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CHECK report for ppiData on riesling1

This page was generated on 2021-01-14 15:59:10 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE ppiData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 267/385HostnameOS / ArchINSTALLBUILDCHECK
ppiData 0.29.0
Bioconductor Package Maintainer
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/ppiData
Branch: master
Last Commit: b2d6691
Last Changed Date: 2020-10-27 09:46:51 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ WARNINGS ]

Summary

Package: ppiData
Version: 0.29.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ppiData.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ppiData_0.29.0.tar.gz
StartedAt: 2021-01-14 11:33:50 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:35:17 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 86.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ppiData.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ppiData.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ppiData_0.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/ppiData.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* 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 '0.29.0'
* 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     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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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:/biocbuild/bbs-3.13-data-experiment/meat/ppiData.Rcheck/00check.log'
for details.



Installation output

ppiData.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/ppiData_0.29.0.tar.gz && rm -rf ppiData.buildbin-libdir && mkdir ppiData.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ppiData.buildbin-libdir ppiData_0.29.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ppiData_0.29.0.zip && rm ppiData_0.29.0.tar.gz ppiData_0.29.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2868k  100 2868k    0     0  28.2M      0 --:--:-- --:--:-- --:--:-- 28.2M

install for i386

* 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
  converting help for package 'ppiData'
    finding HTML links ... done
    Cagney2001BPGraph                       html  
REDIRECT:topic	 Cagney2001BPGraph -> Cagney2001BPGraph.html [ SUCCESS ]
    Gavin2002BPGraph                        html  
REDIRECT:topic	 Gavin2002BPGraph -> Gavin2002BPGraph.html [ SUCCESS ]
    Gavin2006bPGraph                        html  
REDIRECT:topic	 Gavin2006BPGraph -> Gavin2006bPGraph.html [ SUCCESS ]
    Hazbun2003BPGraph                       html  
REDIRECT:topic	 Hazbun2003BPGraph -> Hazbun2003BPGraph.html [ SUCCESS ]
    Ho2002BPGraph                           html  
REDIRECT:topic	 Ho2002BPGraph -> Ho2002BPGraph.html [ SUCCESS ]
    Ito2001BPGraph                          html  
REDIRECT:topic	 Ito2001BPGraph -> Ito2001BPGraph.html [ SUCCESS ]
    ItoCore2001BPGraph                      html  
REDIRECT:topic	 ItoCore2001BPGraph -> ItoCore2001BPGraph.html [ SUCCESS ]
    ItoFull2001BPGraph                      html  
REDIRECT:topic	 ItoFull2001BPGraph -> ItoFull2001BPGraph.html [ SUCCESS ]
    Krogan2004BPGraph                       html  
REDIRECT:topic	 Krogan2004BPGraph -> Krogan2004BPGraph.html [ SUCCESS ]
    Krogan2006BPGraph                       html  
REDIRECT:topic	 Krogan2006BPGraph -> Krogan2006BPGraph.html [ SUCCESS ]
    Tong2002BPGraph                         html  
REDIRECT:topic	 Tong2002BPGraph -> Tong2002BPGraph.html [ SUCCESS ]
    Uetz2000BPGraph1                        html  
REDIRECT:topic	 Uetz2000BPGraph1 -> Uetz2000BPGraph1.html [ SUCCESS ]
    Uetz2000BPGraph2                        html  
REDIRECT:topic	 Uetz2000BPGraph2 -> Uetz2000BPGraph2.html [ SUCCESS ]
    Zhao2005BPGraph                         html  
REDIRECT:topic	 Zhao2005BPGraph -> Zhao2005BPGraph.html [ SUCCESS ]
    bpExperimentNames                       html  
REDIRECT:topic	 bpExperimentNames -> bpExperimentNames.html [ SUCCESS ]
    collectIntactPPIData                    html  
REDIRECT:topic	 collectIntactPPIData -> collectIntactPPIData.html [ SUCCESS ]
    createBPList                            html  
REDIRECT:topic	 createBPList -> createBPList.html [ SUCCESS ]
    intAct2Sys                              html  
REDIRECT:topic	 intAct2Sys -> intAct2Sys.html [ SUCCESS ]
    intActPPIData                           html  
REDIRECT:topic	 intActPPIData -> intActPPIData.html [ SUCCESS ]
    map2Systematic                          html  
REDIRECT:topic	 map2Systematic -> map2Systematic.html [ SUCCESS ]
    map2Systematic2                         html  
REDIRECT:topic	 map2Systematic2 -> map2Systematic2.html [ SUCCESS ]
    ppipred                                 html  
REDIRECT:topic	 ppipred -> ppipred.html [ SUCCESS ]
    sWAC2Sys                                html  
REDIRECT:topic	 sWAC2Sys -> sWAC2Sys.html [ SUCCESS ]
    stochasticBaits                         html  
REDIRECT:topic	 stochasticBaits -> stochasticBaits.html [ SUCCESS ]
    tableList                               html  
REDIRECT:topic	 tableList -> tableList.html [ SUCCESS ]
    twTableAPMS                             html  
REDIRECT:topic	 twTableAPMS -> twTableAPMS.html [ SUCCESS ]
    twTableY2H                              html  
REDIRECT:topic	 twTableY2H -> twTableY2H.html [ SUCCESS ]
    viableProteins                          html  
REDIRECT:topic	 viablePrey -> viableProteins.html [ SUCCESS ]
REDIRECT:topic	 viableBaits -> viableProteins.html [ SUCCESS ]
REDIRECT:file	 viableProteins.html -> viableProteins.html [ SUCCESS ]
    y2h                                     html  
REDIRECT:topic	 y2h -> y2h.html [ SUCCESS ]
    y2hSysGW                                html  
REDIRECT:topic	 y2hSysGW -> y2hSysGW.html [ SUCCESS ]
** 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

install for x64

* installing *source* package 'ppiData' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ppiData' as ppiData_0.29.0.zip
* DONE (ppiData)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'ppiData' successfully unpacked and MD5 sums checked

Tests output


Example timings

ppiData.Rcheck/examples_i386/ppiData-Ex.timings

nameusersystemelapsed
Cagney2001BPGraph0.020.000.01
Gavin2002BPGraph000
Gavin2006bPGraph000
Hazbun2003BPGraph000
Ho2002BPGraph000
Ito2001BPGraph000
ItoCore2001BPGraph000
ItoFull2001BPGraph000
Krogan2004BPGraph0.010.000.02
Krogan2006BPGraph000
Tong2002BPGraph000
Uetz2000BPGraph10.020.000.01
Uetz2000BPGraph2000
Zhao2005BPGraph000
bpExperimentNames000
collectIntactPPIData4.250.004.25
createBPList0.140.000.14
intActPPIData000
map2Systematic000
ppipred000
sWAC2Sys000
stochasticBaits000
tableList000
twTableAPMS000
twTableY2H0.000.020.02
viableProteins0.010.000.01
y2h000
y2hSysGW0.020.000.02

ppiData.Rcheck/examples_x64/ppiData-Ex.timings

nameusersystemelapsed
Cagney2001BPGraph000
Gavin2002BPGraph000
Gavin2006bPGraph000
Hazbun2003BPGraph000
Ho2002BPGraph0.000.020.02
Ito2001BPGraph000
ItoCore2001BPGraph000
ItoFull2001BPGraph000
Krogan2004BPGraph000
Krogan2006BPGraph000
Tong2002BPGraph000
Uetz2000BPGraph1000
Uetz2000BPGraph2000
Zhao2005BPGraph000
bpExperimentNames000
collectIntactPPIData4.310.094.40
createBPList0.160.020.17
intActPPIData000
map2Systematic0.010.000.02
ppipred000
sWAC2Sys0.000.020.01
stochasticBaits000
tableList0.020.000.02
twTableAPMS000
twTableY2H000
viableProteins000
y2h0.000.010.02
y2hSysGW000