BioC 3.2: CHECK report for cobindR on linux1.bioconductor.org

Package: cobindR

Version: 1.8.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings cobindR_1.8.0.tar.gz

StartedAt: 2015-10-27 02:19:32 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:24:15 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 282.2 seconds

RetCode: 0

Status:  OK

CheckDir: cobindR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings cobindR_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/cobindR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cobindR/DESCRIPTION’ ... OK
* this is package ‘cobindR’ version ‘1.8.0’
* 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 ... [17s/17s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
'library' or 'require' calls in package code:
  ‘MotifDb’ ‘parallel’ ‘snowfall’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 ‘mclapply’
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’
get.bindingsite.ranges,cobindr : .local: no visible global function
  definition for ‘GRanges’
get.bindingsite.ranges,cobindr : .local: no visible binding for global
  variable ‘sequence_names’
get.bindingsite.ranges,cobindr : .local: no visible binding for global
  variable ‘pwm’
plot.positions,cobindr : .local: no visible binding for global variable
  ‘n.cpu’
plot.positions,cobindr : .local: no visible global function definition
  for ‘grid.newpage’
plot.positions,cobindr : .local: no visible global function definition
  for ‘pushViewport’
plot.positions,cobindr : .local: no visible global function definition
  for ‘viewport’
plot.positions,cobindr : .local: no visible global function definition
  for ‘plot_gene_map’
plot.positions,cobindr : .local: no visible global function definition
  for ‘popViewport’
plot.positions,cobindr : .local: no visible global function definition
  for ‘gpar’
plot.positions,cobindr : .local: no visible global function definition
  for ‘grid_legend’
plot.tfbs.venndiagram,cobindr : .local: no visible global function
  definition for ‘venn.diagram’
plot.tfbs.venndiagram,cobindr : .local: no visible global function
  definition for ‘grid.draw’
plot.tfbslogo,cobindr : .local : <anonymous>: no visible global
  function definition for ‘makePWM’
plot.tfbslogo,cobindr : .local : <anonymous>: no visible global
  function definition for ‘seqLogo’
plot.tfbslogo,cobindr : .local : <anonymous>: no visible global
  function definition for ‘grid.text’
plot.tfbslogo,cobindr : .local : <anonymous>: no visible global
  function definition for ‘gpar’
search.gadem,cobindr : .local : <anonymous>: no visible global function
  definition for ‘GADEM’
search.gadem,cobindr : .local: no visible global function definition
  for ‘GADEM’
search.gadem,cobindr : .local: no visible global function definition
  for ‘nMotifs’
search.pwm,cobindr : .local: no visible global function definition for
  ‘error’
write.bindingsites.table,cobindr : .local: no visible global function
  definition for ‘mcols’
* 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 ... [175s/107s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
testCpG                21.585  2.535  14.765
rtfbs                  18.871  2.643   9.455
search.pwm             18.084  2.166  12.333
plot.gc                 8.206 10.796   8.475
write.sequences        14.525  1.393  11.072
search.gadem           13.943  1.309  10.493
sequences               7.229  0.754   3.029
bg_binding_sites        5.313  0.683   4.474
bg_sequences            5.239  0.705   4.108
bg_pairs                4.770  0.921   3.438
binding_sites           4.916  0.738   3.929
pairs_of_interest       4.597  0.862   3.729
experiment_description  4.413  0.754   3.399
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [8s/8s]
 [8s/8s] 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-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	0.001	0.000	0.002
bg_binding_sites	5.313	0.683	4.474
bg_pairs	4.770	0.921	3.438
bg_sequence_origin	0.004	0.000	0.005
bg_sequence_source	0.004	0.000	0.004
bg_sequence_type	0.000	0.004	0.004
bg_sequences	5.239	0.705	4.108
binding_sites	4.916	0.738	3.929
cobindRConfiguration	0.002	0.000	0.002
cobindr-class	0.001	0.000	0.001
comment	0.083	0.008	0.091
configuration-class	0.001	0.000	0.001
configuration	4.160	0.645	3.031
downstream	0.003	0.000	0.002
experiment_description	4.413	0.754	3.399
fdrThreshold	0.000	0.004	0.003
get.bindingsite.ranges	0.000	0.000	0.001
id	0.002	0.000	0.003
location	0.094	0.000	0.097
mart	0.003	0.000	0.003
max_distance	0.003	0.000	0.002
name	0.083	0.008	0.090
pValue	0.003	0.000	0.003
pairs	0.002	0.000	0.003
pairs_of_interest	4.597	0.862	3.729
path	0.003	0.000	0.003
pfm	4.038	0.623	3.442
pfm_path	0.005	0.000	0.005
plot.gc	8.206	10.796	8.475
pseudocount	0.003	0.000	0.003
rtfbs	18.871	2.643	9.455
search.gadem	13.943	1.309	10.493
search.pwm	18.084	2.166	12.333
seqObj	0.090	0.004	0.094
sequence	0.098	0.004	0.102
sequence_origin	0.003	0.000	0.003
sequence_source	0.003	0.000	0.003
sequence_type	0.002	0.000	0.003
sequences	7.229	0.754	3.029
species	0.003	0.000	0.003
testCpG	21.585	2.535	14.765
threshold	0.004	0.000	0.004
uid	0.146	0.000	0.146
upstream	0.004	0.000	0.004
write.sequences	14.525	1.393	11.072