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CHECK report for SCOPE on tokay2

This page was generated on 2020-10-17 11:57:46 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE SCOPE PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1605/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SCOPE 1.0.0
Rujin Wang
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/SCOPE
Branch: RELEASE_3_11
Last Commit: e9ad67e
Last Changed Date: 2020-04-27 15:33:59 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SCOPE
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SCOPE.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SCOPE_1.0.0.tar.gz
StartedAt: 2020-10-17 08:03:23 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 08:15:00 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 696.8 seconds
RetCode: 0
Status:  OK  
CheckDir: SCOPE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SCOPE.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SCOPE_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/SCOPE.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SCOPE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SCOPE' version '1.0.0'
* 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 'SCOPE' 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
* 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
plot_EM_fit             29.49   2.61   33.38
normalize_scope         22.58   2.26   24.84
normalize_scope_group   17.53   1.84   19.37
get_coverage_scDNA       8.66   0.31   20.98
normalize_scope_foreach  6.87   0.22   59.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
normalize_scope         29.39   2.25   31.92
plot_EM_fit             27.94   2.42   30.37
normalize_scope_group   19.09   1.35   20.44
get_coverage_scDNA       7.82   0.20    8.03
normalize_scope_foreach  7.64   0.11   57.80
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: OK

Installation output

SCOPE.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/SCOPE_1.0.0.tar.gz && rm -rf SCOPE.buildbin-libdir && mkdir SCOPE.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SCOPE.buildbin-libdir SCOPE_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL SCOPE_1.0.0.zip && rm SCOPE_1.0.0.tar.gz SCOPE_1.0.0.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
100  241k  100  241k    0     0  3881k      0 --:--:-- --:--:-- --:--:-- 4309k

install for i386

* installing *source* package 'SCOPE' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SCOPE'
    finding HTML links ... done
    QCmetric.scopeDemo                      html  
    Y_sim                                   html  
    coverageObj.scopeDemo                   html  
    get_bam_bed                             html  
    get_coverage_scDNA                      html  
    get_gc                                  html  
    get_gini                                html  
    get_mapp                                html  
    get_samp_QC                             html  
    iCN_sim                                 html  
    initialize_ploidy                       html  
    initialize_ploidy_group                 html  
    normObj.scopeDemo                       html  
    normalize_codex2_ns_noK                 html  
    normalize_scope                         html  
    normalize_scope_foreach                 html  
    normalize_scope_group                   html  
    perform_qc                              html  
    plot_EM_fit                             html  
    plot_iCN                                html  
    ref.scopeDemo                           html  
    ref_sim                                 html  
    segment_CBScs                           html  
** building package indices
** installing vignettes
** 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 'SCOPE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SCOPE' as SCOPE_1.0.0.zip
* DONE (SCOPE)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'SCOPE' successfully unpacked and MD5 sums checked

Tests output

SCOPE.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(SCOPE)
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: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: rtracklayer
> 
> test_check("SCOPE")
1 	1 	== testthat results  ===========================================================
[ OK: 7 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  27.82    1.57   29.43

SCOPE.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(SCOPE)
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: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: rtracklayer
> 
> test_check("SCOPE")
1 	1 	== testthat results  ===========================================================
[ OK: 7 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  27.75    0.73   28.50

Example timings

SCOPE.Rcheck/examples_i386/SCOPE-Ex.timings

nameusersystemelapsed
get_bam_bed0.190.080.31
get_coverage_scDNA 8.66 0.3120.98
get_gc000
get_gini0.940.000.94
get_mapp000
get_samp_QC4.070.114.19
initialize_ploidy1.070.081.14
initialize_ploidy_group1.150.021.17
normalize_codex2_ns_noK0.270.000.27
normalize_scope22.58 2.2624.84
normalize_scope_foreach 6.87 0.2259.16
normalize_scope_group17.53 1.8419.37
perform_qc0.060.000.06
plot_EM_fit29.49 2.6133.38
plot_iCN0.480.070.55
segment_CBScs1.020.011.03

SCOPE.Rcheck/examples_x64/SCOPE-Ex.timings

nameusersystemelapsed
get_bam_bed0.190.020.20
get_coverage_scDNA7.820.208.03
get_gc000
get_gini0.090.000.09
get_mapp000
get_samp_QC3.830.113.94
initialize_ploidy2.220.032.25
initialize_ploidy_group1.250.001.25
normalize_codex2_ns_noK0.470.010.48
normalize_scope29.39 2.2531.92
normalize_scope_foreach 7.64 0.1157.80
normalize_scope_group19.09 1.3520.44
perform_qc0.050.000.05
plot_EM_fit27.94 2.4230.37
plot_iCN0.420.080.50
segment_CBScs1.520.011.53