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This page was generated on 2021-10-16 15:51:46 -0400 (Sat, 16 Oct 2021).

CHECK results for ppiData on nebbiolo2

To the developers/maintainers of the ppiData package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 276/404HostnameOS / ArchINSTALLBUILDCHECK
ppiData 0.31.4  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-10-16 09:30:02 -0400 (Sat, 16 Oct 2021)
git_url: https://git.bioconductor.org/packages/ppiData
git_branch: master
git_last_commit: 0be70a2
git_last_commit_date: 2021-09-22 16:53:37 -0400 (Wed, 22 Sep 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

Summary

Package: ppiData
Version: 0.31.4
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ppiData.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ppiData_0.31.4.tar.gz
StartedAt: 2021-10-16 12:28:26 -0400 (Sat, 16 Oct 2021)
EndedAt: 2021-10-16 12:30:46 -0400 (Sat, 16 Oct 2021)
EllapsedTime: 139.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ppiData.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ppiData.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ppiData_0.31.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/ppiData.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘0.31.4’
* 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 ... 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 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 ... OK
* 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     86Kb       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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
collectIntactPPIData 26.670  0.448  27.124
map2Systematic       26.457  0.084  26.542
* 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
See
  ‘/home/biocbuild/bbs-3.14-data-experiment/meat/ppiData.Rcheck/00check.log’
for details.



Installation output

ppiData.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL ppiData
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘ppiData’ ...
** using staged installation
** R
** data
** 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
Cagney2001BPGraph0.0020.0000.002
Gavin2002BPGraph0.0060.0000.006
Gavin2006bPGraph0.0060.0000.006
Hazbun2003BPGraph0.0040.0000.004
Ho2002BPGraph0.0040.0000.004
Ito2001BPGraph0.0070.0000.007
ItoCore2001BPGraph0.0020.0000.002
ItoFull2001BPGraph0.0030.0040.007
Krogan2004BPGraph0.0010.0000.002
Krogan2006BPGraph0.0130.0000.013
Tong2002BPGraph0.0000.0000.001
Uetz2000BPGraph10.0020.0000.002
Uetz2000BPGraph20.0000.0020.001
Zhao2005BPGraph0.0000.0010.000
bpExperimentNames000
collectIntactPPIData26.670 0.44827.124
createBPList3.7980.2324.029
intActPPIData0.0020.0000.001
map2Systematic26.457 0.08426.542
ppipred0.0150.0000.015
sWAC2Sys0.0070.0000.007
stochasticBaits0.0050.0000.005
tableList0.2970.0080.306
twTableAPMS0.0020.0000.003
twTableY2H0.0010.0000.001
viableProteins0.0090.0000.010
y2h0.0110.0000.011
y2hSysGW0.010.000.01