Package: anota2seq

Version: 1.2.0

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_1.2.0.tar.gz

StartedAt: 2018-10-16 19:53:10 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 19:58:01 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 290.9 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/anota2seq.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.2.0’
* 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
anota2seqGetQualityControl   47.702  0.273  48.368
anota2seqGetResidOutlierTest 46.015  0.308  46.658
* 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/3.5/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)

name	user	system	elapsed
anota2seq-plots	0.003	0.000	0.003
anota2seqAnalyze	1.893	0.067	1.990
anota2seqDataSetFromMatrix	0.221	0.004	0.226
anota2seqGetContrasts	0.735	0.019	0.768
anota2seqGetCovariates	0.708	0.013	0.733
anota2seqGetDeltaData	0.745	0.015	0.770
anota2seqGetNormalizedData	0.066	0.001	0.068
anota2seqGetOutput	0.810	0.013	0.838
anota2seqGetQualityControl	47.702	0.273	48.368
anota2seqGetResidOutlierTest	46.015	0.308	46.658
anota2seqGetThresholds	0.689	0.013	0.714
anota2seqPerformQC	0.001	0.000	0.001
anota2seqRegModes	1.964	0.042	2.061
anota2seqResidOutlierTest	0.002	0.001	0.002
anota2seqRun	1.798	0.045	1.883
anota2seqSelSigGenes	0.763	0.027	0.806
anota2seq_data	0.015	0.002	0.017
show-Anota2seqDataSet-method	0.345	0.010	0.358