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CHECK report for multiHiCcompare on celaya2

This page was generated on 2019-10-16 13:03:04 -0400 (Wed, 16 Oct 2019).

Package 1067/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multiHiCcompare 1.2.0
John Stansfield
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/multiHiCcompare
Branch: RELEASE_3_9
Last Commit: 1ac2fa1
Last Changed Date: 2019-05-02 11:54:12 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: multiHiCcompare
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:multiHiCcompare.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings multiHiCcompare_1.2.0.tar.gz
StartedAt: 2019-10-16 04:57:27 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:04:49 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 442.0 seconds
RetCode: 0
Status:  OK 
CheckDir: multiHiCcompare.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:multiHiCcompare.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings multiHiCcompare_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/multiHiCcompare.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multiHiCcompare/DESCRIPTION’ ... OK
* this is package ‘multiHiCcompare’ version ‘1.2.0’
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/multiHiCcompare.Rcheck/00check.log’
for details.



Installation output

multiHiCcompare.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL multiHiCcompare
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages



> 
> test_check("multiHiCcompare")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 17 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 71.597  14.505  63.273 

Example timings

multiHiCcompare.Rcheck/multiHiCcompare-Ex.timings

nameusersystemelapsed
Hicexp-class0.0190.0160.035
MD_composite1.1500.0551.207
MD_hicexp0.8610.2541.120
cyclic_loess4.4770.4453.638
exportJuicebox0.1550.1270.079
fastlo2.1600.8061.799
hic_exactTest0.0000.0010.000
hic_filter2.4860.2951.448
hic_glm0.0010.0010.000
hic_scale0.1490.0970.167
hic_table0.0310.0170.103
make_hicexp2.6920.3052.838
manhattan_hicexp0.7020.1450.758
meta0.0160.0070.025
normalized0.0170.0110.027
perm_test0.0000.0000.001
plot_counts0.3000.1670.219
plot_pvals0.2900.1590.151
pval_heatmap3.5930.6433.356
resolution0.0170.0120.029
results0.0150.0110.026
topDirs0.7140.0420.201