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CHECK report for anota2seq on merida1

This page was generated on 2020-08-07 12:37:21 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE anota2seq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 67/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
anota2seq 1.11.0
Christian Oertlin , Julie Lorent
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/anota2seq
Branch: master
Last Commit: 0e34b88
Last Changed Date: 2020-04-27 15:11:14 -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: anota2seq
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:anota2seq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings anota2seq_1.11.0.tar.gz
StartedAt: 2020-08-07 03:15:32 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 03:22:25 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 412.7 seconds
RetCode: 0
Status:  OK 
CheckDir: anota2seq.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:anota2seq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings anota2seq_1.11.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/anota2seq.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 ‘anota2seq/DESCRIPTION’ ... OK
* this is package ‘anota2seq’ version ‘1.11.0’
* 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 ‘anota2seq’ 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 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
anota2seqGetQualityControl   66.694  0.315  67.269
anota2seqGetResidOutlierTest 66.647  0.253  67.366
* 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

anota2seq.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL anota2seq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘anota2seq’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (anota2seq)

Tests output


Example timings

anota2seq.Rcheck/anota2seq-Ex.timings

nameusersystemelapsed
anota2seq-plots0.0010.0010.001
anota2seqAnalyze2.1740.1182.316
anota2seqDataSetFromMatrix0.1250.0060.130
anota2seqGetContrasts0.9070.0190.949
anota2seqGetCovariates0.9450.0170.983
anota2seqGetDeltaData0.9030.0210.946
anota2seqGetNormalizedData0.0490.0030.052
anota2seqGetOutput0.8610.0120.893
anota2seqGetQualityControl66.694 0.31567.269
anota2seqGetResidOutlierTest66.647 0.25367.366
anota2seqGetThresholds0.9390.0291.076
anota2seqPerformQC0.0000.0010.000
anota2seqRegModes2.5550.0572.694
anota2seqResidOutlierTest0.0000.0010.001
anota2seqRun2.6220.0492.756
anota2seqSelSigGenes0.9290.0170.968
anota2seq_data0.0210.0020.024
show-Anota2seqDataSet-method0.2170.0040.220