocData <- processData(data, times = NULL, experiments = NULL,
do.normalisation = TRUE)
preprocData <- processRawData(rawData, times, experiments = NULL,
is.logged = TRUE, do.normalisation = ifelse(is.logged, TRUE,
FALSE))
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There was 1 warning, see
'/Users/biocbuild/bbs-2.8-bioc/meat/tigre.Rcheck/00check.log'
for details