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This page was generated on 2021-10-22 12:04:06 -0400 (Fri, 22 Oct 2021).

CHECK results for multiHiCcompare on nebbiolo2

To the developers/maintainers of the multiHiCcompare package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/multiHiCcompare.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 1240/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multiHiCcompare 1.11.0  (landing page)
John Stansfield , Mikhail Dozmorov
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/multiHiCcompare
git_branch: master
git_last_commit: c70ffc2
git_last_commit_date: 2021-05-19 12:37:18 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: multiHiCcompare
Version: 1.11.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:multiHiCcompare.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings multiHiCcompare_1.11.0.tar.gz
StartedAt: 2021-10-21 21:01:38 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 21:05:21 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 223.7 seconds
RetCode: 0
Status:   OK  
CheckDir: multiHiCcompare.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:multiHiCcompare.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings multiHiCcompare_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/multiHiCcompare.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multiHiCcompare/DESCRIPTION’ ... OK
* this is package ‘multiHiCcompare’ version ‘1.11.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘multiHiCcompare’ 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
* 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 ... NOTE
.count_manhattan: no visible global function definition for ‘textxy’
cyclic_loess: no visible binding for global variable ‘chr’
cyclic_loess: no visible binding for global variable ‘region1’
cyclic_loess: no visible binding for global variable ‘region2’
exportJuicebox: no visible binding for global variable ‘logCPM’
exportJuicebox: no visible binding for global variable ‘logFC’
exportJuicebox: no visible binding for global variable ‘p.adj’
fastlo: no visible binding for global variable ‘chr’
fastlo: no visible binding for global variable ‘region1’
fastlo: no visible binding for global variable ‘region2’
hic_exactTest: no visible binding for global variable ‘chr’
hic_exactTest: no visible binding for global variable ‘region1’
hic_exactTest: no visible binding for global variable ‘region2’
hic_filter: no visible binding for global variable ‘hg19_cyto’
hic_glm: no visible binding for global variable ‘chr’
hic_glm: no visible binding for global variable ‘region1’
hic_glm: no visible binding for global variable ‘region2’
make_hicexp: no visible binding for global variable ‘hg19_cyto’
make_hicexp: no visible binding for global variable ‘region2’
make_hicexp: no visible binding for global variable ‘region1’
make_hicexp: no visible binding for global variable ‘chr’
perm_test: no visible binding for global variable ‘chr’
perm_test: no visible global function definition for ‘IRanges’
topDirs: no visible binding for global variable ‘logCPM’
topDirs: no visible binding for global variable ‘logFC’
topDirs: no visible binding for global variable ‘p.adj’
Undefined global functions or variables:
  IRanges chr hg19_cyto logCPM logFC p.adj region1 region2 textxy
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/multiHiCcompare.Rcheck/00check.log’
for details.



Installation output

multiHiCcompare.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL multiHiCcompare
###
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##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘multiHiCcompare’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (multiHiCcompare)

Tests output

multiHiCcompare.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(multiHiCcompare)
> 
> test_check("multiHiCcompare")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
 33.020   1.037  33.802 

Example timings

multiHiCcompare.Rcheck/multiHiCcompare-Ex.timings

nameusersystemelapsed
Hicexp-class0.0370.0110.049
MD_composite0.1130.0200.134
MD_hicexp1.3720.0201.392
cyclic_loess1.5890.0521.625
exportJuicebox0.0430.0080.045
fastlo0.8060.0040.793
hic_exactTest000
hic_filter1.2460.0481.283
hic_glm000
hic_scale0.0750.0120.074
hic_table0.0080.0120.020
make_hicexp0.7710.0280.779
manhattan_hicexp0.3740.0200.387
meta0.0110.0010.010
normalized0.0100.0000.009
perm_test000
plot_counts0.0860.0070.094
plot_pvals0.0520.0040.057
pval_heatmap0.7840.0080.786
resolution0.010.000.01
results0.010.000.01
topDirs0.0300.0040.033