SIM 1.10.0
Maarten van Iterson
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/SIM | | Last Changed Rev: 34811 / Revision: 38965 | | Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008) |
| wilson2 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | [ OK ] | OK |
| pelham | Mac OS X Leopard (10.5.6) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/SIM.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ASCII
* checking for file 'SIM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SIM' version '1.10.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'SIM' 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
RESOURCERER.annotation.to.ID: no visible binding for global variable
'expr.data'
RESOURCERER.annotation.to.ID: no visible binding for global variable
'poslist_expr'
acgh.heatmap.with.heatmap: no visible binding for global variable
'chrom.table'
acgh.heatmap.with.heatmap: no visible binding for global variable
'dep.data.only'
assemble.data: no visible binding for global variable 'acgh.data'
assemble.data: no visible binding for global variable 'expr.data'
heatmap.with.clac.plot: no visible binding for global variable
'dep.data.only'
heatmap.with.clac.plot: no visible binding for global variable
'chrom.table'
heatmap.with.plot: no visible binding for global variable 'ddc'
integrated.analysis: no visible binding for global variable
'chrom.table'
integrated.analysis: no visible binding for global variable
'indep.data'
integrated.analysis: no visible binding for global variable 'dep.data'
link.metadata: no visible binding for global variable 'expr.data'
link.metadata: no visible binding for global variable 'hgu133plus2CHR'
link.metadata: no visible binding for global variable
'hgu133plus2CHRLOC'
link.metadata: no visible binding for global variable
'hgu133plus2SYMBOL'
quantsmooth.heatmap: no visible binding for global variable
'chrom.table'
quantsmooth.heatmap: no visible binding for global variable
'dep.data.only'
sim.plot.pvals.on.genome: no visible binding for global variable
'chrom.table'
sim.plot.pvals.on.region: no visible binding for global variable
'chrom.table'
sim.plot.zscore.heatmap: no visible binding for global variable
'chrom.table'
sim.plot.zscore.heatmap: no visible binding for global variable
'dep.data'
sim.plot.zscore.heatmap: no visible binding for global variable
'indep.data'
sim.update.chrom.table : dbConnectEnsembl: no visible global function
definition for 'dbConnect'
sim.update.chrom.table : dbConnectEnsembl: no visible global function
definition for 'MySQL'
sim.update.chrom.table : dbGetChrBands: no visible global function
definition for 'dbGetQuery'
sim.update.chrom.table : dbGetChrBands: no visible binding for global
variable 'ensemblDb'
sim.update.chrom.table: no visible global function definition for
'import'
sim.update.chrom.table: no visible binding for global variable 'RMySQL'
tabulate.pvals: no visible binding for global variable 'chrom.table'
tabulate.top.dep.features: no visible binding for global variable
'chrom.table'
tabulate.top.indep.features: no visible binding for global variable
'chrom.table'
* 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 SIM-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating SIM-manual.tex ... OK
* checking SIM-manual.tex using pdflatex ... OK
* Installing *source* package 'SIM' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: fields
Loading required package: spam
Package 'spam' is loaded. Spam version 0.15-4 (2009-04-15).
Type demo( spam) for some demos, help( Spam) for an overview of this package.
Attaching package: 'spam'
The following object(s) are masked from package:base :
backsolve,
forwardsolve
Try help(fields) for an overview of this library
Loading required package: globaltest
Loading required package: marray
Loading required package: limma
Loading required package: quantsmooth
Loading required package: quantreg
Loading required package: SparseM
Package SparseM (0.79) loaded. To cite, see citation("SparseM")
Attaching package: 'SparseM'
The following object(s) are masked from package:spam :
backsolve,
chol,
norm
The following object(s) are masked from package:stats :
model.response
The following object(s) are masked from package:base :
backsolve,
chol
Loading required package: lodplot
Loading required package: grid
Loading required package: clac
Loading required package: multtest
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)'.
Warning in namespaceImportFrom(self, asNamespace(ns)) :
replacing previous import: summary
** help
>>> Building/Updating help pages for package 'SIM'
Formats: text html latex example
A4 text html latex example
RESOURCERER.annotation.to.ID text html latex example
SIM-package text html latex example
acgh.data text html latex example
acgh.heatmap.with.heatmap text html latex example
adj.bhfdr text html latex example
adj.byfdr text html latex example
assemble.data text html latex example
chrom.table text html latex example
collapse.arms text html latex example
collapse.bands text html latex example
create.color.vector text html latex example
expr.data text html latex example
get.abs.start text html latex example
get.indep.zscores text html latex example
get.pvals text html latex example
get.start.input.regions text html latex example
heatmap.with.clac.plot text html latex example
heatmap.with.plot text html latex example
impute.nas.by.surrounding text html latex example
integrated.analysis text html latex example
link.metadata text html latex example
make.Normal.data text html latex example
quantsmooth.heatmap text html latex example
run.ia text html latex example
samples text html latex example
sim.plot.adj.pvals text html latex example
sim.plot.pvals.on.genome text html latex example
sim.plot.pvals.on.region text html latex example
sim.plot.zscore.heatmap text html latex example
sim.update.chrom.table text html latex example
tabulate.pvals text html latex example
tabulate.top.dep.features text html latex example
tabulate.top.indep.features text html latex example
writeln text html latex example
** building package indices ...
* DONE (SIM)