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 'E:/biocbld/bbs-2.3-bioc/meat/SIM.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* 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 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
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'
RESOURCERER.annotation.to.ID: no visible binding for global variable
'expr.data'
RESOURCERER.annotation.to.ID: no visible binding for global variable
'poslist_expr'
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 R.css in E:/biocbld/bbs-2.3-bioc/meat/SIM.Rcheck
---------- Making package SIM ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
installing R files
installing inst files
installing data files
preparing package SIM for lazy loading
Loading required package: fields
Loading required package: spam
Attaching package: 'spam'
The following object(s) are masked from package:base :
backsolve,
forwardsolve
Loading required package: globaltest
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: marray
Loading required package: limma
Loading required package: quantsmooth
Loading required package: quantreg
Loading required package: 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
Warning in namespaceImportFrom(self, asNamespace(ns)) :
replacing previous import: summary
installing man source files
installing indices
not zipping data
installing help
>>> Building/Updating help pages for package 'SIM'
Formats: text html latex example chm
A4 text html latex example chm
RESOURCERER.annotation.to.ID text html latex example chm
SIM-package text html latex example chm
acgh.data text html latex example chm
acgh.heatmap.with.heatmap text html latex example chm
adj.bhfdr text html latex example chm
adj.byfdr text html latex example chm
assemble.data text html latex example chm
chrom.table text html latex example chm
collapse.arms text html latex example chm
collapse.bands text html latex example chm
create.color.vector text html latex example chm
expr.data text html latex example chm
get.abs.start text html latex example chm
get.indep.zscores text html latex example chm
get.pvals text html latex example chm
get.start.input.regions text html latex example chm
heatmap.with.clac.plot text html latex example chm
heatmap.with.plot text html latex example chm
impute.nas.by.surrounding text html latex example chm
integrated.analysis text html latex example chm
link.metadata text html latex example chm
make.Normal.data text html latex example chm
quantsmooth.heatmap text html latex example chm
run.ia text html latex example chm
samples text html latex example chm
sim.plot.adj.pvals text html latex example chm
sim.plot.pvals.on.genome text html latex example chm
sim.plot.pvals.on.region text html latex example chm
sim.plot.zscore.heatmap text html latex example chm
sim.update.chrom.table text html latex example chm
tabulate.pvals text html latex example chm
tabulate.top.dep.features text html latex example chm
tabulate.top.indep.features text html latex example chm
writeln text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.3-bioc\meat\SIM.Rcheck\00_pkg_src\SIM\chm\SIM.chm
Compile time: 0 minutes, 0 seconds
36 Topics
219 Local links
0 Internet links
1 Graphic
Created e:\biocbld\bbs-2.3-bioc\meat\SIM.Rcheck\00_pkg_src\SIM\chm\SIM.chm, 64,410 bytes
Compression decreased file by 94,680 bytes.
adding MD5 sums
* DONE (SIM)