Package: multiHiCcompare

Version: 1.4.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:multiHiCcompare.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings multiHiCcompare_1.4.0.tar.gz

StartedAt: 2020-04-15 05:56:53 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:02:59 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 365.9 seconds

RetCode: 0

Status:  OK

CheckDir: multiHiCcompare.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:multiHiCcompare.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings multiHiCcompare_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/multiHiCcompare.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.4.0’
* 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
Examples with CPU or elapsed time > 5s
        user system elapsed
fastlo 9.552  0.036   3.832
* 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-3.10-bioc/meat/multiHiCcompare.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL multiHiCcompare
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* installing to library ‘/home/biocbuild/bbs-3.10-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)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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)

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 
 85.164   0.812  60.765 

name	user	system	elapsed
Hicexp-class	0.012	0.008	0.022
MD_composite	0.860	0.028	0.890
MD_hicexp	0.664	0.016	0.688
cyclic_loess	2.740	0.020	2.198
exportJuicebox	0.644	0.000	0.195
fastlo	9.552	0.036	3.832
hic_exactTest	0	0	0
hic_filter	1.368	0.016	0.987
hic_glm	0	0	0
hic_scale	0.356	0.004	0.147
hic_table	0.524	0.012	0.130
make_hicexp	3.280	0.012	2.490
manhattan_hicexp	0.576	0.004	0.579
meta	0.012	0.000	0.015
normalized	0.012	0.000	0.015
perm_test	0	0	0
plot_counts	0.960	0.008	0.449
plot_pvals	0.996	0.000	0.459
pval_heatmap	2.976	0.032	2.890
resolution	0.012	0.000	0.015
results	0.012	0.004	0.017
topDirs	0.344	0.008	0.171