Back to Build/check report for BioC 3.14 experimental data
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2022-01-19 14:50:24 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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 278/408HostnameOS / ArchINSTALLBUILDCHECK
ppiData 0.32.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-01-19 07:30:01 -0500 (Wed, 19 Jan 2022)
git_url: https://git.bioconductor.org/packages/ppiData
git_branch: RELEASE_3_14
git_last_commit: 31334ee
git_last_commit_date: 2021-10-26 11:40:52 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

Summary

Package: ppiData
Version: 0.32.0
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_0.32.0.tar.gz
StartedAt: 2022-01-19 11:41:26 -0500 (Wed, 19 Jan 2022)
EndedAt: 2022-01-19 11:43:42 -0500 (Wed, 19 Jan 2022)
EllapsedTime: 136.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ppiData.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_0.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/ppiData.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘0.32.0’
* 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 ... 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     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 (user + system) or elapsed time > 5s
                       user system elapsed
map2Systematic       26.427  0.180  26.608
collectIntactPPIData 24.941  0.659  25.601
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL ppiData
###
##############################################################################
##############################################################################


* 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
Cagney2001BPGraph0.0020.0000.001
Gavin2002BPGraph0.0030.0000.004
Gavin2006bPGraph0.0060.0000.006
Hazbun2003BPGraph0.0040.0000.005
Ho2002BPGraph0.0030.0000.004
Ito2001BPGraph0.0060.0000.007
ItoCore2001BPGraph0.0020.0000.002
ItoFull2001BPGraph0.0070.0000.006
Krogan2004BPGraph0.0010.0000.002
Krogan2006BPGraph0.0120.0000.013
Tong2002BPGraph0.0010.0000.001
Uetz2000BPGraph10.0020.0000.002
Uetz2000BPGraph20.0010.0000.002
Zhao2005BPGraph0.0000.0000.001
bpExperimentNames0.0000.0010.001
collectIntactPPIData24.941 0.65925.601
createBPList3.1020.0763.180
intActPPIData0.0010.0000.001
map2Systematic26.427 0.18026.608
ppipred0.0150.0000.016
sWAC2Sys0.0070.0000.007
stochasticBaits0.0050.0000.005
tableList0.3090.0000.309
twTableAPMS0.0020.0000.002
twTableY2H0.0010.0000.001
viableProteins0.0110.0000.011
y2h0.0110.0000.011
y2hSysGW0.010.000.01