BioC 2.13: CHECK report for cobindR on zin1

Package: cobindR

Version: 1.0.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings cobindR_1.0.0.tar.gz

StartedAt: 2014-04-05 00:29:04 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:33:24 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 259.6 seconds

RetCode: 0

Status:  OK

CheckDir: cobindR.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/cobindR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ... [13s/13s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [191s/132s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
testCpG                26.010  0.852  20.083
search.pwm             22.998  1.236  15.329
rtfbs                  21.885  1.152  13.198
search.gadem           16.713  0.476  13.107
write.sequences        15.841  0.416  12.571
plot.gc                 9.196  5.876   7.768
sequences               9.508  0.412   4.653
bg_pairs                6.788  0.584   5.167
bg_binding_sites        6.176  0.340   5.264
experiment_description  5.868  0.368   4.719
bg_sequences            5.785  0.384   4.419
binding_sites           5.796  0.344   4.734
configuration           5.756  0.368   4.700
pairs_of_interest       5.641  0.448   4.492
pfm                     5.669  0.388   4.454
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [6s/6s]
 [6s/6s] 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
  ‘/home/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	0.004	0.000	0.004
bg_binding_sites	6.176	0.340	5.264
bg_pairs	6.788	0.584	5.167
bg_sequence_origin	0.008	0.000	0.011
bg_sequence_source	0.004	0.008	0.013
bg_sequence_type	0.012	0.000	0.012
bg_sequences	5.785	0.384	4.419
binding_sites	5.796	0.344	4.734
cobindRConfiguration	0.008	0.000	0.011
cobindr-class	0.004	0.000	0.004
comment	0.104	0.016	0.119
configuration-class	0.000	0.004	0.004
configuration	5.756	0.368	4.700
downstream	0.008	0.004	0.012
experiment_description	5.868	0.368	4.719
fdrThreshold	0.016	0.000	0.015
get.bindingsite.ranges	0.004	0.000	0.003
id	0.008	0.000	0.012
location	0.276	0.040	0.314
mart	0.008	0.000	0.009
max_distance	0.008	0.000	0.009
name	0.104	0.012	0.119
pValue	0.012	0.000	0.010
pairs	0.004	0.004	0.011
pairs_of_interest	5.641	0.448	4.492
path	0.012	0.000	0.010
pfm	5.669	0.388	4.454
pfm_path	0.008	0.000	0.010
plot.gc	9.196	5.876	7.768
pseudocount	0.012	0.000	0.012
rtfbs	21.885	1.152	13.198
search.gadem	16.713	0.476	13.107
search.pwm	22.998	1.236	15.329
seqObj	0.124	0.016	0.141
sequence	0.132	0.000	0.136
sequence_origin	0.012	0.000	0.011
sequence_source	0.012	0.000	0.011
sequence_type	0.008	0.004	0.010
sequences	9.508	0.412	4.653
species	0.008	0.000	0.011
testCpG	26.010	0.852	20.083
threshold	0.012	0.000	0.013
uid	0.132	0.004	0.135
upstream	0.012	0.000	0.011
write.sequences	15.841	0.416	12.571