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Package 414/464HostnameOS / ArchBUILDCHECKBUILD BIN
simulatorAPMS 1.25.0
Tony Chiang
Snapshot Date: 2011-04-20 07:21:46 -0700 (Wed, 20 Apr 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/simulatorAPMS
Last Changed Rev: 54802 / Revision: 54983
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / 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 

Summary

Package: simulatorAPMS
Version: 1.25.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings simulatorAPMS_1.25.0.tar.gz
StartedAt: 2011-04-20 16:02:02 -0700 (Wed, 20 Apr 2011)
EndedAt: 2011-04-20 16:03:25 -0700 (Wed, 20 Apr 2011)
EllapsedTime: 82.9 seconds
RetCode: 0
Status:  OK  
CheckDir: simulatorAPMS.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/simulatorAPMS.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'simulatorAPMS/DESCRIPTION' ... OK
* this is package 'simulatorAPMS' version '1.25.0'
* 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 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 for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... 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 ...
*** tangling vignette sources ...
   'simulatorAPMS.Rnw' 
** 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
APComEX0.000.020.01
PPIEX000
TSNMatrix0.090.000.10
applyDeformationError0.100.000.09
applyFNErrors0.100.000.09
applyFPErrors0.180.000.19
applyStickyError0.100.000.09
compIndep0.000.000.02
filteredProt0.000.020.01
fullSimEX000
missedProtEX000
missedProtHMSPCI0.010.000.02
recordSticky0.020.000.01
runAPComplex000
runCompIndep0.000.010.02
runSimEX000
runSimulators0.010.000.02
simEX000
simulator0.020.000.01
simulatorD0.310.000.39
simulatorS0.330.000.33
vBaits000
vBaitsEX0.000.020.02
vDeformEX000
vDeformed0.020.000.01
vDeformedEX0.010.000.02
vStickyEX0.000.000.03