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CHECK report for appreci8R on merida1

This page was generated on 2020-08-07 12:38:59 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE appreci8R PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 73/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
appreci8R 1.7.0
Sarah Sandmann
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/appreci8R
Branch: master
Last Commit: 8474b30
Last Changed Date: 2020-04-27 15:18:01 -0400 (Mon, 27 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: appreci8R
Version: 1.7.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:appreci8R.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings appreci8R_1.7.0.tar.gz
StartedAt: 2020-08-07 03:52:39 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 04:00:10 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 451.6 seconds
RetCode: 0
Status:  OK 
CheckDir: appreci8R.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:appreci8R.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings appreci8R_1.7.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/appreci8R.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘appreci8R/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘appreci8R’ version ‘1.7.0’
* 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 ‘appreci8R’ 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 sizes of PDF files under ‘inst/doc’ ... 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

appreci8R.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL appreci8R
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘appreci8R’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘GenomicScores’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘GenomicScores’
** testing if installed package can be loaded from final location
No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘GenomicScores’
** testing if installed package keeps a record of temporary installation path
* DONE (appreci8R)

Tests output


Example timings

appreci8R.Rcheck/appreci8R-Ex.timings

nameusersystemelapsed
annotate0.1960.0200.217
appreci8R-package000
appreci8Rshiny0.0000.0000.001
combineOutput0.6240.0640.689
determineCharacteristics0.2180.0220.239
evaluateCovAndBQ0.2370.0120.250
filterTarget0.0020.0010.003
finalFiltration0.2850.0110.296
normalize0.0040.0000.003