Back to Multiple platform build/check report for BioC 3.8
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

CHECK report for multiHiCcompare on merida1

This page was generated on 2019-04-16 12:11:50 -0400 (Tue, 16 Apr 2019).

Package 1022/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multiHiCcompare 1.0.0
John Stansfield
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/multiHiCcompare
Branch: RELEASE_3_8
Last Commit: e315dae
Last Changed Date: 2018-10-30 11:42:10 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: multiHiCcompare
Version: 1.0.0
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_1.0.0.tar.gz
StartedAt: 2019-04-16 01:29:58 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:35:26 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 328.0 seconds
RetCode: 0
Status:  OK 
CheckDir: multiHiCcompare.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/multiHiCcompare.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.0.0’
* 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’
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
Consider adding
  importFrom("graphics", "axis")
  importFrom("stats", "end", "start")
  importFrom("utils", "tail")
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
Examples with CPU or elapsed time > 5s
             user system elapsed
make_hicexp 4.096  2.288    2.61
* 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-3.8-bioc/meat/multiHiCcompare.Rcheck/00check.log’
for details.



Installation output

multiHiCcompare.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL multiHiCcompare
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘multiHiCcompare’ ...
** 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
* DONE (multiHiCcompare)

Tests output

multiHiCcompare.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 62.390  13.058  50.465 

Example timings

multiHiCcompare.Rcheck/multiHiCcompare-Ex.timings

nameusersystemelapsed
Hicexp-class0.0180.0080.025
MD_composite0.1920.0270.219
MD_hicexp1.2020.1311.339
cyclic_loess2.9990.8162.151
fastlo3.3431.2221.398
hic_exactTest0.0020.0020.001
hic_filter1.7921.8600.966
hic_glm0.0010.0020.001
hic_scale1.2250.2770.173
hic_table0.4300.0060.038
make_hicexp4.0962.2882.610
manhattan_hicexp1.0010.8550.616
meta0.0150.0020.018
normalized0.0120.0040.016
perm_test000
plot_counts0.3180.3500.147
plot_pvals0.5290.7900.170
pval_heatmap2.6641.1882.231
resolution0.0100.0030.013
results0.0100.0030.013
topDirs0.1000.0740.082