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CHECK report for keggorthology on malbec1

This page was generated on 2020-04-15 12:05:01 -0400 (Wed, 15 Apr 2020).

Package 888/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
keggorthology 2.38.0
VJ Carey
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/keggorthology
Branch: RELEASE_3_10
Last Commit: 3a59cf9
Last Changed Date: 2019-10-29 13:07:50 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: keggorthology
Version: 2.38.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:keggorthology.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings keggorthology_2.38.0.tar.gz
StartedAt: 2020-04-15 00:25:40 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:27:01 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 81.6 seconds
RetCode: 0
Status:  OK 
CheckDir: keggorthology.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:keggorthology.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings keggorthology_2.38.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/keggorthology.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 ‘keggorthology/DESCRIPTION’ ... OK
* this is package ‘keggorthology’ version ‘2.38.0’
* 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 ‘keggorthology’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘graph’ ‘stats’
A package should be listed in only one of these fields.
* 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
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
Package in Depends field not imported from: ‘hgu95av2.db’
  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
getKOprobes: no visible binding for global variable ‘KOgraph’
getKOtags: no visible binding for global variable ‘KOgraph’
Undefined global functions or variables:
  KOgraph
* 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 ... OK
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/keggorthology.Rcheck/00check.log’
for details.



Installation output

keggorthology.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL keggorthology
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘keggorthology’ ...
** 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 (keggorthology)

Tests output


Example timings

keggorthology.Rcheck/keggorthology-Ex.timings

nameusersystemelapsed
getKOprobes0.7160.0040.719
indRender0.0320.0000.030
keggDF2graph0.0080.0080.014