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CHECK report for InTAD on tokay2

This page was generated on 2020-10-17 11:56:53 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE InTAD PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 880/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
InTAD 1.8.0
Konstantin Okonechnikov
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/InTAD
Branch: RELEASE_3_11
Last Commit: e20dc48
Last Changed Date: 2020-04-27 15:15:46 -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 UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: InTAD
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:InTAD.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings InTAD_1.8.0.tar.gz
StartedAt: 2020-10-17 05:14:11 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:23:23 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 551.4 seconds
RetCode: 0
Status:  OK  
CheckDir: InTAD.Rcheck
Warnings: 0

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:InTAD.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings InTAD_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/InTAD.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 'InTAD/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'InTAD' version '1.8.0'
* 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 'InTAD' 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
plotCorAcrossRef 5.50   0.66    6.15
combineInTAD     3.06   0.83   30.57
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
plotCorAcrossRef 4.77   0.05   24.14
* 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

InTAD.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/InTAD_1.8.0.tar.gz && rm -rf InTAD.buildbin-libdir && mkdir InTAD.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=InTAD.buildbin-libdir InTAD_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL InTAD_1.8.0.zip && rm InTAD_1.8.0.tar.gz InTAD_1.8.0.zip
###
##############################################################################
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  % 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  380k  100  380k    0     0  5569k      0 --:--:-- --:--:-- --:--:-- 6143k

install for i386

* installing *source* package 'InTAD' ...
** 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 'InTAD'
    finding HTML links ... done
    InTADSig                                html  
    combineInTAD                            html  
    enhSel                                  html  
    enhSelGR                                html  
    exprs                                   html  
    filterGeneExpr                          html  
    findCorrelation                         html  
    fnSE                                    html  
    geneCoords                              html  
    get.enr.bg.normfit                      html  
    loadSigInTAD                            html  
    mbAnnData                               html  
    newSigInTAD                             html  
    plotCorAcrossRef                        html  
    plotCorrelation                         html  
    rpkmCountsSel                           html  
    sigCoords                               html  
    signals                                 html  
    tadGR                                   html  
    txsSel                                  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 'InTAD' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'InTAD' as InTAD_1.8.0.zip
* DONE (InTAD)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'InTAD' successfully unpacked and MD5 sums checked

Tests output

InTAD.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(InTAD)
Loading required package: S4Vectors
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


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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: MultiAssayExperiment
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

> 
> test_check("InTAD")
== testthat results  ===========================================================
[ OK: 24 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> 
> proc.time()
   user  system elapsed 
  40.60    2.01   43.21 

InTAD.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(InTAD)
Loading required package: S4Vectors
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


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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: MultiAssayExperiment
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

> 
> test_check("InTAD")
== testthat results  ===========================================================
[ OK: 24 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> 
> proc.time()
   user  system elapsed 
  39.31    1.01   43.07 

Example timings

InTAD.Rcheck/examples_i386/InTAD-Ex.timings

nameusersystemelapsed
combineInTAD 3.06 0.8330.57
exprs0.310.000.32
filterGeneExpr0.560.000.56
findCorrelation3.190.003.19
geneCoords0.490.030.51
loadSigInTAD0.390.000.39
newSigInTAD0.370.000.38
plotCorAcrossRef5.500.666.15
plotCorrelation2.400.002.41
sigCoords0.320.000.31
signals0.310.000.31

InTAD.Rcheck/examples_x64/InTAD-Ex.timings

nameusersystemelapsed
combineInTAD3.140.153.28
exprs0.270.000.26
filterGeneExpr0.420.000.43
findCorrelation2.450.032.48
geneCoords0.270.000.27
loadSigInTAD0.260.000.26
newSigInTAD0.580.010.59
plotCorAcrossRef 4.77 0.0524.14
plotCorrelation2.540.002.55
sigCoords0.270.000.27
signals0.250.010.26