BioC experimental data: CHECK report for ppiData on morelia

Package: ppiData

Version: 0.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ppiData_0.9.0.tar.gz

StartedAt: 2015-11-25 11:02:11 -0800 (Wed, 25 Nov 2015)

EndedAt: 2015-11-25 11:04:22 -0800 (Wed, 25 Nov 2015)

EllapsedTime: 130.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ppiData.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ppiData_0.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/ppiData.Rcheck’
* using R Under development (unstable) (2015-11-08 r69614)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ppiData/DESCRIPTION’ ... OK
* this is package ‘ppiData’ version ‘0.9.0’
* 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 ‘ppiData’ can be installed ... [10s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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’
Undefined global functions or variables:
  org.Sc.sgdALIAS org.Sc.sgdCOMMON2ORF org.Sc.sgdREJECTORF sWAC2Sys
  tableList
* 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     14Kb    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 ... [20s/20s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
collectIntactPPIData 12.889  3.664  16.576
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/ppiData.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
Cagney2001BPGraph	0.021	0.002	0.023
Gavin2002BPGraph	0.002	0.000	0.002
Gavin2006bPGraph	0.001	0.001	0.002
Hazbun2003BPGraph	0.002	0.000	0.002
Ho2002BPGraph	0.001	0.001	0.001
Ito2001BPGraph	0.106	0.000	0.107
ItoCore2001BPGraph	0.002	0.001	0.002
ItoFull2001BPGraph	0.002	0.000	0.002
Krogan2004BPGraph	0.001	0.000	0.001
Krogan2006BPGraph	0.002	0.000	0.002
Tong2002BPGraph	0.002	0.001	0.002
Uetz2000BPGraph1	0.002	0.000	0.002
Uetz2000BPGraph2	0.002	0.001	0.002
Zhao2005BPGraph	0.002	0.000	0.002
bpExperimentNames	0.002	0.004	0.005
collectIntactPPIData	12.889	3.664	16.576
createBPList	0.013	0.001	0.013
intActPPIData	0.003	0.001	0.029
map2Systematic	0.004	0.000	0.005
ppipred	0.001	0.001	0.002
sWAC2Sys	0.001	0.000	0.002
stochasticBaits	0.005	0.000	0.005
tableList	0.002	0.001	0.002
twTableAPMS	0.001	0.001	0.002
twTableY2H	0.001	0.000	0.002
viableProteins	0.010	0.001	0.011
y2h	0.002	0.001	0.002
y2hSysGW	0.010	0.001	0.011