BioC 3.6: CHECK report for HiCcompare on malbec1

Package: HiCcompare

Version: 0.99.13

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings HiCcompare_0.99.13.tar.gz

StartedAt: 2017-08-15 23:55:11 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:58:38 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 207.0 seconds

RetCode: 0

Status:  OK

CheckDir: HiCcompare.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings HiCcompare_0.99.13.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/HiCcompare.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘0.99.13’
* 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 ... 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 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’
.loess.as: no visible global function definition for ‘lines’
.loess.as: no visible global function definition for ‘persp’
.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’
.sim.mat: no visible global function definition for ‘head’
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 global function definition for ‘is’
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_diff: no visible global function definition for ‘is’
hic_simulate: no visible binding for global variable ‘bias.slope’
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’
Undefined global functions or variables:
  D IF IF1 IF2 M adj.IF1 adj.IF2 adj.M bias.slope chr1 chr2 fold.change
  head i is j lines p.adj p.value persp region1 region2
Consider adding
  importFrom("graphics", "lines", "persp")
  importFrom("methods", "is")
  importFrom("stats", "D")
  importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
hic_simulate      12.048  0.036  12.090
sim.other.methods 11.204  0.036  11.245
* 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: 1 NOTE
See
  ‘/home/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)

name	user	system	elapsed
KRnorm	0.000	0.000	0.003
MA_norm	0.100	0.004	0.103
MD.plot1	2.304	0.020	2.325
MD.plot2	4.216	0.028	4.248
SCN	0.000	0.000	0.003
cooler2sparse	1.020	0.016	1.040
create.hic.table	0.012	0.000	0.012
full2sparse	0.004	0.000	0.006
hic_diff	3.512	0.012	3.523
hic_loess	0.464	0.000	0.466
hic_simulate	12.048	0.036	12.090
make_InteractionSet	0.336	0.004	0.342
remove_centromere	0.000	0.000	0.002
sim.other.methods	11.204	0.036	11.245
sparse2full	0.004	0.000	0.002