Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-26 14:06:53 -0400 (Tue, 26 Oct 2021).

CHECK results for BiocSklearn on riesling1

To the developers/maintainers of the BiocSklearn package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocSklearn.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 169/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocSklearn 1.15.0  (landing page)
Vince Carey
Snapshot Date: 2021-10-25 14:50:11 -0400 (Mon, 25 Oct 2021)
git_url: https://git.bioconductor.org/packages/BiocSklearn
git_branch: master
git_last_commit: 0b618b4
git_last_commit_date: 2021-07-29 13:17:36 -0400 (Thu, 29 Jul 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  

Summary

Package: BiocSklearn
Version: 1.15.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:BiocSklearn.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BiocSklearn_1.15.0.tar.gz
StartedAt: 2021-10-26 00:31:49 -0400 (Tue, 26 Oct 2021)
EndedAt: 2021-10-26 00:34:37 -0400 (Tue, 26 Oct 2021)
EllapsedTime: 167.6 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocSklearn.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:BiocSklearn.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BiocSklearn_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/BiocSklearn.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.15.0'
* 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 whether package 'BiocSklearn' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'D:/biocbuild/bbs-3.14-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
* 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
  'D:/biocbuild/bbs-3.14-bioc/meat/BiocSklearn.Rcheck/00check.log'
for details.



Installation output

BiocSklearn.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch BiocSklearn
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
* installing *source* package 'BiocSklearn' ...
** using non-staged installation via StagedInstall field

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** 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  
    SkDecomp                                html  
    SklearnEls                              html  
    h5mat                                   html  
    skIncrPCA                               html  
    skIncrPCA_h5                            html  
    skIncrPPCA                              html  
    skIncrPartialPCA                        html  
    skKMeans                                html  
    skPCA                                   html  
    skPartialPCA_step                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BiocSklearn)
Making 'packages.html' ... done

Tests output

BiocSklearn.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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)
> 
> #test_check("BiocSklearn")
> 
> 
> proc.time()
   user  system elapsed 
   0.12    0.01    0.12 

Example timings

BiocSklearn.Rcheck/BiocSklearn-Ex.timings

nameusersystemelapsed
H5matref000
SklearnEls000
h5mat000
skIncrPCA0.720.524.18
skIncrPCA_h50.060.000.06
skIncrPPCA0.020.000.02
skIncrPartialPCA0.070.000.09
skKMeans0.720.541.37
skPCA0.050.040.03
skPartialPCA_step000