Package: HiCcompare

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HiCcompare.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HiCcompare_1.4.0.tar.gz

StartedAt: 2019-04-16 00:32:26 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:36:59 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 273.4 seconds

RetCode: 0

Status:  OK

CheckDir: HiCcompare.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HiCcompare.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HiCcompare_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/HiCcompare.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 ‘HiCcompare/DESCRIPTION’ ... OK
* this is package ‘HiCcompare’ 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 ‘HiCcompare’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
* 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
.adjust_pval : <anonymous>: no visible binding for global variable
  ‘p.adj’
.adjust_pval : <anonymous>: no visible binding for global variable
  ‘p.value’
.adjust_pval: no visible binding for global variable ‘p.value’
.adjust_pval: no visible binding for global variable ‘p.adj’
.calc.pval: no visible binding for global variable ‘D’
.calc.pval: no visible binding for global variable ‘p.value’
.calc.pval: no visible binding for global variable ‘p.adj’
.calc.pval: no visible binding for global variable ‘adj.M’
.calc.pval: no visible binding for global variable ‘fold.change’
.calc.pval: no visible binding for global variable ‘adj.IF2’
.calc.pval: no visible binding for global variable ‘adj.IF1’
.calc_z2: no visible binding for global variable ‘Z’
.calc_z2: no visible global function definition for ‘pnorm’
.calc_z2: no visible binding for global variable ‘p.value’
.loess.matrix: no visible binding for global variable ‘adj.IF1’
.loess.matrix: no visible binding for global variable ‘IF1’
.loess.matrix: no visible binding for global variable ‘adj.IF2’
.loess.matrix: no visible binding for global variable ‘IF2’
.loess.matrix: no visible binding for global variable ‘adj.M’
.loess.matrix: no visible binding for global variable ‘A’
.split_cent: no visible binding for global variable
  ‘centromere_locations’
.split_cent: no visible binding for global variable ‘start1’
.split_cent: no visible binding for global variable ‘start2’
.split_cent: no visible binding for global variable ‘chr1’
.split_cent: no visible binding for global variable ‘chr2’
MA_norm: no visible binding for global variable ‘D’
MA_norm: no visible binding for global variable ‘M’
MA_norm: no visible binding for global variable ‘adj.IF1’
MA_norm: no visible binding for global variable ‘IF1’
MA_norm: no visible binding for global variable ‘adj.IF2’
MA_norm: no visible binding for global variable ‘IF2’
MA_norm: no visible binding for global variable ‘adj.M’
cooler2sparse: no visible binding for global variable ‘chr1’
cooler2sparse: no visible binding for global variable ‘chr2’
cooler2sparse: no visible binding for global variable ‘IF’
create.hic.table: no visible binding for global variable ‘D’
create.hic.table: no visible binding for global variable ‘region2’
create.hic.table: no visible binding for global variable ‘region1’
create.hic.table: no visible binding for global variable ‘IF2’
create.hic.table: no visible binding for global variable ‘M’
create.hic.table: no visible binding for global variable ‘IF1’
create.hic.table: no visible binding for global variable ‘i’
create.hic.table: no visible binding for global variable ‘j’
filter_params: no visible binding for global variable ‘M’
filter_params: no visible binding for global variable ‘IF1’
filter_params: no visible binding for global variable ‘IF2’
filter_params: no visible global function definition for ‘axis’
full2sparse: no visible binding for global variable ‘IF’
hic_compare : <anonymous>: no visible binding for global variable
  ‘p.adj’
hic_simulate: no visible binding for global variable ‘bias.slope’
hicpro2bedpe: no visible binding for global variable ‘chr1’
hicpro2bedpe: no visible binding for global variable ‘chr2’
manhattan_plot: no visible binding for global variable ‘bp’
manhattan_plot: no visible binding for global variable ‘count’
sim.other.methods: no visible binding for global variable ‘adj.IF1’
sim.other.methods: no visible binding for global variable ‘IF1’
sim.other.methods: no visible binding for global variable ‘adj.IF2’
sim.other.methods: no visible binding for global variable ‘IF2’
sim.other.methods: no visible binding for global variable ‘adj.M’
sim.other.methods: no visible binding for global variable ‘M’
sim_matrix: no visible binding for global variable ‘bias.slope’
total_sum: no visible binding for global variable ‘IF2’
total_sum: no visible binding for global variable ‘M’
total_sum: no visible binding for global variable ‘IF1’
total_sum: no visible binding for global variable ‘chr1’
volcano: no visible binding for global variable ‘A’
volcano: no visible binding for global variable ‘adj.IF1’
volcano: no visible binding for global variable ‘adj.IF2’
volcano: no visible binding for global variable ‘p.value’
volcano: no visible binding for global variable ‘D’
Undefined global functions or variables:
  A D IF IF1 IF2 M Z adj.IF1 adj.IF2 adj.M axis bias.slope bp
  centromere_locations chr1 chr2 count fold.change i j p.adj p.value
  pnorm region1 region2 start1 start2
Consider adding
  importFrom("graphics", "axis")
  importFrom("stats", "D", "pnorm")
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
filter_params     48.094 39.898  10.852
hic_diff          20.799 21.349   5.503
sim_matrix         4.650  5.670   1.858
hic_simulate       4.689  5.094   1.939
sim.other.methods  4.559  3.734   1.270
* 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/HiCcompare.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL HiCcompare
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘HiCcompare’ ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to 'ceiling' 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HiCcompare)

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(HiCcompare)
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> 
> test_check("HiCcompare")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 28 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 16.853   7.450  12.957 

name	user	system	elapsed
KRnorm	0.010	0.001	0.011
MA_norm	0.141	0.010	0.155
MD.plot1	0.804	0.017	0.830
MD.plot2	1.215	1.547	0.460
SCN	0.003	0.001	0.004
cooler2sparse	2.764	1.561	0.803
create.hic.table	0.077	0.115	0.023
filter_params	48.094	39.898	10.852
full2sparse	0.029	0.032	0.009
get_CNV	0.001	0.001	0.001
hic_compare	1.884	2.375	0.632
hic_diff	20.799	21.349	5.503
hic_loess	0.261	0.022	0.287
hic_simulate	4.689	5.094	1.939
hicpro2bedpe	0	0	0
make_InteractionSet	0.184	0.002	0.191
manhattan_plot	1.590	1.410	0.824
remove_centromere	0.002	0.001	0.002
sim.other.methods	4.559	3.734	1.270
sim_matrix	4.650	5.670	1.858
sparse2full	0.005	0.001	0.005
split_centromere	0.036	0.032	0.021
total_sum	1.389	0.848	0.281
visualize_pvals	2.898	2.055	1.018