BioC 2.14: CHECK report for cobindR on petty

Package: cobindR

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cobindR_1.2.0.tar.gz

StartedAt: 2014-10-07 21:27:09 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:37:29 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 619.6 seconds

RetCode: 0

Status:  OK

CheckDir: cobindR.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 --no-multiarch cobindR_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/cobindR.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cobindR/DESCRIPTION’ ... OK
* this is package ‘cobindR’ version ‘1.2.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘genoPlotR’
* 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 ‘cobindR’ can be installed ... [33s/34s] 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
parallelize: no visible global function definition for ‘sfCpus’
parallelize: no visible global function definition for ‘sfInit’
parallelize: no visible global function definition for ‘sfLapply’
parallelize: no visible global function definition for ‘sfStop’
query.motifDb: no visible binding for global variable ‘MotifDb’
* 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 ... [555s/277s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
plot.gc                27.123 45.100  16.916
testCpG                56.715 10.269  43.649
search.pwm             51.548 10.637  32.600
rtfbs                  46.364 12.005  23.560
write.sequences        44.270 11.107  26.161
search.gadem           37.003  5.261  27.030
sequences              22.492  5.037   9.843
pairs_of_interest      15.245  6.765   9.578
binding_sites          13.801  5.511   9.920
configuration          13.891  5.162  10.056
bg_binding_sites       14.327  4.661  11.241
bg_pairs               13.100  4.908   9.535
pfm                    13.270  4.676   9.492
bg_sequences           12.912  4.712   9.698
experiment_description 11.929  3.585   9.494
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [16s/16s]
 [16s/17s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/cobindR.Rcheck/00check.log’
for details.

* installing *source* package ‘cobindR’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘sequence’ in package ‘cobindR’
Creating a generic function for ‘write’ from package ‘base’ in package ‘cobindR’
Creating a generic function for ‘write.fasta’ from package ‘seqinr’ in package ‘cobindR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cobindR)

name	user	system	elapsed
SeqObj-class	0.003	0.000	0.003
bg_binding_sites	14.327	4.661	11.241
bg_pairs	13.100	4.908	9.535
bg_sequence_origin	0.011	0.002	0.013
bg_sequence_source	0.011	0.002	0.013
bg_sequence_type	0.011	0.001	0.013
bg_sequences	12.912	4.712	9.698
binding_sites	13.801	5.511	9.920
cobindRConfiguration	0.011	0.002	0.014
cobindr-class	0.003	0.001	0.003
comment	0.366	0.020	0.403
configuration-class	0.004	0.001	0.005
configuration	13.891	5.162	10.056
downstream	0.011	0.001	0.014
experiment_description	11.929	3.585	9.494
fdrThreshold	0.010	0.002	0.011
get.bindingsite.ranges	0.001	0.000	0.001
id	0.010	0.002	0.011
location	0.371	0.022	0.396
mart	0.011	0.002	0.013
max_distance	0.011	0.001	0.012
name	0.383	0.020	0.403
pValue	0.012	0.002	0.014
pairs	0.012	0.002	0.013
pairs_of_interest	15.245	6.765	9.578
path	0.010	0.002	0.012
pfm	13.270	4.676	9.492
pfm_path	0.011	0.001	0.013
plot.gc	27.123	45.100	16.916
pseudocount	0.013	0.003	0.017
rtfbs	46.364	12.005	23.560
search.gadem	37.003	5.261	27.030
search.pwm	51.548	10.637	32.600
seqObj	0.377	0.032	0.410
sequence	0.385	0.031	0.424
sequence_origin	0.011	0.002	0.013
sequence_source	0.012	0.001	0.013
sequence_type	0.012	0.002	0.013
sequences	22.492	5.037	9.843
species	0.011	0.002	0.013
testCpG	56.715	10.269	43.649
threshold	0.011	0.001	0.013
uid	0.373	0.016	0.392
upstream	0.011	0.002	0.012
write.sequences	44.270	11.107	26.161