Package: HiCcompare

Version: 1.5.3

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:HiCcompare.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings HiCcompare_1.5.3.tar.gz

StartedAt: 2019-04-09 01:12:35 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:20:31 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 475.3 seconds

RetCode: 0

Status:  OK

CheckDir: HiCcompare.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:HiCcompare.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings HiCcompare_1.5.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/HiCcompare.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCcompare/DESCRIPTION’ ... OK
* this is package ‘HiCcompare’ version ‘1.5.3’
* 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     787.280  2.957 126.808
hic_simulate       77.116  0.340  13.892
sim_matrix         64.707  0.288  11.232
sim.other.methods  49.628  0.148   8.000
visualize_pvals    30.523  0.108   5.532
hic_diff           27.412  0.088   7.129
hic_compare        17.311  0.014   2.935
manhattan_plot      9.281  0.060   1.957
cooler2sparse       8.854  0.044   2.028
* 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-3.9-bioc/meat/HiCcompare.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL HiCcompare
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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(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 
132.821   0.918  32.686 

name	user	system	elapsed
KRnorm	0.006	0.000	0.007
MA_norm	0.107	0.004	0.110
MD.plot1	0.882	0.004	0.886
MD.plot2	3.073	0.013	0.729
SCN	0.003	0.000	0.003
cooler2sparse	8.854	0.044	2.028
create.hic.table	0.534	0.000	0.085
filter_params	787.280	2.957	126.808
full2sparse	0.140	0.000	0.024
get_CNV	0.000	0.001	0.001
hic_compare	17.311	0.014	2.935
hic_diff	27.412	0.088	7.129
hic_loess	0.326	0.008	0.334
hic_simulate	77.116	0.340	13.892
hicpro2bedpe	0	0	0
make_InteractionSet	0.243	0.000	0.243
manhattan_plot	9.281	0.060	1.957
remove_centromere	0.001	0.000	0.002
sim.other.methods	49.628	0.148	8.000
sim_matrix	64.707	0.288	11.232
sparse2full	0.004	0.000	0.004
split_centromere	0.449	0.004	0.090
total_sum	0.687	0.004	0.268
visualize_pvals	30.523	0.108	5.532