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CHECK report for NCIgraph on malbec1

This page was generated on 2021-03-03 12:10:31 -0500 (Wed, 03 Mar 2021).

To the developers/maintainers of the NCIgraph package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1206/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NCIgraph 1.38.0
Laurent Jacob
Snapshot Date: 2021-03-02 14:50:31 -0500 (Tue, 02 Mar 2021)
URL: https://git.bioconductor.org/packages/NCIgraph
Branch: RELEASE_3_12
Last Commit: 1f618f0
Last Changed Date: 2020-10-27 10:41:10 -0500 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  
tokay1Windows Server 2012 R2 Standard / x64... NOT SUPPORTED ...
merida1macOS 10.14.6 Mojave / x86_64... NOT SUPPORTED ...

Summary

Package: NCIgraph
Version: 1.38.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:NCIgraph.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings NCIgraph_1.38.0.tar.gz
StartedAt: 2021-03-03 04:24:24 -0500 (Wed, 03 Mar 2021)
EndedAt: 2021-03-03 04:25:21 -0500 (Wed, 03 Mar 2021)
EllapsedTime: 56.8 seconds
RetCode: 0
Status:   OK  
CheckDir: NCIgraph.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:NCIgraph.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings NCIgraph_1.38.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/NCIgraph.Rcheck’
* using R version 4.0.4 (2021-02-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NCIgraph/DESCRIPTION’ ... OK
* this is package ‘NCIgraph’ version ‘1.38.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
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 ‘NCIgraph’ 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/NCIgraph.Rcheck/00check.log’
for details.



Installation output

NCIgraph.Rcheck/00install.out

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

Tests output


Example timings

NCIgraph.Rcheck/NCIgraph-Ex.timings

nameusersystemelapsed
NCI.demo.cyList0.5720.0280.600
getNCIPathways4.2040.0244.230
getSubtype.NCIgraph3.9320.0003.938
parseNCInetwork0.1400.0000.138
translateNCI2GeneID3.0640.0003.069