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CHECK report for GenomicInteractions on tokay2

This page was generated on 2020-10-17 11:56:40 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE GenomicInteractions PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 710/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicInteractions 1.22.0
Liz Ing-Simmons
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/GenomicInteractions
Branch: RELEASE_3_11
Last Commit: c0b8798
Last Changed Date: 2020-04-27 14:43:28 -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 [ WARNINGS ] 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: GenomicInteractions
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicInteractions.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings GenomicInteractions_1.22.0.tar.gz
StartedAt: 2020-10-17 04:24:06 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:35:00 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 653.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GenomicInteractions.Rcheck
Warnings: 1

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:GenomicInteractions.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings GenomicInteractions_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/GenomicInteractions.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 'GenomicInteractions/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GenomicInteractions' version '1.22.0'
* 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 'GenomicInteractions' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpiS8fmr/R.INSTALL2d1813b8ec/GenomicInteractions/man/getters.Rd:43: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpiS8fmr/R.INSTALL2d1813b8ec/GenomicInteractions/man/setters.Rd:27: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/GenomicInteractions.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   7.9Mb
* 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
** running examples for arch 'x64' ... OK
* 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/GenomicInteractions.Rcheck/00check.log'
for details.



Installation output

GenomicInteractions.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/GenomicInteractions_1.22.0.tar.gz && rm -rf GenomicInteractions.buildbin-libdir && mkdir GenomicInteractions.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicInteractions.buildbin-libdir GenomicInteractions_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL GenomicInteractions_1.22.0.zip && rm GenomicInteractions_1.22.0.tar.gz GenomicInteractions_1.22.0.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 3315k  100 3315k    0     0  29.5M      0 --:--:-- --:--:-- --:--:-- 31.4M

install for i386

* installing *source* package 'GenomicInteractions' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomicInteractions'
    finding HTML links ... done
    GInteractions-subsetByFeatures-methods
                                            html  
    GenomicInteractions-class               html  
    GenomicInteractions-package             html  
    GenomicInteractions                     html  
    InteractionHelpers                      html  
    InteractionTrack-class                  html  
    InteractionTrack                        html  
    annotateInteractions                    html  
    annotateRegions                         html  
    asBED-GInteractions-method              html  
    availableDisplayPars                    html  
    calculateDistances                      html  
    categoriseInteractions                  html  
    countsBetweenAnchors-methods            html  
    dot-importHicLib                        html  
    dot-importHomer                         html  
    dot-processChiapetName                  html  
    dot-readBam                             html  
    dot-readTwoBams                         html  
    dot-validateInput                       html  
    export.bed12                            html  
    export.bedpe                            html  
    export.chiasig                          html  
    export.igraph                           html  
    get_binom_ligation_threshold            html  
    get_self_ligation_threshold             html  
    getters                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpiS8fmr/R.INSTALL2d1813b8ec/GenomicInteractions/man/getters.Rd:43: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    hg19.refseq.transcripts                 html  
    hic_example_data                        html  
    makeGenomicInteractionsFromFile         html  
    mm9_refseq_promoters                    html  
    plotAvgViewpoint                        html  
    plotCisTrans                            html  
    plotCounts                              html  
    plotDists                               html  
    plotInteractionAnnotations              html  
    plotSummaryStats                        html  
    plotViewpoint                           html  
    removeDups                              html  
    resetAnnotations                        html  
    sameStrand                              html  
    setters                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpiS8fmr/R.INSTALL2d1813b8ec/GenomicInteractions/man/setters.Rd:27: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    sum-GInteractions-method                html  
    summariseByFeaturePairs                 html  
    summariseByFeatures                     html  
    thymus_enh                              html  
    updateObject-GenomicInteractions-method
                                            html  
    viewPoint                               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 'GenomicInteractions' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicInteractions' as GenomicInteractions_1.22.0.zip
* DONE (GenomicInteractions)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'GenomicInteractions' successfully unpacked and MD5 sums checked

Tests output

GenomicInteractions.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(GenomicInteractions)
Loading required package: InteractionSet
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: 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("GenomicInteractions")
== testthat results  ===========================================================
[ OK: 51 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  27.68    2.53   33.53 

GenomicInteractions.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(GenomicInteractions)
Loading required package: InteractionSet
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: 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("GenomicInteractions")
== testthat results  ===========================================================
[ OK: 51 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  30.85    1.21   35.35 

Example timings

GenomicInteractions.Rcheck/examples_i386/GenomicInteractions-Ex.timings

nameusersystemelapsed
GInteractions-subsetByFeatures-methods0.170.010.19
GenomicInteractions-class0.170.000.17
GenomicInteractions0.110.000.11
InteractionHelpers0.030.040.07
InteractionTrack1.160.561.71
annotateInteractions0.410.000.41
annotateRegions0.090.000.09
asBED-GInteractions-method0.450.120.57
availableDisplayPars0.030.000.04
calculateDistances0.110.000.10
categoriseInteractions0.310.030.35
export.bed121.100.001.09
export.bedpe0.380.000.37
export.chiasig0.230.020.25
export.igraph0.140.000.14
getters0.110.000.11
makeGenomicInteractionsFromFile2.170.142.44
plotAvgViewpoint0.380.000.50
plotCisTrans0.340.020.36
plotCounts0.390.000.39
plotDists0.220.010.23
plotInteractionAnnotations0.310.000.32
plotSummaryStats0.720.000.72
plotViewpoint0.620.270.89
resetAnnotations0.050.010.06
setters0.050.190.24
summariseByFeaturePairs1.170.031.20
summariseByFeatures0.620.020.64
viewPoint0.380.060.44

GenomicInteractions.Rcheck/examples_x64/GenomicInteractions-Ex.timings

nameusersystemelapsed
GInteractions-subsetByFeatures-methods0.20.00.2
GenomicInteractions-class0.20.00.2
GenomicInteractions0.090.000.09
InteractionHelpers0.050.010.07
InteractionTrack0.720.030.75
annotateInteractions0.310.000.31
annotateRegions0.050.000.05
asBED-GInteractions-method0.430.040.45
availableDisplayPars0.030.000.04
calculateDistances0.140.000.14
categoriseInteractions0.290.000.29
export.bed120.940.010.96
export.bedpe0.360.000.36
export.chiasig0.250.000.25
export.igraph0.160.000.15
getters0.210.000.20
makeGenomicInteractionsFromFile1.950.052.00
plotAvgViewpoint0.260.010.28
plotCisTrans0.220.000.22
plotCounts0.240.000.23
plotDists0.140.000.15
plotInteractionAnnotations0.280.000.28
plotSummaryStats0.530.020.54
plotViewpoint0.390.000.39
resetAnnotations0.030.010.05
setters0.090.000.09
summariseByFeaturePairs1.050.071.11
summariseByFeatures0.420.000.42
viewPoint0.240.000.24