Package: anota2seq

Version: 1.6.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:anota2seq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings anota2seq_1.6.0.tar.gz

StartedAt: 2019-10-15 23:46:45 -0400 (Tue, 15 Oct 2019)

EndedAt: 2019-10-15 23:51:13 -0400 (Tue, 15 Oct 2019)

EllapsedTime: 267.6 seconds

RetCode: 0

Status:  OK

CheckDir: anota2seq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:anota2seq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings anota2seq_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/anota2seq.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
anota2seqGetResidOutlierTest 41.366  0.020  41.399
anota2seqGetQualityControl   34.399  0.043  34.449
* 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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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL anota2seq
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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	0	0
anota2seqAnalyze	0.943	0.023	0.966
anota2seqDataSetFromMatrix	0.057	0.001	0.057
anota2seqGetContrasts	0.537	0.000	0.537
anota2seqGetCovariates	0.748	0.000	0.749
anota2seqGetDeltaData	0.976	0.004	0.981
anota2seqGetNormalizedData	0.024	0.004	0.029
anota2seqGetOutput	0.459	0.004	0.464
anota2seqGetQualityControl	34.399	0.043	34.449
anota2seqGetResidOutlierTest	41.366	0.020	41.399
anota2seqGetThresholds	0.785	0.004	0.789
anota2seqPerformQC	0.000	0.000	0.001
anota2seqRegModes	2.185	0.004	2.190
anota2seqResidOutlierTest	0	0	0
anota2seqRun	1.311	0.000	1.311
anota2seqSelSigGenes	0.504	0.000	0.505
anota2seq_data	0.012	0.000	0.013
show-Anota2seqDataSet-method	0.084	0.000	0.085