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ppiData 0.1.17
Tony Chiang
Snapshot Date: 2012-09-23 10:15:26 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/ppiData
Last Changed Rev: 2037 / Revision: 2159
Last Changed Date: 2012-03-30 15:20:09 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: ppiData
Version: 0.1.17
Command: rm -rf ppiData.buildbin-libdir && mkdir ppiData.buildbin-libdir && E:\biocbld\bbs-2.10-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ppiData.buildbin-libdir ppiData_0.1.17.tar.gz >ppiData-install.out 2>&1 && E:\biocbld\bbs-2.10-bioc\R\bin\R.exe CMD check --library=ppiData.buildbin-libdir --install="check:ppiData-install.out" --force-multiarch --no-vignettes --timings ppiData_0.1.17.tar.gz && mv ppiData.buildbin-libdir/* ppiData.Rcheck/ && rmdir ppiData.buildbin-libdir
StartedAt: 2012-09-23 13:16:45 -0700 (Sun, 23 Sep 2012)
EndedAt: 2012-09-23 13:19:34 -0700 (Sun, 23 Sep 2012)
EllapsedTime: 168.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ppiData.Rcheck
Warnings: 2

Command output

* using log directory 'E:/biocbld/bbs-2.10-data-experiment/meat/ppiData.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ppiData/DESCRIPTION' ... OK
* this is package 'ppiData' version '0.1.17'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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     85Kb       xz
  sWAC2Sys.rda               35Kb     18Kb       xz
  stochasticBaits.rda        31Kb     20Kb    bzip2
  tableList.rda             2.0Mb    783Kb       xz
  twTableAPMS.rda            24Kb     14Kb    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:
  'ppiStats.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
   'ppiStats.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
  'E:/biocbld/bbs-2.10-data-experiment/meat/ppiData.Rcheck/00check.log'
for details.

ppiData.Rcheck/00install.out:


install for i386

* 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
   'ppiStats.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



install for x64

* installing *source* package 'ppiData' ...
** testing if installed package can be loaded

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


* MD5 sums
packaged installation of 'ppiData' as ppiData_0.1.17.zip

* DONE (ppiData)