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CHECK report for ppiData on malbec1

This page was generated on 2020-04-14 17:46:15 -0400 (Tue, 14 Apr 2020).

Package 271/384HostnameOS / ArchINSTALLBUILDCHECK
ppiData 0.24.0
Bioconductor Package Maintainer
Snapshot Date: 2020-04-14 09:30:11 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/ppiData
Branch: RELEASE_3_10
Last Commit: cf373d5
Last Changed Date: 2019-10-29 13:29:34 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository

Summary

Package: ppiData
Version: 0.24.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ppiData.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ppiData_0.24.0.tar.gz
StartedAt: 2020-04-14 12:54:41 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 12:56:00 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 78.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ppiData.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ppiData.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ppiData_0.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-data-experiment/meat/ppiData.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ppiData/DESCRIPTION’ ... OK
* this is package ‘ppiData’ version ‘0.24.0’
* 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 ... 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 ‘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     15Kb    bzip2
  viableBaits.rda            22Kb     14Kb       xz
  viablePrey.rda             47Kb     30Kb    bzip2
  y2h.rda                    76Kb     47Kb    bzip2
  y2hSysGW.rda               71Kb     44Kb    bzip2
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
collectIntactPPIData 6.244  0.028   6.276
* 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
  ‘/home/biocbuild/bbs-3.10-data-experiment/meat/ppiData.Rcheck/00check.log’
for details.



Installation output

ppiData.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL ppiData
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘ppiData’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ppiData)

Tests output


Example timings

ppiData.Rcheck/ppiData-Ex.timings

nameusersystemelapsed
Cagney2001BPGraph0.0080.0040.013
Gavin2002BPGraph0.0000.0000.001
Gavin2006bPGraph0.0040.0000.001
Hazbun2003BPGraph0.0000.0000.001
Ho2002BPGraph0.0000.0000.001
Ito2001BPGraph0.0040.0000.000
ItoCore2001BPGraph0.0000.0000.001
ItoFull2001BPGraph0.0000.0000.001
Krogan2004BPGraph0.0040.0000.001
Krogan2006BPGraph0.0000.0000.001
Tong2002BPGraph0.0000.0000.001
Uetz2000BPGraph10.0040.0000.001
Uetz2000BPGraph2000
Zhao2005BPGraph0.0000.0000.001
bpExperimentNames0.0040.0000.003
collectIntactPPIData6.2440.0286.276
createBPList0.2040.0000.204
intActPPIData0.0000.0000.001
map2Systematic0.0000.0000.002
ppipred0.0000.0000.001
sWAC2Sys0.0000.0000.001
stochasticBaits0.0040.0000.003
tableList000
twTableAPMS0.0040.0000.001
twTableY2H0.0000.0000.001
viableProteins0.0040.0000.006
y2h000
y2hSysGW0.0000.0040.006