BioC 2.13: CHECK report for cobindR on perceval

Package: cobindR

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cobindR_1.0.0.tar.gz

StartedAt: 2014-04-05 00:31:50 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:39:07 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 436.6 seconds

RetCode: 0

Status:  OK

CheckDir: cobindR.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/cobindR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.0.0’
* 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 ... [21s/22s] 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 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 ... [375s/211s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
plot.gc                19.649 39.691  19.918
testCpG                39.128  7.776  29.528
search.pwm             36.077  8.654  23.664
rtfbs                  30.859  6.412  18.343
search.gadem           26.709  4.115  20.673
write.sequences        25.167  3.840  19.267
sequences              13.396  2.218   7.306
binding_sites          10.627  4.475   9.232
configuration           9.977  4.284   6.891
pairs_of_interest       8.768  3.558   7.271
bg_pairs                9.083  2.661   7.373
bg_binding_sites        8.687  2.501   8.011
bg_sequences            8.404  2.439   6.778
experiment_description  8.064  2.726   6.651
pfm                     7.469  2.488   6.853
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [10s/10s]
 [10s/11s] 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-2.13-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	0.383	0.004	0.397
bg_binding_sites	8.687	2.501	8.011
bg_pairs	9.083	2.661	7.373
bg_sequence_origin	0.020	0.003	0.023
bg_sequence_source	0.023	0.002	0.025
bg_sequence_type	0.020	0.003	0.023
bg_sequences	8.404	2.439	6.778
binding_sites	10.627	4.475	9.232
cobindRConfiguration	0.018	0.004	0.021
cobindr-class	0.009	0.003	0.012
comment	0.281	0.016	0.297
configuration-class	0.012	0.003	0.014
configuration	9.977	4.284	6.891
downstream	0.021	0.004	0.027
experiment_description	8.064	2.726	6.651
fdrThreshold	0.019	0.004	0.024
get.bindingsite.ranges	0.013	0.002	0.014
id	0.016	0.002	0.018
location	0.284	0.018	0.314
mart	0.019	0.003	0.022
max_distance	0.021	0.002	0.022
name	0.755	0.080	0.853
pValue	0.015	0.004	0.019
pairs	0.015	0.004	0.021
pairs_of_interest	8.768	3.558	7.271
path	0.016	0.004	0.022
pfm	7.469	2.488	6.853
pfm_path	0.022	0.005	0.029
plot.gc	19.649	39.691	19.918
pseudocount	0.016	0.005	0.021
rtfbs	30.859	6.412	18.343
search.gadem	26.709	4.115	20.673
search.pwm	36.077	8.654	23.664
seqObj	0.298	0.024	0.322
sequence	0.280	0.013	0.292
sequence_origin	0.022	0.002	0.025
sequence_source	0.026	0.002	0.027
sequence_type	0.027	0.002	0.029
sequences	13.396	2.218	7.306
species	0.022	0.005	0.027
testCpG	39.128	7.776	29.528
threshold	0.018	0.004	0.021
uid	0.263	0.013	0.279
upstream	0.018	0.003	0.022
write.sequences	25.167	3.840	19.267