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CHECK report for simpIntLists on malbec2

This page was generated on 2021-01-21 16:01:21 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE simpIntLists PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 334/386HostnameOS / ArchINSTALLBUILDCHECK
simpIntLists 1.27.0
Kircicegi Korkmaz
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/simpIntLists
Branch: master
Last Commit: 4013f06
Last Changed Date: 2020-10-27 09:52:37 -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: simpIntLists
Version: 1.27.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:simpIntLists.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings simpIntLists_1.27.0.tar.gz
StartedAt: 2021-01-21 12:47:15 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 12:48:10 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 54.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: simpIntLists.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:simpIntLists.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings simpIntLists_1.27.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/simpIntLists.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘simpIntLists/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘simpIntLists’ version ‘1.27.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘simpIntLists’ 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 ... NOTE
findInteractionList: no visible global function definition for ‘data’
findInteractionList: no visible binding for global variable
  ‘ArabidopsisBioGRIDInteractionEntrezId’
findInteractionList: no visible binding for global variable
  ‘ArabidopsisBioGRIDInteractionOfficial’
findInteractionList: no visible binding for global variable
  ‘ArabidopsisBioGRIDInteractionUniqueId’
findInteractionList: no visible binding for global variable
  ‘C.elegansBioGRIDInteractionEntrezId’
findInteractionList: no visible binding for global variable
  ‘C.elegansBioGRIDInteractionOfficial’
findInteractionList: no visible binding for global variable
  ‘C.elegansBioGRIDInteractionUniqueId’
findInteractionList: no visible binding for global variable
  ‘FruitFlyBioGRIDInteractionEntrezId’
findInteractionList: no visible binding for global variable
  ‘FruitFlyBioGRIDInteractionOfficial’
findInteractionList: no visible binding for global variable
  ‘FruitFlyBioGRIDInteractionUniqueId’
findInteractionList: no visible binding for global variable
  ‘HumanBioGRIDInteractionEntrezId’
findInteractionList: no visible binding for global variable
  ‘HumanBioGRIDInteractionOfficial’
findInteractionList: no visible binding for global variable
  ‘HumanBioGRIDInteractionUniqueId’
findInteractionList: no visible binding for global variable
  ‘MouseBioGRIDInteractionEntrezId’
findInteractionList: no visible binding for global variable
  ‘MouseBioGRIDInteractionOfficial’
findInteractionList: no visible binding for global variable
  ‘MouseBioGRIDInteractionUniqueId’
findInteractionList: no visible binding for global variable
  ‘YeastBioGRIDInteractionEntrezId’
findInteractionList: no visible binding for global variable
  ‘YeastBioGRIDInteractionOfficial’
findInteractionList: no visible binding for global variable
  ‘YeastBioGRIDInteractionUniqueId’
findInteractionList: no visible binding for global variable
  ‘S.pombeBioGRIDInteractionEntrezId’
findInteractionList: no visible binding for global variable
  ‘S.pombeBioGRIDInteractionOfficial’
findInteractionList: no visible binding for global variable
  ‘S.pombeBioGRIDInteractionUniqueId’
Undefined global functions or variables:
  ArabidopsisBioGRIDInteractionEntrezId
  ArabidopsisBioGRIDInteractionOfficial
  ArabidopsisBioGRIDInteractionUniqueId
  C.elegansBioGRIDInteractionEntrezId
  C.elegansBioGRIDInteractionOfficial
  C.elegansBioGRIDInteractionUniqueId
  FruitFlyBioGRIDInteractionEntrezId FruitFlyBioGRIDInteractionOfficial
  FruitFlyBioGRIDInteractionUniqueId HumanBioGRIDInteractionEntrezId
  HumanBioGRIDInteractionOfficial HumanBioGRIDInteractionUniqueId
  MouseBioGRIDInteractionEntrezId MouseBioGRIDInteractionOfficial
  MouseBioGRIDInteractionUniqueId S.pombeBioGRIDInteractionEntrezId
  S.pombeBioGRIDInteractionOfficial S.pombeBioGRIDInteractionUniqueId
  YeastBioGRIDInteractionEntrezId YeastBioGRIDInteractionOfficial
  YeastBioGRIDInteractionUniqueId data
Consider adding
  importFrom("utils", "data")
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
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                                            old_size new_size compress
  ArabidopsisBioGRIDInteractionEntrezId.rda     26Kb     19Kb    bzip2
  ArabidopsisBioGRIDInteractionOfficial.rda     34Kb     22Kb    bzip2
  ArabidopsisBioGRIDInteractionUniqueId.rda     32Kb     21Kb    bzip2
  C.ElegansBioGRIDInteractionEntrezId.rda       44Kb     32Kb    bzip2
  C.ElegansBioGRIDInteractionOfficial.rda       65Kb     38Kb    bzip2
  C.ElegansBioGRIDInteractionUniqueId.rda       64Kb     36Kb    bzip2
  FruitFlyBioGRIDInteractionEntrezId.rda       165Kb    112Kb    bzip2
  FruitFlyBioGRIDInteractionOfficial.rda       252Kb    139Kb    bzip2
  FruitFlyBioGRIDInteractionUniqueId.rda       208Kb    121Kb    bzip2
  HumanBioGRIDInteractionEntrezId.rda          222Kb    157Kb    bzip2
  HumanBioGRIDInteractionOfficial.rda          318Kb    190Kb    bzip2
  HumanBioGRIDInteractionUniqueId.rda           29Kb     18Kb    bzip2
  MouseBioGRIDInteractionEntrezId.rda           25Kb     20Kb    bzip2
  MouseBioGRIDInteractionOfficial.rda           34Kb     23Kb    bzip2
  S.PombeBioGRIDInteractionEntrezId.rda         55Kb     37Kb    bzip2
  S.PombeBioGRIDInteractionOfficial.rda         76Kb     44Kb    bzip2
  S.PombeBioGRIDInteractionUniqueId.rda         89Kb     43Kb    bzip2
  YeastBioGRIDInteractionEntrezId.rda          685Kb    469Kb    bzip2
  YeastBioGRIDInteractionOfficial.rda          958Kb    572Kb    bzip2
  YeastBioGRIDInteractionUniqueId.rda          903Kb    533Kb    bzip2
* checking files in ‘vignettes’ ... OK
* checking examples ... 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/simpIntLists.Rcheck/00check.log’
for details.



Installation output

simpIntLists.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL simpIntLists
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘simpIntLists’ ...
** using staged installation
** R
** data
** 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 (simpIntLists)

Tests output


Example timings

simpIntLists.Rcheck/simpIntLists-Ex.timings

nameusersystemelapsed
ArabidopsisBioGRIDInteractionEntrezId0.0310.0440.076
ArabidopsisBioGRIDInteractionOfficial0.0490.0230.073
ArabidopsisBioGRIDInteractionUniqueId0.0510.0230.076
C.ElegansBioGRIDInteractionEntrezId0.0650.0440.110
C.ElegansBioGRIDInteractionOfficial0.0540.0790.133
C.ElegansBioGRIDInteractionUniqueId0.0970.0450.141
FruitFlyBioGRIDInteractionEntrezId0.2240.2000.425
FruitFlyBioGRIDInteractionOfficial0.2310.2080.439
FruitFlyBioGRIDInteractionUniqueId0.2670.1670.435
HumanBioGRIDInteractionEntrezId0.2030.2110.415
HumanBioGRIDInteractionOfficial0.300.220.52
HumanBioGRIDInteractionUniqueId0.0320.0280.059
MouseBioGRIDInteractionEntrezId0.0130.0650.076
MouseBioGRIDInteractionOfficial0.0470.0390.086
MouseBioGRIDInteractionUniqueId0.0080.0040.012
S.PombeBioGRIDInteractionEntrezId0.0390.0760.114
S.PombeBioGRIDInteractionOfficial0.0840.0640.147
S.PombeBioGRIDInteractionUniqueId0.1010.0650.166
YeastBioGRIDInteractionEntrezId0.4280.5040.931
YeastBioGRIDInteractionOfficial0.7160.5481.263
YeastBioGRIDInteractionUniqueId0.7870.5351.321
findInteractionList0.0290.0410.070
simpIntLists0.1990.0360.236