Package: anota2seq

Version: 1.6.0

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_1.6.0.tar.gz

StartedAt: 2019-10-16 00:33:33 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 00:40:24 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 411.3 seconds

RetCode: 0

Status:  OK

CheckDir: anota2seq.Rcheck

Warnings: 0

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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_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/anota2seq.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.6.0’
* 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 or elapsed time > 5s
                               user system elapsed
anota2seqGetResidOutlierTest 61.328  0.456  61.835
anota2seqGetQualityControl   60.920  0.537  61.484
* 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

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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/3.6/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)

name	user	system	elapsed
anota2seq-plots	0.000	0.001	0.001
anota2seqAnalyze	1.943	0.154	2.125
anota2seqDataSetFromMatrix	0.114	0.002	0.115
anota2seqGetContrasts	1.747	0.051	1.810
anota2seqGetCovariates	1.211	0.066	1.290
anota2seqGetDeltaData	1.100	0.025	1.139
anota2seqGetNormalizedData	0.034	0.002	0.037
anota2seqGetOutput	0.714	0.020	0.747
anota2seqGetQualityControl	60.920	0.537	61.484
anota2seqGetResidOutlierTest	61.328	0.456	61.835
anota2seqGetThresholds	1.132	0.025	1.170
anota2seqPerformQC	0.000	0.001	0.000
anota2seqRegModes	2.896	0.103	3.054
anota2seqResidOutlierTest	0.000	0.001	0.001
anota2seqRun	2.921	0.069	3.044
anota2seqSelSigGenes	0.918	0.022	0.954
anota2seq_data	0.016	0.005	0.020
show-Anota2seqDataSet-method	0.171	0.010	0.181