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CHECK report for anota2seq on merida1

This page was generated on 2019-04-16 12:01:51 -0400 (Tue, 16 Apr 2019).

Package 63/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
anota2seq 1.4.2
Christian Oertlin , Julie Lorent
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/anota2seq
Branch: RELEASE_3_8
Last Commit: 571252c
Last Changed Date: 2019-04-02 03:37:23 -0400 (Tue, 02 Apr 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: anota2seq
Version: 1.4.2
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_1.4.2.tar.gz
StartedAt: 2019-04-15 22:22:31 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:27:45 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 314.2 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_1.4.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/anota2seq.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘anota2seq/DESCRIPTION’ ... OK
* this is package ‘anota2seq’ version ‘1.4.2’
* 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 or elapsed time > 5s
                               user system elapsed
anota2seqGetQualityControl   54.434  0.278  55.360
anota2seqGetResidOutlierTest 52.131  0.346  52.981
* 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/3.5/Resources/library’
* installing *source* package ‘anota2seq’ ...
** 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
* DONE (anota2seq)

Tests output


Example timings

anota2seq.Rcheck/anota2seq-Ex.timings

nameusersystemelapsed
anota2seq-plots0.0000.0000.001
anota2seqAnalyze1.9800.0682.077
anota2seqDataSetFromMatrix0.2020.0050.207
anota2seqGetContrasts0.9000.0170.930
anota2seqGetCovariates0.8930.0150.922
anota2seqGetDeltaData0.8550.0160.889
anota2seqGetNormalizedData0.0710.0020.073
anota2seqGetOutput0.8000.0120.825
anota2seqGetQualityControl54.434 0.27855.360
anota2seqGetResidOutlierTest52.131 0.34652.981
anota2seqGetThresholds0.8840.0130.914
anota2seqPerformQC0.0000.0000.001
anota2seqRegModes2.2420.0482.339
anota2seqResidOutlierTest0.0010.0010.001
anota2seqRun2.2230.0352.307
anota2seqSelSigGenes0.7960.0150.823
anota2seq_data0.0160.0020.019
show-Anota2seqDataSet-method0.2890.0050.295