Package: cobindR

Version: 1.18.0

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_1.18.0.tar.gz

StartedAt: 2018-10-16 20:36:08 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 20:42:04 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 355.6 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_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/cobindR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.18.0’
* 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-3.7-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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
plot.gc                18.708 25.569  12.439
testCpG                25.944 10.188  14.859
rtfbs                  24.688 10.151   8.451
search.pwm             23.214  7.049  12.471
write.sequences        14.534  6.106   8.523
search.gadem           14.163  3.853   9.087
bg_sequences            7.096  6.929   3.798
bg_binding_sites        7.628  3.252   5.294
pfm                     5.462  2.650   3.544
bg_pairs                5.631  2.152   3.750
sequences               5.452  2.089   3.736
pairs_of_interest       5.219  2.037   3.404
configuration           5.279  1.800   3.493
binding_sites           5.201  1.871   3.380
experiment_description  5.152  1.864   3.306
* 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, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/cobindR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cobindR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘cobindR’ ...
** 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
Warning: multiple methods tables found for ‘path’
Warning: multiple methods tables found for ‘path<-’
* DONE (cobindR)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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 Oct 16 20:41:56 2018 
*********************************************** 
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 
 11.316   0.550  11.880 

name	user	system	elapsed
SeqObj-class	0.001	0.000	0.002
bg_binding_sites	7.628	3.252	5.294
bg_pairs	5.631	2.152	3.750
bg_sequence_origin	0.005	0.000	0.005
bg_sequence_source	0.005	0.000	0.006
bg_sequence_type	0.004	0.001	0.004
bg_sequences	7.096	6.929	3.798
binding_sites	5.201	1.871	3.380
cobindRConfiguration	0.004	0.001	0.004
cobindr-class	0.001	0.000	0.002
comment	0.124	0.006	0.137
configuration-class	0.003	0.000	0.004
configuration	5.279	1.800	3.493
downstream	0.004	0.000	0.004
experiment_description	5.152	1.864	3.306
fdrThreshold	0.003	0.000	0.004
get.bindingsite.ranges	0.001	0.000	0.001
id	0.003	0.000	0.003
location	0.091	0.006	0.096
mart	0.005	0.000	0.006
max_distance	0.005	0.000	0.006
name	0.117	0.007	0.124
pValue	0.003	0.000	0.004
pairs	0.003	0.001	0.004
pairs_of_interest	5.219	2.037	3.404
path	0.006	0.000	0.006
pfm	5.462	2.650	3.544
pfm_path	0.006	0.001	0.007
plot.gc	18.708	25.569	12.439
pseudocount	0.005	0.002	0.007
rtfbs	24.688	10.151	8.451
search.gadem	14.163	3.853	9.087
search.pwm	23.214	7.049	12.471
seqObj	0.143	0.018	0.162
sequence	0.114	0.010	0.125
sequence_origin	0.006	0.001	0.008
sequence_source	0.006	0.001	0.007
sequence_type	0.006	0.000	0.007
sequences	5.452	2.089	3.736
species	0.006	0.001	0.006
testCpG	25.944	10.188	14.859
threshold	0.005	0.000	0.006
uid	0.115	0.007	0.121
upstream	0.004	0.000	0.004
write.sequences	14.534	6.106	8.523