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BioC experimental data: CHECK report for ppiData on moscato1

This page was generated on 2016-05-28 20:31:02 -0700 (Sat, 28 May 2016).

Package 206/292HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ppiData 0.11.0
Bioconductor Package Maintainer
Snapshot Date: 2016-05-28 09:20:19 -0700 (Sat, 28 May 2016)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/ppiData
Last Changed Rev: 3763 / Revision: 3781
Last Changed Date: 2016-05-03 14:48:02 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ WARNINGS ] OK 

Summary

Package: ppiData
Version: 0.11.0
Command: rm -rf ppiData.buildbin-libdir ppiData.Rcheck && mkdir ppiData.buildbin-libdir ppiData.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ppiData.buildbin-libdir ppiData_0.11.0.tar.gz >ppiData.Rcheck\00install.out 2>&1 && cp ppiData.Rcheck\00install.out ppiData-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ppiData.buildbin-libdir --install="check:ppiData-install.out" --force-multiarch --no-vignettes --timings ppiData_0.11.0.tar.gz
StartedAt: 2016-05-28 15:52:54 -0700 (Sat, 28 May 2016)
EndedAt: 2016-05-28 15:57:15 -0700 (Sat, 28 May 2016)
EllapsedTime: 261.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ppiData.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ppiData.buildbin-libdir ppiData.Rcheck && mkdir ppiData.buildbin-libdir ppiData.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ppiData.buildbin-libdir ppiData_0.11.0.tar.gz >ppiData.Rcheck\00install.out 2>&1 && cp ppiData.Rcheck\00install.out ppiData-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ppiData.buildbin-libdir --install="check:ppiData-install.out" --force-multiarch --no-vignettes --timings ppiData_0.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-data-experiment/meat/ppiData.Rcheck'
* using R version 3.3.0 (2016-05-03)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ppiData/DESCRIPTION' ... OK
* this is package 'ppiData' version '0.11.0'
* 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 whether package 'ppiData' can be installed ... 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
* 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 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 'recover'
collectIntactPPIData: no visible global function definition for 'data'
collectIntactPPIData: no visible binding for global variable
  'tableList'
collectIntactPPIData: no visible binding for global variable 'sWAC2Sys'
collectIntactPPIData : <anonymous>: no visible binding for global
  variable 'tableList'
collectIntactPPIData : <anonymous> : <anonymous>: no visible binding
  for global variable 'tableList'
intAct2Sys: no visible binding for global variable 'recover'
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:
  data org.Sc.sgdALIAS org.Sc.sgdCOMMON2ORF org.Sc.sgdREJECTORF recover
  sWAC2Sys tableList
Consider adding
  importFrom("utils", "data", "recover")
to your NAMESPACE file.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
collectIntactPPIData 10.18      0   10.17
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
collectIntactPPIData 9.37   0.05    9.43
* 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
  'D:/biocbld/bbs-3.4-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
** testing if installed package can be loaded

install for x64

* installing *source* package 'ppiData' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ppiData' as ppiData_0.11.0.zip
* DONE (ppiData)

ppiData.Rcheck/examples_i386/ppiData-Ex.timings:

nameusersystemelapsed
Cagney2001BPGraph0.030.000.03
Gavin2002BPGraph000
Gavin2006bPGraph0.010.000.38
Hazbun2003BPGraph000
Ho2002BPGraph0.020.000.01
Ito2001BPGraph000
ItoCore2001BPGraph0.010.000.02
ItoFull2001BPGraph000
Krogan2004BPGraph000
Krogan2006BPGraph000
Tong2002BPGraph0.000.010.02
Uetz2000BPGraph1000
Uetz2000BPGraph2000
Zhao2005BPGraph0.000.020.02
bpExperimentNames000
collectIntactPPIData10.18 0.0010.17
createBPList0.010.000.01
intActPPIData000
map2Systematic0.020.000.02
ppipred000
sWAC2Sys000
stochasticBaits0.000.010.01
tableList000
twTableAPMS000
twTableY2H0.010.000.02
viableProteins0.020.000.01
y2h000
y2hSysGW0.010.000.02

ppiData.Rcheck/examples_x64/ppiData-Ex.timings:

nameusersystemelapsed
Cagney2001BPGraph0.030.000.03
Gavin2002BPGraph000
Gavin2006bPGraph0.000.020.01
Hazbun2003BPGraph000
Ho2002BPGraph000
Ito2001BPGraph0.000.010.02
ItoCore2001BPGraph000
ItoFull2001BPGraph000
Krogan2004BPGraph0.020.000.01
Krogan2006BPGraph000
Tong2002BPGraph000
Uetz2000BPGraph1000
Uetz2000BPGraph2000
Zhao2005BPGraph000
bpExperimentNames0.000.010.01
collectIntactPPIData9.370.059.43
createBPList0.030.000.43
intActPPIData000
map2Systematic000
ppipred000
sWAC2Sys0.000.020.02
stochasticBaits000
tableList000
twTableAPMS000
twTableY2H000
viableProteins0.000.010.02
y2h000
y2hSysGW0.020.000.01