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Package 262/294HostnameOS / ArchBUILDCHECKBUILD BIN
simulatorAPMS 1.14.0
Tony Chiang
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/simulatorAPMS
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: simulatorAPMS
Version: 1.14.0
Command: E:\biocbld\bbs-2.3-bioc\R\bin\R.exe CMD check --no-vignettes simulatorAPMS_1.14.0.tar.gz
StartedAt: 2009-04-18 20:01:25 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 20:03:25 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 119.3 seconds
RetCode: 0
Status: OK
CheckDir: simulatorAPMS.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.3-bioc/meat/simulatorAPMS.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* checking for file 'simulatorAPMS/DESCRIPTION' ... OK
* this is package 'simulatorAPMS' version '1.14.0'
* 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 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 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 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 simulatorAPMS-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating simulatorAPMS-manual.tex ... OK
* checking simulatorAPMS-manual.tex using pdflatex ... OK

simulatorAPMS.Rcheck/00install.out:

installing R.css in E:/biocbld/bbs-2.3-bioc/meat/simulatorAPMS.Rcheck


---------- Making package simulatorAPMS ------------
  adding build stamp to DESCRIPTION
  installing R files
  installing inst files
  installing data files
  preparing package simulatorAPMS for lazy loading
Loading required package: graph
Loading required package: apComplex
Loading required package: RBGL
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: org.Sc.sgd.db
Loading required package: AnnotationDbi
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: DBI
Loading required package: ScISI
Loading required package: GO.db
Loading required package: GOstats
Loading required package: annotate
Loading required package: xtable

Attaching package: 'annotate'


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

	 toFile 

Loading required package: Category
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: RpsiXML
Loading required package: XML

Attaching package: 'XML'


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

	 addNode 

Loading required package: hypergraph

Attaching package: 'hypergraph'


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

	 label,
	 label<- 


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

	 head,
	 tail 


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

	 head,
	 tail 


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

	 head,
	 tail 

Loading required package: ppiStats
Loading required package: ppiData
Loading required package: lattice
Loading required package: RColorBrewer
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'simulatorAPMS'
     Formats: text html latex example chm 
Note: removing empty section \source in file 'APComEX.Rd'
Note: removing empty section \references in file 'APComEX.Rd'
Note: removing empty section \source in file 'APComEX.Rd'
Note: removing empty section \references in file 'APComEX.Rd'
  APComEX                           text    html    latex   example chm
Note: removing empty section \source in file 'PPIEX.Rd'
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  PPIEX                             text    html    latex   example chm
Note: removing empty section \details in file 'TSNMatrix.Rd'
Note: removing empty section \details in file 'TSNMatrix.Rd'
  TSNMatrix                         text    html    latex   example chm
  applyDeformationError             text    html    latex   example chm
  applyFNErrors                     text    html    latex   example chm
  applyFPErrors                     text    html    latex   example chm
  applyStickyError                  text    html    latex   example chm
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  compIndep                         text    html    latex   example chm
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Note: unmatched right brace in file 'filteredProt.Rd' on or after line 14
  filteredProt                      text    html    latex   example chm
Note: removing empty section \source in file 'fullSimEX.Rd'
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  fullSimEX                         text    html    latex   example chm
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  missedProtEX                      text    html    latex   example chm
Note: removing empty section \source in file 'missedProtHMSPCI.Rd'
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  missedProtHMSPCI                  text    html    latex   example chm
  recordSticky                      text    html    latex   example chm
  runAPComplex                      text    html    latex   example chm
  runCompIndep                      text    html    latex   example chm
Note: removing empty section \source in file 'runSimEX.Rd'
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Note: removing empty section \source in file 'runSimEX.Rd'
Note: removing empty section \references in file 'runSimEX.Rd'
  runSimEX                          text    html    latex   example chm
  runSimulators                     text    html    latex   example chm
Note: removing empty section \source in file 'simEX.Rd'
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Note: removing empty section \source in file 'simEX.Rd'
Note: removing empty section \references in file 'simEX.Rd'
  simEX                             text    html    latex   example chm
  simulator                         text    html    latex   example chm
  simulatorD                        text    html    latex   example chm
  simulatorS                        text    html    latex   example chm
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  vBaits                            text    html    latex   example chm
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  vBaitsEX                          text    html    latex   example chm
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  vDeformEX                         text    html    latex   example chm
  vDeformed                         text    html    latex   example chm
Note: removing empty section \source in file 'vDeformedEX.Rd'
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  vDeformedEX                       text    html    latex   example chm
Note: removing empty section \source in file 'vStickyEX.Rd'
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  vStickyEX                         text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.3-bioc\meat\simulatorAPMS.Rcheck\00_pkg_src\simulatorAPMS\chm\simulatorAPMS.chm


Compile time: 0 minutes, 0 seconds
28	Topics
78	Local links
0	Internet links
1	Graphic


Created e:\biocbld\bbs-2.3-bioc\meat\simulatorAPMS.Rcheck\00_pkg_src\simulatorAPMS\chm\simulatorAPMS.chm, 36,594 bytes
Compression decreased file by 29,656 bytes.
  adding MD5 sums

* DONE (simulatorAPMS)