Package: HiCcompare

Version: 1.9.0

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_1.9.0.tar.gz

StartedAt: 2020-01-16 05:22:51 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 05:29:55 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 424.4 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_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/HiCcompare.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.9.0’
* 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.diff.thresh: no visible global function definition for ‘sd’
.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 global function definition for ‘sd’
.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’
.sim.mat: no visible global function definition for ‘head’
.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’
hic_simulate: no visible global function definition for ‘na.omit’
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.other.methods: no visible global function definition for ‘na.omit’
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 head i j na.omit
  p.adj p.value pnorm region1 region2 sd start1 start2
Consider adding
  importFrom("graphics", "axis")
  importFrom("stats", "D", "na.omit", "pnorm", "sd")
  importFrom("utils", "head")
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 (user + system) or elapsed time > 5s
                    user system elapsed
filter_params     50.016 25.268  15.365
hic_diff          18.287 11.698   5.876
sim_matrix         5.531  2.104   2.407
hic_simulate       5.639  1.960   2.369
sim.other.methods  3.472  1.697   1.679
* 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-3.11-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/4.0/Resources/library’
* installing *source* package ‘HiCcompare’ ...
** using staged installation
** 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 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 (HiCcompare)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 26.081   6.169  21.533 

name	user	system	elapsed
KRnorm	0.007	0.002	0.009
MA_norm	0.124	0.016	0.141
MD.plot1	0.340	0.042	0.383
MD.plot2	2.122	0.480	0.651
SCN	0.004	0.002	0.005
cooler2bedpe	0.001	0.001	0.000
cooler2sparse	1.789	0.790	1.552
create.hic.table	0.032	0.012	0.040
filter_params	50.016	25.268	15.365
full2sparse	0.042	0.036	0.011
get_CNV	0.002	0.001	0.000
hic_compare	3.479	1.013	0.812
hic_diff	18.287	11.698	5.876
hic_loess	0.328	0.055	0.384
hic_simulate	5.639	1.960	2.369
hicpro2bedpe	0.001	0.000	0.001
make_InteractionSet	0.467	0.006	0.473
manhattan_plot	1.627	0.654	1.102
remove_centromere	0.001	0.001	0.003
sim.other.methods	3.472	1.697	1.679
sim_matrix	5.531	2.104	2.407
sparse2full	0.005	0.002	0.006
split_centromere	0.038	0.015	0.031
total_sum	0.677	0.411	0.362
visualize_pvals	2.924	0.363	0.970