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CHECK report for BrainSABER on malbec1

This page was generated on 2020-08-06 11:48:11 -0400 (Thu, 06 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BrainSABER PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 193/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BrainSABER 0.99.4
USD Biomedical Engineering
Snapshot Date: 2020-08-05 14:50:59 -0400 (Wed, 05 Aug 2020)
URL: https://git.bioconductor.org/packages/BrainSABER
Branch: master
Last Commit: 4d2527c
Last Changed Date: 2020-04-20 22:30:39 -0400 (Mon, 20 Apr 2020)
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 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BrainSABER
Version: 0.99.4
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BrainSABER.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BrainSABER_0.99.4.tar.gz
StartedAt: 2020-08-06 05:43:00 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 05:45:55 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 174.5 seconds
RetCode: 0
Status:  OK 
CheckDir: BrainSABER.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BrainSABER.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BrainSABER_0.99.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BrainSABER.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BrainSABER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BrainSABER’ version ‘0.99.4’
* package encoding: UTF-8
* 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 ‘BrainSABER’ 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 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

BrainSABER.Rcheck/00install.out

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

Tests output


Example timings

BrainSABER.Rcheck/BrainSABER-Ex.timings

nameusersystemelapsed
CellScabbard-methods0.3520.0320.385
CellScabbard0.1960.0000.196
buildAIBSARNA0.0040.0040.009
getExampleVector0.0440.0000.045
getExternalVector0.0320.0000.030
getRelevantGenes0.2080.0000.206
getSimDataFrame0.2720.0000.274
getSimMatrix0.240.000.24
getSimScores0.4080.0000.408
getTrimmedExternalSet0.2560.0040.263
getUNDmatrix0.3520.0000.353