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CHECK report for SCOPE on tokay1

This page was generated on 2021-05-06 12:33:29 -0400 (Thu, 06 May 2021).

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 1652/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SCOPE 1.2.0  (landing page)
Rujin Wang
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/SCOPE
Branch: RELEASE_3_12
Last Commit: b63bbf0
Last Changed Date: 2020-10-27 11:53:33 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: SCOPE
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SCOPE.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings SCOPE_1.2.0.tar.gz
StartedAt: 2021-05-06 06:43:31 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:54:49 -0400 (Thu, 06 May 2021)
EllapsedTime: 678.2 seconds
RetCode: 0
Status:   WARNINGS   
CheckDir: SCOPE.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SCOPE.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings SCOPE_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/SCOPE.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.2.0'
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'DescTools::%:%' by 'foreach::%:%' when loading 'SCOPE'
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/SCOPE.Rcheck/00install.out' for details.
* 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             28.53   2.14   30.69
normalize_scope         21.19   2.20   23.39
normalize_scope_group   17.41   1.16   18.56
get_coverage_scDNA       7.92   0.38   17.89
normalize_scope_foreach  5.79   0.48   66.14
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
plot_EM_fit             25.59   2.66   28.28
normalize_scope         24.20   2.26   26.47
normalize_scope_group   21.33   1.95   23.28
normalize_scope_foreach  9.11   0.02   66.77
get_coverage_scDNA       6.69   0.12    6.82
* 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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/SCOPE.Rcheck/00check.log'
for details.

Installation output

SCOPE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/SCOPE_1.2.0.tar.gz && rm -rf SCOPE.buildbin-libdir && mkdir SCOPE.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SCOPE.buildbin-libdir SCOPE_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL SCOPE_1.2.0.zip && rm SCOPE_1.2.0.tar.gz SCOPE_1.2.0.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  239k  100  239k    0     0  11.8M      0 --:--:-- --:--:-- --:--:-- 12.3M

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
Warning: replacing previous import 'DescTools::%:%' by 'foreach::%:%' when loading 'SCOPE'
** 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
Warning: replacing previous import 'DescTools::%:%' by 'foreach::%:%' when loading 'SCOPE'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'DescTools::%:%' by 'foreach::%:%' when loading 'SCOPE'
** 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
Warning: replacing previous import 'DescTools::%:%' by 'foreach::%:%' when loading 'SCOPE'
* MD5 sums
packaged installation of 'SCOPE' as SCOPE_1.2.0.zip
* DONE (SCOPE)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'SCOPE' successfully unpacked and MD5 sums checked

Tests output

SCOPE.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.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
Warning message:
replacing previous import 'DescTools::%:%' by 'foreach::%:%' when loading 'SCOPE' 
> 
> test_check("SCOPE")
1 	1 	[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
  19.37    1.03   20.39

SCOPE.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(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.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
Warning message:
replacing previous import 'DescTools::%:%' by 'foreach::%:%' when loading 'SCOPE' 
> 
> test_check("SCOPE")
1 	1 	[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
  21.01    0.40   21.40

Example timings

SCOPE.Rcheck/examples_i386/SCOPE-Ex.timings

nameusersystemelapsed
get_bam_bed0.170.010.24
get_coverage_scDNA 7.92 0.3817.89
get_gc000
get_gini0.040.000.05
get_mapp000
get_samp_QC3.110.073.19
initialize_ploidy0.970.051.02
initialize_ploidy_group0.970.131.09
normalize_codex2_ns_noK0.230.000.24
normalize_scope21.19 2.2023.39
normalize_scope_foreach 5.79 0.4866.14
normalize_scope_group17.41 1.1618.56
perform_qc0.050.020.06
plot_EM_fit28.53 2.1430.69
plot_iCN0.300.080.37
segment_CBScs1.090.021.11

SCOPE.Rcheck/examples_x64/SCOPE-Ex.timings

nameusersystemelapsed
get_bam_bed0.140.020.15
get_coverage_scDNA6.690.126.82
get_gc000
get_gini0.030.000.03
get_mapp0.020.000.02
get_samp_QC3.120.063.19
initialize_ploidy1.390.021.40
initialize_ploidy_group1.410.001.41
normalize_codex2_ns_noK0.270.000.26
normalize_scope24.20 2.2626.47
normalize_scope_foreach 9.11 0.0266.77
normalize_scope_group21.33 1.9523.28
perform_qc0.060.000.06
plot_EM_fit25.59 2.6628.28
plot_iCN0.320.090.41
segment_CBScs0.340.000.34