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ppiData 0.1.18
Tony Chiang
Snapshot Date: 2013-03-24 09:15:27 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/ppiData
Last Changed Rev: 2237 / Revision: 2286
Last Changed Date: 2013-03-11 21:43:46 -0700 (Mon, 11 Mar 2013)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ WARNINGS ] OK 

Summary

Package: ppiData
Version: 0.1.18
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ppiData_0.1.18.tar.gz
StartedAt: 2013-03-24 12:24:56 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 12:30:38 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 341.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ppiData.Rcheck
Warnings: 2

Command output

* using log directory '/Users/biocbuild/bbs-2.11-data-experiment/meat/ppiData.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ppiData/DESCRIPTION' ... OK
* this is package 'ppiData' version '0.1.18'
* 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 whether package 'ppiData' 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 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 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 ... NOTE
File 'ppiData/R/zzz.R':
  .onLoad has wrong argument list 'libname, pkgname, where'

Package startup functions should have two arguments with names starting
  with 'lib' and 'pkg', respectively.
See section 'Good practice' in ?.onAttach.

* checking Rd files ... NOTE
prepare_Rd: intAct2Sys.Rd:33-35: Dropping empty section \examples
prepare_Rd: twTableAPMS.Rd:22-23: Dropping empty section \details
prepare_Rd: twTableAPMS.Rd:24-26: Dropping empty section \source
prepare_Rd: twTableAPMS.Rd:27-28: Dropping empty section \references
prepare_Rd: twTableY2H.Rd:22-23: Dropping empty section \details
prepare_Rd: twTableY2H.Rd:24-26: Dropping empty section \source
prepare_Rd: twTableY2H.Rd:27-28: 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 ... WARNING
  Warning: large data file(s) 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     86Kb       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 installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'ppiData.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
collectIntactPPIData 14.819  5.965  20.965
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
   'ppiData.Rnw'

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings.
NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.11-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
   'ppiData.Rnw' 
** testing if installed package can be loaded

*** Deprecation warning ***:
The package 'ppiData' is deprecated and will not be supported after Bioconductor release 2.11



* DONE (ppiData)

ppiData.Rcheck/ppiData-Ex.timings:

nameusersystemelapsed
Cagney2001BPGraph0.0030.0010.004
Gavin2002BPGraph0.0010.0010.002
Gavin2006bPGraph0.0010.0010.002
Hazbun2003BPGraph0.0010.0000.001
Ho2002BPGraph0.0030.0000.004
Ito2001BPGraph0.0010.0010.002
ItoCore2001BPGraph0.0010.0000.002
ItoFull2001BPGraph0.0010.0010.001
Krogan2004BPGraph0.0010.0000.001
Krogan2006BPGraph0.0010.0010.001
Tong2002BPGraph0.0010.0000.001
Uetz2000BPGraph10.0010.0010.002
Uetz2000BPGraph20.0010.0000.002
Zhao2005BPGraph0.0010.0010.002
bpExperimentNames0.0030.0080.012
collectIntactPPIData14.819 5.96520.965
createBPList0.0130.0010.015
intActPPIData0.0030.0010.003
map2Systematic0.0020.0000.003
ppipred0.0010.0000.002
sWAC2Sys0.0010.0010.002
stochasticBaits0.0060.0010.007
tableList0.0010.0000.001
twTableAPMS0.0010.0000.002
twTableY2H0.0010.0010.002
viableProteins0.0100.0020.013
y2h0.0010.0000.003
y2hSysGW0.0110.0010.013