Package: HiCcompare

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HiCcompare_1.0.0.tar.gz

StartedAt: 2018-04-12 05:01:26 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 05:06:22 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 295.1 seconds

RetCode: 0

Status:  OK

CheckDir: HiCcompare.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HiCcompare_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/HiCcompare.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.0.0’
* 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 ‘HiCcompare’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    doc    1.3Mb
* 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 loading without being on the library search path ... 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
.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’
.internal_weight_M: no visible binding for global variable ‘A’
.internal_weight_M: no visible binding for global variable ‘adj.IF1’
.internal_weight_M: no visible binding for global variable ‘adj.IF2’
.internal_weight_M: no visible binding for global variable ‘adj.M’
.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’
.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’
full2sparse: no visible binding for global variable ‘IF’
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’
plot_A : <anonymous>: no visible binding for global variable ‘adj.IF1’
plot_A : <anonymous>: no visible binding for global variable ‘adj.IF2’
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’
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 adj.IF1 adj.IF2 adj.M bias.slope
  centromere_locations chr1 chr2 fold.change i j p.adj p.value region1
  region2 start1 start2
Consider adding
  importFrom("stats", "D")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
sim.other.methods 12.402  2.586  15.313
hic_simulate      12.681  1.925  14.868
* 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-3.6-bioc/meat/HiCcompare.Rcheck/00check.log’
for details.

* installing *source* package ‘HiCcompare’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HiCcompare)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: 27 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 34.770   1.742  37.212 

name	user	system	elapsed
KRnorm	0.007	0.001	0.012
MA_norm	0.148	0.007	0.157
MD.plot1	0.807	0.021	0.846
MD.plot2	4.328	0.345	4.820
SCN	0.002	0.001	0.002
cooler2sparse	1.441	0.047	1.511
create.hic.table	0.014	0.003	0.016
full2sparse	0.006	0.001	0.008
get_CNV	0.001	0.000	0.000
hic_diff	3.580	0.466	4.124
hic_loess	0.251	0.010	0.268
hic_simulate	12.681	1.925	14.868
hicpro2bedpe	0.000	0.000	0.001
make_InteractionSet	0.453	0.005	0.466
plot_A	3.169	0.032	3.648
remove_centromere	0.003	0.000	0.003
sim.other.methods	12.402	2.586	15.313
sparse2full	0.003	0.000	0.004
split_centromere	0.013	0.002	0.014
total_sum	0.228	0.014	0.243
visualize_pvals	3.692	0.671	4.418
weight_M	0.562	0.039	0.612