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BioC 3.2: CHECK report for ppiStats on zin1

This page was generated on 2015-08-24 10:47:11 -0700 (Mon, 24 Aug 2015).

Package 767/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ppiStats 1.35.0
Bioconductor Package Maintainer
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ppiStats
Last Changed Rev: 102594 / Revision: 107696
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ppiStats
Version: 1.35.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ppiStats_1.35.0.tar.gz
StartedAt: 2015-08-24 02:38:26 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 02:40:34 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 128.9 seconds
RetCode: 0
Status:  OK 
CheckDir: ppiStats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ppiStats_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ppiStats.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ppiStats/DESCRIPTION’ ... OK
* this is package ‘ppiStats’ version ‘1.35.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ppiStats’ can be installed ... [12s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘ScISI’ ‘ppiData’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/19s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/ppiStats.Rcheck/00check.log’
for details.


ppiStats.Rcheck/00install.out:

* installing *source* package ‘ppiStats’ ...
** R
** inst
** preparing package for lazy loading
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
* DONE (ppiStats)

ppiStats.Rcheck/ppiStats-Ex.timings:

nameusersystemelapsed
assessSymmetry3.4230.1883.609
bpMatrix0.3970.2120.609
calcInOutDegStats0.0030.0000.002
createSummaryTables0.1570.0120.168
degreeEstimates0.0020.0000.002
estErrProbMethodOfMoments0.0010.0000.001
estimateCCMErrorRates1.4510.0481.498
estimatePPIErrorRates3.7580.1043.859
genBPGraph0.0860.0000.086
idProteinErrorType2.3470.1122.456
idProteinType0.0370.0040.041
inOutScatterCharts0.0010.0000.000
nullDistDoublyTestedEdges0.3530.0160.369
twPERM0.0010.0000.001
viabilityCharts0.2320.0280.260