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CHECK report for SELEX on machv2

This page was generated on 2020-10-17 11:59:33 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE SELEX PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1620/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SELEX 1.20.0
Harmen J. Bussemaker
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/SELEX
Branch: RELEASE_3_11
Last Commit: 50e157b
Last Changed Date: 2020-04-27 14:46:52 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SELEX
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SELEX.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SELEX_1.20.0.tar.gz
StartedAt: 2020-10-17 05:11:16 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:13:40 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 143.8 seconds
RetCode: 0
Status:  OK 
CheckDir: SELEX.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SELEX.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SELEX_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SELEX.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SELEX/DESCRIPTION’ ... OK
* this is package ‘SELEX’ version ‘1.20.0’
* 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 ‘SELEX’ 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
SELEX           28.680  3.139  11.353
selex.seqfilter 13.105  1.605   5.062
* 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

SELEX.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SELEX
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘SELEX’ ...
** 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 (SELEX)

Tests output


Example timings

SELEX.Rcheck/SELEX-Ex.timings

nameusersystemelapsed
SELEX28.680 3.13911.353
selex.affinities1.3020.0470.547
selex.config0.2620.0090.067
selex.countSummary1.3350.0670.587
selex.counts2.0250.0650.823
selex.defineSample0.0880.0130.068
selex.exampledata0.1090.0100.051
selex.fastqPSFM0.9410.0420.419
selex.getAttributes0.2570.0150.100
selex.getRound00.3430.0170.170
selex.getSeqfilter0.1000.0040.048
selex.infogain2.2500.0830.809
selex.infogainSummary1.3340.0370.416
selex.jvmStatus0.1730.0050.060
selex.kmax2.4750.3781.229
selex.kmerPSFM0.8250.0710.351
selex.loadAnnotation0.7520.0160.190
selex.mm0.6830.0380.380
selex.mmProb0.7170.0350.359
selex.mmSummary0.6390.0400.390
selex.revcomp1.1460.0480.619
selex.run2.3640.0740.832
selex.sample0.4610.0190.147
selex.samplePSFM1.0360.0330.396
selex.sampleSummary0.1780.0130.130
selex.saveAnnotation0.0620.0110.074
selex.seqfilter13.105 1.605 5.062
selex.setwd0.1130.0030.034
selex.split0.8080.0310.262
selex.summary1.9510.1000.893