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Package 347/389HostnameOS / ArchBUILDCHECKBUILD BIN
simulatorAPMS 1.20.0
Tony Chiang
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/simulatorAPMS
Last Changed Rev: 46401 / Revision: 49923
Last Changed Date: 2010-04-22 11:21:23 -0700 (Thu, 22 Apr 2010)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ OK ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: simulatorAPMS
Version: 1.20.0
Command: D:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings simulatorAPMS_1.20.0.tar.gz
StartedAt: 2010-10-04 18:46:42 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 18:48:16 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 93.5 seconds
RetCode: 0
Status:  OK  
CheckDir: simulatorAPMS.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'D:/biocbld/bbs-2.6-bioc/meat/simulatorAPMS.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'simulatorAPMS/DESCRIPTION' ... OK
* this is package 'simulatorAPMS' version '1.20.0'
* 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 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 ... NOTE
prepare_Rd: APComEX.Rd:25-27: Dropping empty section \source
prepare_Rd: APComEX.Rd:28-30: Dropping empty section \references
prepare_Rd: PPIEX.Rd:22-24: Dropping empty section \source
prepare_Rd: PPIEX.Rd:25-27: Dropping empty section \references
prepare_Rd: TSNMatrix.Rd:17-19: Dropping empty section \details
prepare_Rd: compIndep.Rd:23-25: Dropping empty section \details
prepare_Rd: fullSimEX.Rd:24-26: Dropping empty section \source
prepare_Rd: fullSimEX.Rd:27-29: Dropping empty section \references
prepare_Rd: missedProtEX.Rd:18-20: Dropping empty section \source
prepare_Rd: missedProtEX.Rd:21-23: Dropping empty section \references
prepare_Rd: missedProtHMSPCI.Rd:15-17: Dropping empty section \details
prepare_Rd: missedProtHMSPCI.Rd:18-20: Dropping empty section \source
prepare_Rd: missedProtHMSPCI.Rd:21-23: Dropping empty section \references
prepare_Rd: runSimEX.Rd:20-22: Dropping empty section \source
prepare_Rd: runSimEX.Rd:23-25: Dropping empty section \references
prepare_Rd: simEX.Rd:20-22: Dropping empty section \source
prepare_Rd: simEX.Rd:23-25: Dropping empty section \references
prepare_Rd: vBaits.Rd:15-17: Dropping empty section \details
prepare_Rd: vBaits.Rd:18-20: Dropping empty section \source
prepare_Rd: vBaits.Rd:21-23: Dropping empty section \references
prepare_Rd: vBaitsEX.Rd:16-18: Dropping empty section \source
prepare_Rd: vBaitsEX.Rd:19-21: Dropping empty section \references
prepare_Rd: vDeformEX.Rd:13-15: Dropping empty section \details
prepare_Rd: vDeformEX.Rd:16-18: Dropping empty section \source
prepare_Rd: vDeformEX.Rd:19-21: Dropping empty section \references
prepare_Rd: vDeformedEX.Rd:13-15: Dropping empty section \details
prepare_Rd: vDeformedEX.Rd:16-18: Dropping empty section \source
prepare_Rd: vDeformedEX.Rd:19-21: Dropping empty section \references
prepare_Rd: vStickyEX.Rd:13-15: Dropping empty section \details
prepare_Rd: vStickyEX.Rd:16-18: Dropping empty section \source
prepare_Rd: vStickyEX.Rd:19-21: Dropping empty section \references
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... 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:

* install options are ' --no-html'

* 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: 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:AnnotationDbi':

    head, tail

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

    head, tail

Loading required package: apComplex
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

*** Deprecation warning ***:
The package 'simulatorAPMS' is deprecated and will not be supported after Bioconductor release 2.4. The methods and functions will be ported over to ppiStats within the next two releases.



* DONE (simulatorAPMS)

simulatorAPMS.Rcheck/simulatorAPMS-Ex.timings:

nameusersystemelapsed
APComEX000
PPIEX0.000.020.02
TSNMatrix0.060.000.06
applyDeformationError0.160.010.17
applyFNErrors0.060.000.06
applyFPErrors0.160.000.16
applyStickyError0.060.000.06
compIndep0.020.000.02
filteredProt0.010.000.01
fullSimEX000
missedProtEX000
missedProtHMSPCI0.020.000.02
recordSticky000
runAPComplex000
runCompIndep0.000.020.01
runSimEX0.000.020.02
runSimulators0.010.000.01
simEX000
simulator0.020.000.02
simulatorD0.250.010.38
simulatorS0.230.020.25
vBaits0.020.000.01
vBaitsEX000
vDeformEX000
vDeformed0.000.010.02
vDeformedEX000
vStickyEX0.000.020.01