BioC 3.5: CHECK report for chipenrich on oaxaca

Package: chipenrich

Version: 1.13.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chipenrich_1.13.3.tar.gz

StartedAt: 2017-03-04 00:25:09 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 00:28:37 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 207.3 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_1.13.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/chipenrich.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.13.3’
* 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 ... 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
single_gam_fast: no visible global function definition for ‘predict’
single_gam_nb_fast: no visible global function definition for ‘predict’
test_gam_fast: no visible binding for global variable ‘geneid’
test_gam_fast: no visible global function definition for ‘predict’
test_gam_nb: no visible binding for global variable ‘geneid’
test_gam_nb_fast: no visible binding for global variable ‘geneid’
test_gam_nb_fast: no visible global function definition for ‘predict’
Undefined global functions or variables:
  geneid predict
Consider adding
  importFrom("stats", "predict")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
plot_spline_length 17.666  0.428  22.430
chipenrich         12.447  0.294  13.410
plot_gene_coverage  9.187  0.043   9.282
* 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
  ‘/Users/biocbuild/bbs-3.5-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
assign_peak_segments	0.862	0.049	3.868
assign_peaks	1.298	0.024	1.323
calc_peak_gene_overlap	0.588	0.036	0.665
chipenrich	12.447	0.294	13.410
load_peaks	0.050	0.002	0.137
num_peaks_per_gene	0.551	0.031	0.583
plot_dist_to_tss	0.278	0.019	0.298
plot_gene_coverage	9.187	0.043	9.282
plot_spline_length	17.666	0.428	22.430
read_bed	0.072	0.001	0.073
read_bedgff	0.083	0.001	0.084
supported_genesets	0.008	0.001	0.009
supported_genomes	0.003	0.000	0.003
supported_locusdefs	0.006	0.001	0.007
supported_methods	0	0	0
supported_read_lengths	0.006	0.001	0.007