Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-22 15:05:13 -0400 (Wed, 22 Sep 2021).

CHECK results for diffloop on tokay2

To the developers/maintainers of the diffloop package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/diffloop.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 501/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffloop 1.20.0  (landing page)
Caleb Lareau
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/diffloop
git_branch: RELEASE_3_13
git_last_commit: 900a5e1
git_last_commit_date: 2021-05-19 12:20:17 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: diffloop
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:diffloop.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings diffloop_1.20.0.tar.gz
StartedAt: 2021-09-21 21:57:11 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 22:02:55 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 344.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: diffloop.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:diffloop.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings diffloop_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/diffloop.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'diffloop/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'diffloop' version '1.20.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'diffloop' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'diffloop'
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/diffloop.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 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-3.13-bioc/meat/diffloop.Rcheck/00check.log'
for details.



Installation output

diffloop.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/diffloop_1.20.0.tar.gz && rm -rf diffloop.buildbin-libdir && mkdir diffloop.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=diffloop.buildbin-libdir diffloop_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL diffloop_1.20.0.zip && rm diffloop_1.20.0.tar.gz diffloop_1.20.0.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 1144k  100 1144k    0     0  1781k      0 --:--:-- --:--:-- --:--:-- 1785k

install for i386

* installing *source* package 'diffloop' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'diffloop'
** help
*** installing help indices
  converting help for package 'diffloop'
    finding HTML links ... done
    addchr                                  html  
    annotateAnchors                         html  
    annotateAnchors.bed                     html  
    annotateAnchors.bigwig                  html  
    annotateLoops                           html  
    annotateLoops.dge                       html  
    bedToGRanges                            html  
    calcLDSizeFactors                       html  
    callCCDs                                html  
    computeBoundaryScores                   html  
    diffloop                                html  
    dim-loops-method                        html  
    featureTest                             html  
    filterLoops                             html  
    filterSpanningLoops                     html  
    geneinfo                                html  
    getHumanGenes                           html  
    getHumanTSS                             html  
    getMouseGenes                           html  
    getMouseTSS                             html  
    head-loops-method                       html  
    human.genes                             html  
    interchromosomal                        html  
    intrachromosomal                        html  
    keepCTCFloops                           html  
    keepEPloops                             html  
    loopAssoc                               html  
    loopDistancePlot                        html  
    loopGenes                               html  
    loopMetrics                             html  
    loopPlot                                html  
    loopWidth                               html  
    loops-class                             html  
    loops.small                             html  
    loopsMake                               html  
    loopsMake.mango                         html  
    loopsSubset                             html  
    mangoCorrection                         html  
    manyLoopPlots                           html  
    mergeAnchors                            html  
    numAnchors                              html  
    numLoops                                html  
    padGRanges                              html  
    pcaPlot                                 html  
    plotTopLoops                            html  
    quickAssoc                              html  
    quickAssocVoom                          html  
    removeRegion                            html  
    removeSelfLoops                         html  
    rmchr                                   html  
    sampleNames-loops-method                html  
    slidingWindowTest                       html  
    splitSamples                            html  
    sub-loops-numeric-numeric-missing-method
                                            html  
    subsetLoops                             html  
    subsetRegion                            html  
    subsetRegionAB                          html  
    summary-loops-method                    html  
    tail-loops-method                       html  
    topLoops                                html  
    union-loops-loops-method                html  
    updateLDGroups                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'diffloop'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'diffloop'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'diffloop' ...
** testing if installed package can be loaded
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'diffloop'
* MD5 sums
packaged installation of 'diffloop' as diffloop_1.20.0.zip
* DONE (diffloop)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'diffloop' successfully unpacked and MD5 sums checked

Tests output

diffloop.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(diffloop)
Warning message:
replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'diffloop' 
> 
> test_check("diffloop")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
  10.31    0.78   11.07 

diffloop.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(diffloop)
Warning message:
replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'diffloop' 
> 
> test_check("diffloop")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
  13.34    0.48   13.81 

Example timings

diffloop.Rcheck/examples_i386/diffloop-Ex.timings

nameusersystemelapsed
addchr0.250.040.28
annotateAnchors0.170.000.19
annotateAnchors.bed0.120.020.14
annotateAnchors.bigwig0.080.010.10
annotateLoops0.870.081.15
annotateLoops.dge0.440.000.44
bedToGRanges0.060.000.06
calcLDSizeFactors0.020.000.01
callCCDs000
computeBoundaryScores000
featureTest000
filterLoops0.170.000.18
filterSpanningLoops0.020.000.01
getHumanGenes0.060.000.06
getHumanTSS0.190.010.21
getMouseGenes0.260.000.50
getMouseTSS0.250.000.25
interchromosomal0.030.000.03
intrachromosomal0.040.000.03
keepCTCFloops0.150.000.16
keepEPloops0.380.000.37
loopAssoc000
loopDistancePlot0.030.000.03
loopGenes0.090.020.11
loopMetrics0.020.000.02
loopPlot0.620.060.68
loopWidth0.020.000.02
loopsMake0.000.000.03
loopsMake.mango000
loopsSubset0.260.000.27
mangoCorrection0.110.000.11
manyLoopPlots0.080.020.09
mergeAnchors0.140.040.19
numAnchors0.020.000.01
numLoops0.010.000.02
padGRanges0.130.030.16
pcaPlot000
plotTopLoops1.020.021.03
quickAssoc0.030.030.06
quickAssocVoom0.020.030.05
removeRegion0.150.020.17
removeSelfLoops000
rmchr0.110.010.13
sampleNames-loops-method0.020.000.01
slidingWindowTest000
splitSamples0.080.000.08
subsetLoops0.010.000.02
subsetRegion0.410.000.40
subsetRegionAB0.340.050.39
summary-loops-method0.110.050.16
topLoops0.070.010.09
union-loops-loops-method0.320.110.42
updateLDGroups000

diffloop.Rcheck/examples_x64/diffloop-Ex.timings

nameusersystemelapsed
addchr0.180.000.17
annotateAnchors0.110.010.13
annotateAnchors.bed0.060.020.08
annotateAnchors.bigwig0.040.000.04
annotateLoops0.520.010.54
annotateLoops.dge0.360.000.36
bedToGRanges0.060.000.06
calcLDSizeFactors000
callCCDs000
computeBoundaryScores000
featureTest000
filterLoops0.080.000.08
filterSpanningLoops0.010.000.02
getHumanGenes0.050.000.04
getHumanTSS0.170.000.18
getMouseGenes0.110.000.11
getMouseTSS0.190.000.18
interchromosomal0.010.000.02
intrachromosomal0.020.000.01
keepCTCFloops0.100.000.09
keepEPloops0.310.000.32
loopAssoc000
loopDistancePlot0.020.000.01
loopGenes0.090.020.11
loopMetrics000
loopPlot0.860.030.89
loopWidth0.030.000.03
loopsMake000
loopsMake.mango000
loopsSubset0.310.000.32
mangoCorrection0.140.000.14
manyLoopPlots0.080.000.07
mergeAnchors0.140.000.14
numAnchors000
numLoops0.010.000.02
padGRanges0.100.030.12
pcaPlot000
plotTopLoops1.450.001.45
quickAssoc0.050.000.05
quickAssocVoom0.030.000.03
removeRegion0.170.000.17
removeSelfLoops0.020.000.02
rmchr0.170.000.17
sampleNames-loops-method000
slidingWindowTest000
splitSamples0.090.000.10
subsetLoops0.030.000.03
subsetRegion0.420.020.43
subsetRegionAB0.220.010.23
summary-loops-method0.090.000.10
topLoops0.030.000.03
union-loops-loops-method0.220.000.22
updateLDGroups000