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Package 395/444HostnameOS / ArchBUILDCHECKBUILD BIN
simulatorAPMS 1.23.0
Tony Chiang
Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/simulatorAPMS
Last Changed Rev: 50295 / Revision: 53825
Last Changed Date: 2010-10-17 22:57:44 -0700 (Sun, 17 Oct 2010)
lamb1 Linux (openSUSE 11.3) / 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 
petty Mac OS X Snow Leopard (10.6.6) / i386  OK [ OK ] OK 

Summary

Package: simulatorAPMS
Version: 1.23.0
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch simulatorAPMS_1.23.0.tar.gz
StartedAt: 2011-03-17 17:33:54 -0700 (Thu, 17 Mar 2011)
EndedAt: 2011-03-17 17:35:12 -0700 (Thu, 17 Mar 2011)
EllapsedTime: 77.2 seconds
RetCode: 0
Status:  OK 
CheckDir: simulatorAPMS.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/simulatorAPMS.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'simulatorAPMS/DESCRIPTION' ... OK
* this is package 'simulatorAPMS' version '1.23.0'
* 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 installed package size ... 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 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 for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
  'browseVignettes()'. 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
APComEX0.0020.0000.003
PPIEX0.0020.0010.002
TSNMatrix0.0740.0030.076
applyDeformationError0.0760.0010.076
applyFNErrors0.1450.0000.144
applyFPErrors0.0750.0000.076
applyStickyError0.1470.0010.148
compIndep0.0120.0010.013
filteredProt0.0020.0010.003
fullSimEX0.0010.0000.002
missedProtEX0.0020.0010.002
missedProtHMSPCI0.0060.0000.006
recordSticky0.0050.0000.006
runAPComplex000
runCompIndep0.0100.0010.011
runSimEX0.0020.0010.002
runSimulators0.0100.0020.011
simEX0.0020.0010.002
simulator0.0050.0010.006
simulatorD0.2510.0140.325
simulatorS0.2400.0060.247
vBaits0.0030.0000.003
vBaitsEX0.0020.0000.002
vDeformEX0.0050.0010.006
vDeformed0.0040.0010.005
vDeformedEX0.0050.0010.006
vStickyEX0.0050.0010.005