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CHECK report for BiocSklearn on merida1

This page was generated on 2020-08-11 12:00:46 -0400 (Tue, 11 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BiocSklearn PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 161/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocSklearn 1.11.5
VJ Carey
Snapshot Date: 2020-08-10 14:50:56 -0400 (Mon, 10 Aug 2020)
URL: https://git.bioconductor.org/packages/BiocSklearn
Branch: master
Last Commit: 5ced25f
Last Changed Date: 2020-07-21 12:30:19 -0400 (Tue, 21 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocSklearn
Version: 1.11.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiocSklearn.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiocSklearn_1.11.5.tar.gz
StartedAt: 2020-08-11 03:20:33 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-11 03:23:37 -0400 (Tue, 11 Aug 2020)
EllapsedTime: 184.7 seconds
RetCode: 0
Status:  OK 
CheckDir: BiocSklearn.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiocSklearn.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiocSklearn_1.11.5.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/BiocSklearn.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocSklearn/DESCRIPTION’ ... OK
* this is package ‘BiocSklearn’ version ‘1.11.5’
* package encoding: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BiocSklearn’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.12-bioc/meat/BiocSklearn.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 32.7Mb
  sub-directories of 1Mb or more:
    ban_6_17  29.1Mb
    hdf5       3.1Mb
* 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 ... 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 line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
skIncrPCA 3.959  1.425   4.729
* 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
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/BiocSklearn.Rcheck/00check.log’
for details.



Installation output

BiocSklearn.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BiocSklearn
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘BiocSklearn’ ...
** using non-staged installation via StagedInstall field
** R
** 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 (BiocSklearn)

Tests output

BiocSklearn.Rcheck/tests/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(restfulSE)
> 
> #test_check("BiocSklearn")
> 
> 
> proc.time()
   user  system elapsed 
  0.299   0.071   0.345 

Example timings

BiocSklearn.Rcheck/BiocSklearn-Ex.timings

nameusersystemelapsed
H5matref0.0000.0010.002
SklearnEls0.0000.0000.001
h5mat0.0030.0010.003
skIncrPCA3.9591.4254.729
skIncrPCA_h50.0130.0020.015
skIncrPPCA0.0080.0020.009
skIncrPartialPCA0.2670.0080.274
skKMeans1.2500.6640.574
skPCA0.2450.1140.055
skPartialPCA_step0.0070.0010.007