BioC 3.3: CHECK report for chipenrich on zin2

Package: chipenrich

Version: 1.10.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings chipenrich_1.10.0.tar.gz

StartedAt: 2016-10-13 00:20:47 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 00:25:13 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 266.2 seconds

RetCode: 0

Status:  OK

CheckDir: chipenrich.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings chipenrich_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/chipenrich.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chipenrich/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chipenrich’ version ‘1.10.0’
* 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 ‘chipenrich’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
  Chee Lee <cheelee@umich.edu> [aut, cre]
  Raymond G. Cavalcante <rcavalca@umich.edu> [aut, cre]
* 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
..plot_expected_peaks: no visible global function definition for
  ‘qpois’
..plot_expected_peaks: no visible global function definition for
  ‘as.formula’
calc_approx_weights: no visible global function definition for
  ‘as.formula’
calc_approx_weights: no visible global function definition for ‘fitted’
calc_approx_weights: no visible global function definition for ‘resid’
calc_spline_mappa: no visible global function definition for
  ‘as.formula’
calc_spline_mappa: no visible global function definition for ‘fitted’
calc_weights_gam: no visible global function definition for
  ‘as.formula’
calc_weights_gam: no visible global function definition for ‘fitted’
calc_weights_gam: no visible global function definition for ‘resid’
chipenrich: no visible global function definition for ‘data’
chipenrich: no visible global function definition for ‘na.omit’
chipenrich: no visible binding for global variable ‘P.value’
chipenrich: no visible global function definition for ‘write.table’
chipenrich: no visible global function definition for ‘pdf’
chipenrich: no visible global function definition for ‘dev.off’
get_ext: no visible global function definition for ‘tail’
load_peaks: no visible binding for global variable ‘chrom’
plot_dist_to_tss: no visible global function definition for ‘data’
plot_expected_peaks: no visible global function definition for ‘data’
plot_expected_peaks: no visible global function definition for
  ‘na.omit’
plot_gene_coverage: no visible global function definition for ‘data’
plot_spline_length: no visible global function definition for ‘data’
randomize_locusdef : <anonymous>: no visible binding for global
  variable ‘chrom’
read_bed: no visible global function definition for ‘read.table’
read_bed: no visible binding for global variable ‘chrom’
read_bedgff: no visible global function definition for ‘read.table’
read_bedgff: no visible binding for global variable ‘chrom’
read_mappa: no visible global function definition for ‘read.table’
read_peaks: no visible global function definition for ‘read.table’
read_peaks: no visible binding for global variable ‘chrom’
setup_geneset: no visible global function definition for ‘read.table’
setup_geneset: no visible global function definition for
  ‘complete.cases’
setup_geneset: no visible global function definition for ‘na.omit’
setup_ldef: no visible global function definition for ‘read.table’
setup_ldef: no visible global function definition for ‘complete.cases’
setup_ldef: no visible global function definition for ‘na.omit’
setup_ldef: no visible binding for global variable ‘chrom’
single_approx : lrm.fast: no visible global function definition for
  ‘pchisq’
single_gam: no visible global function definition for ‘as.formula’
single_gam: no visible global function definition for ‘coef’
supported_genesets: no visible global function definition for ‘data’
supported_genomes: no visible global function definition for ‘data’
supported_genomes: no visible global function definition for ‘na.omit’
supported_locusdefs: no visible global function definition for ‘data’
supported_read_lengths: no visible global function definition for
  ‘data’
test_approx: no visible binding for global variable ‘geneid’
test_approx: no visible global function definition for ‘p.adjust’
test_binomial: no visible binding for global variable ‘geneid’
test_binomial: no visible global function definition for ‘binom.test’
test_binomial: no visible global function definition for ‘p.adjust’
test_fisher_exact: no visible binding for global variable ‘geneid’
test_fisher_exact : <anonymous>: no visible global function definition
  for ‘fisher.test’
test_fisher_exact: no visible global function definition for ‘p.adjust’
test_gam: no visible binding for global variable ‘geneid’
test_gam: no visible global function definition for ‘p.adjust’
test_gam_ratio: no visible binding for global variable ‘geneid’
test_gam_ratio: no visible global function definition for ‘p.adjust’
test_gam_ratio_splineless: no visible binding for global variable
  ‘geneid’
test_gam_ratio_splineless: no visible global function definition for
  ‘p.adjust’
Undefined global functions or variables:
  P.value as.formula binom.test chrom coef complete.cases data dev.off
  fisher.test fitted geneid na.omit p.adjust pchisq pdf qpois
  read.table resid tail write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "as.formula", "binom.test", "coef",
             "complete.cases", "fisher.test", "fitted", "na.omit",
             "p.adjust", "pchisq", "qpois", "resid")
  importFrom("utils", "data", "read.table", "tail", "write.table")
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 sizes of PDF files under ‘inst/doc’ ... 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
chipenrich          42.385  0.183  45.667
plot_spline_length  24.669  0.076  24.944
plot_expected_peaks 23.421  0.023  23.801
plot_gene_coverage   5.700  0.016   5.732
* 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-3.3-bioc/meat/chipenrich.Rcheck/00check.log’
for details.

* installing *source* package ‘chipenrich’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (chipenrich)

name	user	system	elapsed
chipenrich	42.385	0.183	45.667
plot_dist_to_tss	0.578	0.000	0.583
plot_expected_peaks	23.421	0.023	23.801
plot_gene_coverage	5.700	0.016	5.732
plot_spline_length	24.669	0.076	24.944
supported_genesets	0.003	0.000	0.002
supported_genomes	0.002	0.000	0.003
supported_locusdefs	0.002	0.000	0.002
supported_methods	0.001	0.000	0.000
supported_read_lengths	0.003	0.000	0.004