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Package 282/319HostnameOS / ArchBUILDCHECKBUILD BIN
simulatorAPMS 1.16.0
Tony Chiang
Bioconductor Changelog
Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/simulatorAPMS
Last Changed Rev: 39013 / Revision: 42512
Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009)
wilson1 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 (10.5.8) / i386  OK  OK  OK 
Package: simulatorAPMS
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/2.9/Resources/bin/R CMD check --no-vignettes simulatorAPMS_1.16.0.tar.gz
StartedAt: 2009-10-20 18:57:36 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 18:59:36 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 119.9 seconds
RetCode: 0
Status: OK
CheckDir: simulatorAPMS.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.4-bioc/meat/simulatorAPMS.Rcheck'
* using R version 2.9.2 Patched (2009-08-24 r49419)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'simulatorAPMS/DESCRIPTION' ... OK
* this is package 'simulatorAPMS' version '1.16.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'simulatorAPMS' 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 ... OK
* checking Rd files ... OK
* checking Rd files against version 2 parser ... 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
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

simulatorAPMS.Rcheck/00install.out:

* Installing *source* package ‘simulatorAPMS’ ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: Biobase

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: DBI
Loading required package: RpsiXML
Loading required package: annotate
Loading required package: graph
Loading required package: RBGL
Loading required package: hypergraph

Attaching package: 'hypergraph'


	The following object(s) are masked from package:AnnotationDbi :

	 head,
	 tail 


	The following object(s) are masked from package:utils :

	 head,
	 tail 

Warning in namespaceImportFrom(self, asNamespace(ns)) :
  replacing previous import: addNode
Loading required package: apComplex
** help
*** installing help indices
 >>> Building/Updating help pages for package 'simulatorAPMS'
     Formats: text html latex example 
Note: removing empty section \source in file 'APComEX.Rd'
Note: removing empty section \references in file 'APComEX.Rd'
  APComEX                           text    html    latex   example
Note: removing empty section \source in file 'PPIEX.Rd'
Note: removing empty section \references in file 'PPIEX.Rd'
  PPIEX                             text    html    latex   example
Note: removing empty section \details in file 'TSNMatrix.Rd'
  TSNMatrix                         text    html    latex   example
  applyDeformationError             text    html    latex   example
  applyFNErrors                     text    html    latex   example
  applyFPErrors                     text    html    latex   example
  applyStickyError                  text    html    latex   example
Note: removing empty section \details in file 'compIndep.Rd'
  compIndep                         text    html    latex   example
  filteredProt                      text    html    latex   example
Note: removing empty section \source in file 'fullSimEX.Rd'
Note: removing empty section \references in file 'fullSimEX.Rd'
  fullSimEX                         text    html    latex   example
Note: removing empty section \source in file 'missedProtEX.Rd'
Note: removing empty section \references in file 'missedProtEX.Rd'
  missedProtEX                      text    html    latex   example
Note: removing empty section \source in file 'missedProtHMSPCI.Rd'
Note: removing empty section \details in file 'missedProtHMSPCI.Rd'
Note: removing empty section \references in file 'missedProtHMSPCI.Rd'
  missedProtHMSPCI                  text    html    latex   example
  recordSticky                      text    html    latex   example
  runAPComplex                      text    html    latex   example
  runCompIndep                      text    html    latex   example
Note: removing empty section \source in file 'runSimEX.Rd'
Note: removing empty section \references in file 'runSimEX.Rd'
  runSimEX                          text    html    latex   example
  runSimulators                     text    html    latex   example
Note: removing empty section \source in file 'simEX.Rd'
Note: removing empty section \references in file 'simEX.Rd'
  simEX                             text    html    latex   example
  simulator                         text    html    latex   example
  simulatorD                        text    html    latex   example
  simulatorS                        text    html    latex   example
Note: removing empty section \source in file 'vBaits.Rd'
Note: removing empty section \details in file 'vBaits.Rd'
Note: removing empty section \references in file 'vBaits.Rd'
  vBaits                            text    html    latex   example
Note: removing empty section \source in file 'vBaitsEX.Rd'
Note: removing empty section \references in file 'vBaitsEX.Rd'
  vBaitsEX                          text    html    latex   example
Note: removing empty section \source in file 'vDeformEX.Rd'
Note: removing empty section \details in file 'vDeformEX.Rd'
Note: removing empty section \references in file 'vDeformEX.Rd'
  vDeformEX                         text    html    latex   example
  vDeformed                         text    html    latex   example
Note: removing empty section \source in file 'vDeformedEX.Rd'
Note: removing empty section \details in file 'vDeformedEX.Rd'
Note: removing empty section \references in file 'vDeformedEX.Rd'
  vDeformedEX                       text    html    latex   example
Note: removing empty section \source in file 'vStickyEX.Rd'
Note: removing empty section \details in file 'vStickyEX.Rd'
Note: removing empty section \references in file 'vStickyEX.Rd'
  vStickyEX                         text    html    latex   example
** building package indices ...
* DONE (simulatorAPMS)