Package: BiocSklearn

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:BiocSklearn.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings BiocSklearn_1.2.0.tar.gz

StartedAt: 2018-10-17 00:44:43 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:48:00 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 196.6 seconds

RetCode: 0

Status:  OK

CheckDir: BiocSklearn.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:BiocSklearn.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings BiocSklearn_1.2.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/BiocSklearn.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocSklearn/DESCRIPTION' ... OK
* this is package 'BiocSklearn' 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'BiocSklearn' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 35.7Mb
  sub-directories of 1Mb or more:
    ban_6_17  29.1Mb
    hdf5       6.1Mb
* 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
Package in Depends field not imported from: 'HDF5Array'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
H5matref 5.53   0.65    28.6
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/BiocSklearn.Rcheck/00check.log'
for details.

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch BiocSklearn
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* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
* installing *source* package 'BiocSklearn' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BiocSklearn'
    finding HTML links ... done
    H5matref                                html  
    SkDecomp-class                          html  
    SklearnEls                              html  
    h5mat                                   html  
    skIncrPCA                               html  
    skIncrPPCA                              html  
    skPCA                                   html  
    skPartialPCA_step                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BiocSklearn)
Making 'packages.html' ... done
In R CMD INSTALL

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(restfulSE)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply


> 
> test_check("BiocSklearn")
Loading required package: BiocSklearn
Loading required package: reticulate
Loading required package: knitr
Loading required package: HDF5Array
Loading required package: rhdf5
checking python library availability...
done.
== testthat results  ===========================================================
OK: 2 SKIPPED: 0 FAILED: 0
> 
> 
> proc.time()
   user  system elapsed 
   9.42    0.50   10.85 

name	user	system	elapsed
H5matref	5.53	0.65	28.60
SklearnEls	0.02	0.00	0.01
h5mat	0	0	0
skIncrPCA	0.05	0.00	0.08
skIncrPPCA	2.66	0.29	3.26
skPCA	0	0	0
skPartialPCA_step	0.03	0.00	0.03