Package: cobindR

Version: 1.21.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cobindR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cobindR_1.21.0.tar.gz

StartedAt: 2019-04-09 00:51:28 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:59:50 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 502.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: cobindR.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cobindR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cobindR_1.21.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/cobindR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cobindR/DESCRIPTION’ ... OK
* this is package ‘cobindR’ version ‘1.21.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: multiple methods tables found for ‘path’
  Warning: multiple methods tables found for ‘path<-’
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/cobindR.Rcheck/00install.out’ for details.
* 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 ... NOTE
Warning: multiple methods tables found for ‘path’
Warning: multiple methods tables found for ‘path<-’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.detrending plot.gc plot.pairdistance plot.positionprofile
  plot.positions plot.positions.simple plot.tfbs.heatmap
  plot.tfbs.venndiagram plot.tfbslogo
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
plot.gc                28.747 44.007  19.561
rtfbs                  35.083 17.177  12.511
search.pwm             30.960 11.965  17.539
testCpG                30.719 11.794  18.697
write.sequences        22.073 17.001  12.632
search.gadem           18.164  6.049  12.536
bg_binding_sites       11.253  4.396   8.741
bg_pairs                8.888  6.623   5.845
sequences               7.583  3.430   5.880
bg_sequences            6.885  3.521   4.872
configuration           7.010  3.009   5.135
pairs_of_interest       6.814  3.081   4.758
experiment_description  6.740  3.102   4.852
pfm                     6.781  3.051   4.735
binding_sites           6.652  3.157   4.605
* 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: 1 WARNING, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/cobindR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cobindR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘cobindR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘sequence’ in package ‘cobindR’
Creating a new generic function for ‘path’ in package ‘cobindR’
Creating a new generic function for ‘path<-’ 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 from temporary location
Warning: multiple methods tables found for ‘path’
Warning: multiple methods tables found for ‘path<-’
** testing if installed package can be loaded from final location
Warning: multiple methods tables found for ‘path’
Warning: multiple methods tables found for ‘path<-’
** testing if installed package keeps a record of temporary installation path
* DONE (cobindR)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage('cobindR', pattern="runit_.*\\.R$")

Attaching package: 'cobindR'

The following object is masked from 'package:base':

    sequence



RUNIT TEST PROTOCOL -- Tue Apr  9 00:59:40 2019 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
cobindR RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: multiple methods tables found for 'path' 
2: multiple methods tables found for 'path<-' 
> 
> proc.time()
   user  system elapsed 
 15.200   1.305  16.458 

name	user	system	elapsed
SeqObj-class	0.003	0.001	0.003
bg_binding_sites	11.253	4.396	8.741
bg_pairs	8.888	6.623	5.845
bg_sequence_origin	0.005	0.001	0.005
bg_sequence_source	0.004	0.001	0.005
bg_sequence_type	0.005	0.001	0.005
bg_sequences	6.885	3.521	4.872
binding_sites	6.652	3.157	4.605
cobindRConfiguration	0.005	0.001	0.005
cobindr-class	0.002	0.001	0.002
comment	0.203	0.016	0.219
configuration-class	0.003	0.001	0.004
configuration	7.010	3.009	5.135
downstream	0.005	0.001	0.005
experiment_description	6.740	3.102	4.852
fdrThreshold	0.006	0.001	0.007
get.bindingsite.ranges	0.000	0.000	0.001
id	0.005	0.001	0.006
location	0.185	0.016	0.200
mart	0.003	0.001	0.004
max_distance	0.003	0.001	0.004
name	0.173	0.012	0.184
pValue	0.004	0.001	0.004
pairs	0.004	0.001	0.004
pairs_of_interest	6.814	3.081	4.758
path	0.006	0.002	0.007
pfm	6.781	3.051	4.735
pfm_path	0.003	0.001	0.003
plot.gc	28.747	44.007	19.561
pseudocount	0.004	0.001	0.005
rtfbs	35.083	17.177	12.511
search.gadem	18.164	6.049	12.536
search.pwm	30.960	11.965	17.539
seqObj	0.207	0.027	0.233
sequence	0.209	0.021	0.230
sequence_origin	0.006	0.002	0.008
sequence_source	0.006	0.001	0.008
sequence_type	0.006	0.001	0.008
sequences	7.583	3.430	5.880
species	0.005	0.001	0.007
testCpG	30.719	11.794	18.697
threshold	0.005	0.001	0.006
uid	0.197	0.013	0.211
upstream	0.003	0.001	0.003
write.sequences	22.073	17.001	12.632