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CHECK report for Rariant on tokay2

This page was generated on 2020-05-29 14:46:43 -0400 (Fri, 29 May 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Rariant PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1419/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rariant 1.24.0
Julian Gehring
Snapshot Date: 2020-05-28 16:50:23 -0400 (Thu, 28 May 2020)
URL: https://git.bioconductor.org/packages/Rariant
Branch: RELEASE_3_11
Last Commit: f187b1f
Last Changed Date: 2020-04-27 14:39:42 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rariant
Version: 1.24.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rariant.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings Rariant_1.24.0.tar.gz
StartedAt: 2020-05-29 05:19:54 -0400 (Fri, 29 May 2020)
EndedAt: 2020-05-29 05:29:30 -0400 (Fri, 29 May 2020)
EllapsedTime: 575.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: Rariant.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rariant.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings Rariant_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/Rariant.Rcheck'
* using R version 4.0.0 (2020-04-24)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rariant/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rariant' version '1.24.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'Rariant' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
tallyBamRegion: no visible global function definition for 'PileupParam'
tallyBamRegion: no visible global function definition for
  'ScanBamParam'
tallyBamRegion: no visible global function definition for 'pileup'
Undefined global functions or variables:
  PileupParam ScanBamParam pileup
* 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 installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'rariant-inspect-ci.png', 'rariant-inspect-shift.png'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... WARNING
Found the following significant warnings:

  Warning: 'rbind_all' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
mismatch-plot  5.9   1.74    7.89
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:

  Warning: 'rbind_all' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test_all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test_all.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: 2 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/Rariant.Rcheck/00check.log'
for details.



Installation output

Rariant.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/Rariant_1.24.0.tar.gz && rm -rf Rariant.buildbin-libdir && mkdir Rariant.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rariant.buildbin-libdir Rariant_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL Rariant_1.24.0.zip && rm Rariant_1.24.0.tar.gz Rariant_1.24.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 5500k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 5500k  100 5500k    0     0  25.3M      0 --:--:-- --:--:-- --:--:-- 26.0M

install for i386

* installing *source* package 'Rariant' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Rariant'
    finding HTML links ... done
    Rariant-package                         html  
    ci-adjust                               html  
    ci-assessment                           html  
    ci-utils                                html  
    colorscales                             html  
    convert-utils                           html  
    evidence-heatmap                        html  
    mismatch-plot                           html  
    mismatch-utils                          html  
    multi-utils                             html  
    plot-cis                                html  
    prop-cis                                html  
    prop-tests                              html  
    rariant                                 html  
    shiny                                   html  
    split-sample                            html  
    tally                                   html  
    yesnomaybe                              html  
** building package indices
** installing vignettes
   'Rariant-vignette.Rhtml' using 'UTF-8' 
** 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

install for x64

* installing *source* package 'Rariant' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rariant' as Rariant_1.24.0.zip
* DONE (Rariant)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'Rariant' successfully unpacked and MD5 sums checked

Tests output

Rariant.Rcheck/tests_i386/test_all.Rout


R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(Rariant)
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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, 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: VariantAnnotation
Loading required package: SummarizedExperiment
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


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, rowsum

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit


Attaching package: 'VariantAnnotation'

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

    tabulate

> 
> test_package("Rariant")
== testthat results  ===========================================================
[ OK: 21 | SKIPPED: 1 | WARNINGS: 4 | FAILED: 0 ]
Warning message:
Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
> 
> proc.time()
   user  system elapsed 
  26.71    2.82   31.50 

Rariant.Rcheck/tests_x64/test_all.Rout


R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 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(Rariant)
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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, 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: VariantAnnotation
Loading required package: SummarizedExperiment
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


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, rowsum

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit


Attaching package: 'VariantAnnotation'

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

    tabulate

> 
> test_package("Rariant")
== testthat results  ===========================================================
[ OK: 21 | SKIPPED: 1 | WARNINGS: 4 | FAILED: 0 ]
Warning message:
Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
> 
> proc.time()
   user  system elapsed 
  25.35    0.98   26.68 

Example timings

Rariant.Rcheck/examples_i386/Rariant-Ex.timings

nameusersystemelapsed
Rariant-package0.280.040.64
ci-adjust0.010.000.01
ci-assessment0.030.000.03
ci-utils000
convert-utils0.270.040.30
mismatch-plot5.901.747.89
plot-cis1.140.001.14
prop-cis000
prop-tests000
rariant0.340.000.34
shiny000
split-sample000

Rariant.Rcheck/examples_x64/Rariant-Ex.timings

nameusersystemelapsed
Rariant-package0.220.080.29
ci-adjust000
ci-assessment0.030.000.03
ci-utils000
convert-utils0.350.000.35
mismatch-plot4.640.174.81
plot-cis1.390.011.41
prop-cis000
prop-tests0.010.000.01
rariant0.280.030.32
shiny000
split-sample000