BioC 3.2: CHECK report for chipenrich on perceval

Package: chipenrich

Version: 1.7.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chipenrich_1.7.2.tar.gz

StartedAt: 2015-08-23 23:01:37 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 23:08:41 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 423.8 seconds

RetCode: 0

Status:  OK

CheckDir: chipenrich.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chipenrich_1.7.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/chipenrich.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.7.2’
* 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 ... [18s/18s] 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:
  Ryan P. Welch <welchr@umich.edu> [aut, cre, cph]
  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
chipenrich: no visible binding for global variable ‘P.value’
load_peaks: no visible binding for global variable ‘chrom’
randomize_locusdef : <anonymous>: no visible binding for global
  variable ‘chrom’
read_bed: no visible binding for global variable ‘chrom’
read_bedgff: no visible binding for global variable ‘chrom’
read_peaks: no visible binding for global variable ‘chrom’
setup_ldef: no visible binding for global variable ‘chrom’
test_approx: no visible binding for global variable ‘geneid’
test_binomial: no visible binding for global variable ‘geneid’
test_fisher_exact: no visible binding for global variable ‘geneid’
test_gam: no visible binding for global variable ‘geneid’
test_gam_ratio: no visible binding for global variable ‘geneid’
test_gam_ratio_splineless: no visible binding for global variable
  ‘geneid’
* 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 ... [162s/162s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
chipenrich          62.688  1.674  64.497
plot_expected_peaks 37.627  1.711  39.426
plot_spline_length  36.967  2.211  39.209
plot_gene_coverage   8.966  0.087   9.054
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [84s/84s]
 [85s/84s] 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-3.2-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	62.688	1.674	64.497
plot_dist_to_tss	1.470	0.030	1.502
plot_expected_peaks	37.627	1.711	39.426
plot_gene_coverage	8.966	0.087	9.054
plot_spline_length	36.967	2.211	39.209
supported_genesets	0.003	0.000	0.003
supported_genomes	0.003	0.001	0.003
supported_locusdefs	0.003	0.000	0.004
supported_methods	0.000	0.000	0.001
supported_read_lengths	0.005	0.000	0.006