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CHECK report for multiHiCcompare on malbec2

This page was generated on 2020-10-17 11:55:13 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE multiHiCcompare PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1154/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multiHiCcompare 1.6.0
John Stansfield
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/multiHiCcompare
Branch: RELEASE_3_11
Last Commit: 6522884
Last Changed Date: 2020-04-27 15:18:41 -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: multiHiCcompare
Version: 1.6.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:multiHiCcompare.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings multiHiCcompare_1.6.0.tar.gz
StartedAt: 2020-10-17 03:31:33 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:37:07 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 333.9 seconds
RetCode: 0
Status:  OK 
CheckDir: multiHiCcompare.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:multiHiCcompare.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings multiHiCcompare_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/multiHiCcompare.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.6.0’
* 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 ... NOTE
Namespace in Imports field not imported from: ‘GenomeInfoDbData’
  All declared Imports should be used.
* 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 ‘tail’
.count_manhattan: no visible global function definition for ‘axis’
.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’
exportJuicebox: no visible global function definition for ‘write.table’
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 global function definition for ‘seqlevelsStyle<-’
perm_test: no visible binding for global variable ‘chr’
perm_test: no visible binding for global variable ‘start’
perm_test: no visible binding for global variable ‘end’
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’
topDirs: no visible binding for global variable ‘avgLogCPM’
topDirs: no visible binding for global variable ‘avgLogFC’
topDirs: no visible binding for global variable ‘avgP.adj’
topDirs: no visible binding for global variable ‘avgD’
Undefined global functions or variables:
  IRanges avgD avgLogCPM avgLogFC avgP.adj axis chr end hg19_cyto
  logCPM logFC p.adj region1 region2 seqlevelsStyle<- start tail textxy
  write.table
Consider adding
  importFrom("graphics", "axis")
  importFrom("stats", "end", "start")
  importFrom("utils", "tail", "write.table")
to your NAMESPACE file.
* 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 ... 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/multiHiCcompare.Rcheck/00check.log’
for details.



Installation output

multiHiCcompare.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL multiHiCcompare
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘multiHiCcompare’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 17 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 54.675   0.586  49.609 

Example timings

multiHiCcompare.Rcheck/multiHiCcompare-Ex.timings

nameusersystemelapsed
Hicexp-class0.0140.0000.014
MD_composite0.1170.0160.133
MD_hicexp0.6000.0080.608
cyclic_loess2.9720.0202.423
exportJuicebox0.0620.0000.042
fastlo1.6940.0151.208
hic_exactTest0.0000.0000.001
hic_filter1.2500.0400.882
hic_glm000
hic_scale0.3360.0120.136
hic_table0.0160.0040.020
make_hicexp2.1320.0271.420
manhattan_hicexp0.4560.0080.446
meta0.010.000.01
normalized0.0090.0000.009
perm_test000
plot_counts0.1180.0000.118
plot_pvals0.0910.0000.090
pval_heatmap1.5520.0201.386
resolution0.0140.0000.014
results0.0140.0000.014
topDirs0.0380.0120.050