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BioC experimental data: CHECK report for ppiData on perceval

This page was generated on 2015-04-08 17:41:22 -0700 (Wed, 08 Apr 2015).

Package 168/219HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ppiData 0.3.1
Bioconductor Package Maintainer
Snapshot Date: 2015-04-08 06:15:26 -0700 (Wed, 08 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_0/experiment/pkgs/ppiData
Last Changed Rev: 3075 / Revision: 3266
Last Changed Date: 2014-10-13 14:52:40 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ WARNINGS ] OK 

Summary

Package: ppiData
Version: 0.3.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ppiData_0.3.1.tar.gz
StartedAt: 2015-04-08 10:26:53 -0700 (Wed, 08 Apr 2015)
EndedAt: 2015-04-08 10:30:37 -0700 (Wed, 08 Apr 2015)
EllapsedTime: 224.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ppiData.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ppiData_0.3.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-data-experiment/meat/ppiData.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ppiData/DESCRIPTION’ ... OK
* this is package ‘ppiData’ version ‘0.3.1’
* 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 ‘ppiData’ can be installed ... [18s/19s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
Package in Depends field not imported from: ‘graph’
  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 ... NOTE
collectIntactPPIData: no visible binding for global variable
  ‘tableList’
collectIntactPPIData : <anonymous>: no visible binding for global
  variable ‘tableList’
collectIntactPPIData : <anonymous> : <anonymous>: no visible binding
  for global variable ‘tableList’
collectIntactPPIData: no visible binding for global variable ‘sWAC2Sys’
map2Systematic: no visible binding for global variable
  ‘org.Sc.sgdCOMMON2ORF’
map2Systematic: no visible binding for global variable
  ‘org.Sc.sgdALIAS’
map2Systematic: no visible binding for global variable
  ‘org.Sc.sgdREJECTORF’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING
  Warning: large data file saved inefficiently:
               size ASCII compress
  ppipred.rda 896Kb FALSE     none
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                         old_size new_size compress
  Gavin2002BPGraph.rda       17Kb     10Kb       xz
  Gavin2006BPGraph.rda       50Kb     27Kb    bzip2
  Hazbun2003BPGraph.rda      20Kb      8Kb       xz
  Ho2002BPGraph.rda          19Kb      9Kb       xz
  Ito2001BPGraph.rda         33Kb     15Kb       xz
  ItoFull2001BPGraph.rda     33Kb     15Kb       xz
  Krogan2006BPGraph.rda     151Kb     84Kb    bzip2
  intActPPIData.rda         114Kb     63Kb       xz
  ppipred.rda               896Kb     85Kb       xz
  sWAC2Sys.rda               35Kb     18Kb       xz
  stochasticBaits.rda        31Kb     20Kb    bzip2
  tableList.rda             2.0Mb    783Kb       xz
  twTableAPMS.rda            24Kb     15Kb    bzip2
  viableBaits.rda            22Kb     14Kb       xz
  viablePrey.rda             47Kb     30Kb    bzip2
  y2h.rda                    76Kb     47Kb    bzip2
  y2hSysGW.rda               71Kb     44Kb    bzip2
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [36s/36s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
collectIntactPPIData 21.57  7.373  29.087
* 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

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-data-experiment/meat/ppiData.Rcheck/00check.log’
for details.

ppiData.Rcheck/00install.out:

* installing *source* package ‘ppiData’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ppiData)

ppiData.Rcheck/ppiData-Ex.timings:

nameusersystemelapsed
Cagney2001BPGraph0.0040.0010.005
Gavin2002BPGraph0.0030.0010.003
Gavin2006bPGraph0.0020.0010.003
Hazbun2003BPGraph0.0020.0000.002
Ho2002BPGraph0.0020.0000.002
Ito2001BPGraph0.0020.0000.002
ItoCore2001BPGraph0.0010.0000.002
ItoFull2001BPGraph0.0020.0000.002
Krogan2004BPGraph0.0020.0000.003
Krogan2006BPGraph0.0020.0010.003
Tong2002BPGraph0.0020.0010.002
Uetz2000BPGraph10.0030.0010.003
Uetz2000BPGraph20.0030.0010.004
Zhao2005BPGraph0.0020.0010.002
bpExperimentNames0.0020.0070.010
collectIntactPPIData21.570 7.37329.087
createBPList0.0150.0010.015
intActPPIData0.0040.0020.024
map2Systematic0.0060.0010.006
ppipred0.0020.0000.002
sWAC2Sys0.0020.0000.003
stochasticBaits0.0060.0010.006
tableList0.0020.0000.002
twTableAPMS0.0010.0010.003
twTableY2H0.0020.0000.002
viableProteins0.0110.0020.013
y2h0.0010.0010.002
y2hSysGW0.0130.0010.014