BioC 3.4: CHECK report for cobindR on morelia

Package: cobindR

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cobindR_1.12.0.tar.gz

StartedAt: 2017-04-15 00:11:33 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:18:08 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 395.8 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 cobindR_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/cobindR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cobindR/DESCRIPTION’ ... OK
* this is package ‘cobindR’ version ‘1.12.0’
* 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 ... 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
compare.samples: no visible global function definition for
  ‘wilcox.test’
input.pfm.similarity: no visible global function definition for ‘combn’
parallelize: no visible global function definition for
  ‘installed.packages’
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’
find.pairs,cobindr: no visible global function definition for ‘combn’
get.bindingsite.ranges,cobindr: no visible global function definition
  for ‘GRanges’
get.bindingsite.ranges,cobindr: no visible binding for global variable
  ‘sequence_names’
get.bindingsite.ranges,cobindr: no visible binding for global variable
  ‘pwm’
plot.detrending,cobindr: no visible global function definition for
  ‘par’
plot.detrending,cobindr: no visible global function definition for
  ‘plot’
plot.detrending,cobindr: no visible global function definition for
  ‘lines’
plot.detrending,cobindr: no visible global function definition for
  ‘title’
plot.gc,cobindr: no visible global function definition for
  ‘txtProgressBar’
plot.gc,cobindr: no visible global function definition for
  ‘setTxtProgressBar’
plot.gc,cobindr: no visible global function definition for ‘rainbow’
plot.gc,cobindr: no visible global function definition for ‘par’
plot.gc,cobindr: no visible global function definition for ‘matplot’
plot.gc,cobindr: no visible global function definition for ‘points’
plot.gc,cobindr: no visible global function definition for ‘legend’
plot.pairdistance,cobindr: no visible global function definition for
  ‘hist’
plot.pairdistribution,cobindr: no visible global function definition
  for ‘plot’
plot.positionprofile,cobindr: no visible global function definition for
  ‘rainbow’
plot.positionprofile,cobindr: no visible global function definition for
  ‘matplot’
plot.positionprofile,cobindr: no visible global function definition for
  ‘legend’
plot.positions.simple,cobindr: no visible global function definition
  for ‘rainbow’
plot.positions.simple,cobindr: no visible global function definition
  for ‘par’
plot.positions.simple,cobindr: no visible global function definition
  for ‘plot’
plot.positions.simple,cobindr: no visible global function definition
  for ‘points’
plot.positions.simple,cobindr: no visible global function definition
  for ‘legend’
plot.positions,cobindr: no visible global function definition for
  ‘rainbow’
plot.positions,cobindr: no visible binding for global variable ‘n.cpu’
plot.positions,cobindr: no visible global function definition for
  ‘hclust’
plot.positions,cobindr: no visible global function definition for
  ‘dist’
plot.positions,cobindr: no visible global function definition for
  ‘order.dendrogram’
plot.positions,cobindr: no visible global function definition for
  ‘as.dendrogram’
plot.positions,cobindr: no visible global function definition for
  ‘grid.newpage’
plot.positions,cobindr: no visible global function definition for
  ‘pushViewport’
plot.positions,cobindr: no visible global function definition for
  ‘viewport’
plot.positions,cobindr: no visible global function definition for
  ‘plot_gene_map’
plot.positions,cobindr: no visible global function definition for
  ‘popViewport’
plot.positions,cobindr: no visible global function definition for
  ‘gpar’
plot.positions,cobindr: no visible global function definition for
  ‘grid_legend’
plot.tfbs.heatmap,cobindr: no visible global function definition for
  ‘phyper’
plot.tfbs.heatmap,cobindr: no visible global function definition for
  ‘heat.colors’
plot.tfbs.venndiagram,cobindr: no visible global function definition
  for ‘venn.diagram’
plot.tfbs.venndiagram,cobindr: no visible global function definition
  for ‘grid.draw’
plot.tfbslogo,cobindr : <anonymous>: no visible global function
  definition for ‘makePWM’
plot.tfbslogo,cobindr : <anonymous>: no visible global function
  definition for ‘seqLogo’
plot.tfbslogo,cobindr : <anonymous>: no visible global function
  definition for ‘grid.text’
plot.tfbslogo,cobindr : <anonymous>: no visible global function
  definition for ‘gpar’
read.pfm,configuration: no visible global function definition for
  ‘read.table’
read.sequences,configuration: no visible global function definition for
  ‘txtProgressBar’
read.sequences,configuration: no visible global function definition for
  ‘setTxtProgressBar’
read.sequences,configuration: no visible global function definition for
  ‘read.table’
search.gadem,cobindr : <anonymous>: no visible global function
  definition for ‘GADEM’
search.gadem,cobindr: no visible global function definition for ‘GADEM’
search.gadem,cobindr: no visible global function definition for
  ‘nMotifs’
search.pwm,cobindr: no visible global function definition for ‘error’
testCpG,cobindr: no visible global function definition for ‘hist’
testCpG,cobindr: no visible global function definition for ‘layout’
testCpG,cobindr: no visible global function definition for ‘par’
testCpG,cobindr: no visible global function definition for ‘barplot’
write.bindingsites.table,cobindr: no visible global function definition
  for ‘mcols’
write.bindingsites.table,cobindr: no visible global function definition
  for ‘write.table’
write.bindingsites,cobindr: no visible global function definition for
  ‘write.table’
write,cobindr-character: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  GADEM GRanges MotifDb as.dendrogram barplot combn dist error gpar
  grid.draw grid.newpage grid.text grid_legend hclust heat.colors hist
  installed.packages layout legend lines makePWM matplot mclapply mcols
  n.cpu nMotifs order.dendrogram par phyper plot plot_gene_map points
  popViewport pushViewport pwm rainbow read.table seqLogo
  sequence_names setTxtProgressBar sfCpus sfInit sfLapply sfStop title
  txtProgressBar venn.diagram viewport wilcox.test write.table
Consider adding
  importFrom("grDevices", "heat.colors", "rainbow")
  importFrom("graphics", "barplot", "hist", "layout", "legend", "lines",
             "matplot", "par", "plot", "points", "title")
  importFrom("stats", "as.dendrogram", "dist", "hclust",
             "order.dendrogram", "phyper", "wilcox.test")
  importFrom("utils", "combn", "installed.packages", "read.table",
             "setTxtProgressBar", "txtProgressBar", "write.table")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
plot.gc                13.171 13.020   8.322
search.pwm             20.125  4.450  12.102
write.sequences        17.093  4.330   9.935
testCpG                17.404  3.084  19.028
search.gadem           17.007  2.668   9.589
rtfbs                  14.821  3.457  10.112
sequences               8.272  1.701   3.767
bg_sequences            5.331  1.344   3.866
bg_binding_sites        4.943  1.319  69.259
binding_sites           4.816  1.225   3.302
pairs_of_interest       4.521  1.091   3.396
bg_pairs                4.261  1.302   3.000
experiment_description  4.464  1.098   3.183
pfm                     4.160  0.959   3.553
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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
  ‘/Users/biocbuild/bbs-3.4-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	0.002	0.000	0.002
bg_binding_sites	4.943	1.319	69.259
bg_pairs	4.261	1.302	3.000
bg_sequence_origin	0.005	0.001	0.005
bg_sequence_source	0.004	0.000	0.004
bg_sequence_type	0.005	0.001	0.019
bg_sequences	5.331	1.344	3.866
binding_sites	4.816	1.225	3.302
cobindRConfiguration	0.004	0.001	0.005
cobindr-class	0.001	0.000	0.001
comment	0.097	0.005	0.101
configuration-class	0.002	0.000	0.002
configuration	3.989	0.872	2.898
downstream	0.004	0.000	0.005
experiment_description	4.464	1.098	3.183
fdrThreshold	0.005	0.000	0.005
get.bindingsite.ranges	0.001	0.000	0.000
id	0.003	0.000	0.004
location	0.088	0.004	0.091
mart	0.004	0.000	0.005
max_distance	0.003	0.000	0.004
name	0.110	0.004	0.115
pValue	0.004	0.000	0.004
pairs	0.003	0.000	0.003
pairs_of_interest	4.521	1.091	3.396
path	0.002	0.000	0.003
pfm	4.160	0.959	3.553
pfm_path	0.004	0.001	0.005
plot.gc	13.171	13.020	8.322
pseudocount	0.005	0.001	0.006
rtfbs	14.821	3.457	10.112
search.gadem	17.007	2.668	9.589
search.pwm	20.125	4.450	12.102
seqObj	0.139	0.012	0.152
sequence	0.153	0.021	0.174
sequence_origin	0.005	0.000	0.006
sequence_source	0.005	0.000	0.005
sequence_type	0.005	0.001	0.005
sequences	8.272	1.701	3.767
species	0.005	0.001	0.015
testCpG	17.404	3.084	19.028
threshold	0.004	0.000	0.005
uid	0.125	0.005	0.129
upstream	0.005	0.000	0.005
write.sequences	17.093	4.330	9.935