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Package 260/294HostnameOS / ArchBUILDCHECKBUILD BIN
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 
Package: SIM
Version: 1.10.0
Command: /home/biocbuild/bbs-2.3-bioc/R/bin/R CMD check --no-vignettes SIM_1.10.0.tar.gz
StartedAt: 2009-04-18 16:41:50 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 16:43:47 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 116.5 seconds
RetCode: 0
Status: OK
CheckDir: SIM.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.3-bioc/meat/SIM.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: UTF-8
* 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
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

SIM.Rcheck/00install.out:

* 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)