Package: MLSeq

Version: 1.20.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MLSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MLSeq_1.20.3.tar.gz

StartedAt: 2018-10-16 22:43:35 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 22:47:33 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 238.6 seconds

RetCode: 0

Status:  OK

CheckDir: MLSeq.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:MLSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MLSeq_1.20.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/MLSeq.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 ‘MLSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MLSeq’ version ‘1.20.3’
* 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 ‘MLSeq’ 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 ... NOTE
Namespace in Imports field not imported from: ‘xtable’
  All declared Imports should be used.
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/MLSeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MLSeq
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘MLSeq’ ...
** R
** data
** 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 (MLSeq)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(MLSeq)
Loading required package: caret
Loading required package: lattice
Loading required package: ggplot2


NOTE: MLSeq has major changes after version 1.20.1 and this will bump following versions to 2.y.z in the next release of Bioconductor (ver. 3.8). Most of the functions from previous versions were changed and new functions are included. Please see Beginner's Guide before continue with the analysis.
> test_check("MLSeq")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 0 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 11.559   0.617  12.247 

name	user	system	elapsed
cervical	0.001	0.000	0.001
classify	0.005	0.001	0.005
confusionMat	0.005	0.001	0.005
control	0.004	0.001	0.004
discreteControl	0.001	0.000	0.001
input	0.003	0.001	0.003
isUpdated	0.004	0.000	0.004
metaData	0.003	0.000	0.004
method	0.003	0.001	0.004
modelInfo	0.003	0.000	0.003
normalization	0.003	0.001	0.003
preProcessing	0.004	0.000	0.004
predict	0.006	0.001	0.007
ref	0.005	0.000	0.005
selectedGenes	0.003	0.000	0.004
trainParameters	0.004	0.001	0.004
trained	0.003	0.001	0.003
transformation	0.003	0.000	0.003
update	0.003	0.001	0.003
voomControl	0.002	0.000	0.001