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CHECK report for annotationTools on nebbiolo1

This page was generated on 2020-12-01 11:55:47 -0500 (Tue, 01 Dec 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE annotationTools PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 68/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotationTools 1.64.0
Alexandre Kuhn
Snapshot Date: 2020-11-30 14:42:56 -0500 (Mon, 30 Nov 2020)
URL: https://git.bioconductor.org/packages/annotationTools
Branch: RELEASE_3_12
Last Commit: 8b4f650
Last Changed Date: 2020-10-27 10:30:36 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: annotationTools
Version: 1.64.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:annotationTools.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings annotationTools_1.64.0.tar.gz
StartedAt: 2020-11-30 19:57:01 -0500 (Mon, 30 Nov 2020)
EndedAt: 2020-11-30 19:57:35 -0500 (Mon, 30 Nov 2020)
EllapsedTime: 33.6 seconds
RetCode: 0
Status:  OK 
CheckDir: annotationTools.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:annotationTools.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings annotationTools_1.64.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/annotationTools.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotationTools/DESCRIPTION’ ... OK
* this is package ‘annotationTools’ version ‘1.64.0’
* 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 ‘annotationTools’ 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 ... 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: OK


Installation output

annotationTools.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL annotationTools
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘annotationTools’ ...
** 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 (annotationTools)

Tests output


Example timings

annotationTools.Rcheck/annotationTools-Ex.timings

nameusersystemelapsed
compactList0.0000.0010.001
getANNOTATION0.0020.0010.004
getGENEID0.0740.0000.074
getGENEONTOLOGY0.010.000.01
getGENESYMBOL0.0060.0000.006
getGENETITLE0.0060.0000.006
getHOMOLOG0.0150.0000.016
getMULTIANNOTATION0.0030.0000.004
getOrthologousProbesets0.0260.0040.029
getPROBESET0.0060.0020.008
listToCharacterVector000
ps2ps0.0010.0000.000