BioC 3.1: CHECK report for cobindR on zin2

Package: cobindR

Version: 1.6.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings cobindR_1.6.0.tar.gz

StartedAt: 2015-10-08 23:47:07 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:53:12 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 364.6 seconds

RetCode: 0

Status:  OK

CheckDir: cobindR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings cobindR_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-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 ‘1.6.0’
* 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 ... [14s/19s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [140s/148s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
testCpG                16.949  1.048  19.910
rtfbs                  15.358  1.161  12.480
search.pwm             14.654  1.282  14.860
plot.gc                 6.907  7.444  13.920
search.gadem           11.881  0.582  14.142
write.sequences        11.014  0.542  13.406
sequences               6.474  0.618   5.543
pfm                     4.297  0.716   4.810
binding_sites           4.376  0.510   5.560
configuration           4.138  0.507   6.197
bg_pairs                4.074  0.499   5.470
bg_binding_sites        4.190  0.376   6.149
experiment_description  4.034  0.494   5.433
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [6s/10s]
 [7s/10s] 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-3.1-bioc/meat/cobindR.Rcheck/00check.log’
for details.

* installing *source* package ‘cobindR’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (cobindR)

name	user	system	elapsed
SeqObj-class	0.001	0.000	0.001
bg_binding_sites	4.190	0.376	6.149
bg_pairs	4.074	0.499	5.470
bg_sequence_origin	0.004	0.000	0.004
bg_sequence_source	0.003	0.000	0.014
bg_sequence_type	0.004	0.000	0.004
bg_sequences	4.111	0.416	4.812
binding_sites	4.376	0.510	5.560
cobindRConfiguration	0.003	0.000	0.015
cobindr-class	0.001	0.000	0.001
comment	0.117	0.000	0.234
configuration-class	0.001	0.000	0.001
configuration	4.138	0.507	6.197
downstream	0.004	0.000	0.004
experiment_description	4.034	0.494	5.433
fdrThreshold	0.003	0.000	0.003
get.bindingsite.ranges	0.001	0.000	0.001
id	0.003	0.000	0.004
location	0.100	0.004	0.105
mart	0.000	0.004	0.003
max_distance	0.003	0.000	0.003
name	0.102	0.004	0.110
pValue	0.003	0.000	0.006
pairs	0.003	0.000	0.003
pairs_of_interest	3.713	0.458	4.054
path	0.003	0.000	0.003
pfm	4.297	0.716	4.810
pfm_path	0.003	0.000	0.003
plot.gc	6.907	7.444	13.920
pseudocount	0.004	0.000	0.004
rtfbs	15.358	1.161	12.480
search.gadem	11.881	0.582	14.142
search.pwm	14.654	1.282	14.860
seqObj	0.107	0.007	0.123
sequence	0.105	0.012	0.234
sequence_origin	0.004	0.000	0.012
sequence_source	0.004	0.000	0.004
sequence_type	0.004	0.000	0.004
sequences	6.474	0.618	5.543
species	0.004	0.000	0.003
testCpG	16.949	1.048	19.910
threshold	0.003	0.000	0.003
uid	0.098	0.003	0.107
upstream	0.003	0.000	0.003
write.sequences	11.014	0.542	13.406