Package: cobindR

Version: 1.22.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:cobindR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings cobindR_1.22.0.tar.gz

StartedAt: 2019-10-16 00:40:41 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 00:46:41 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 359.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: cobindR.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:cobindR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings cobindR_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/cobindR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.22.0’
* 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 ‘/home/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 : : no visible global function
  definition for ‘makePWM’
plot.tfbslogo,cobindr : : no visible global function
  definition for ‘seqLogo’
plot.tfbslogo,cobindr : : no visible global function
  definition for ‘grid.text’
plot.tfbslogo,cobindr : : 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 : : 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
plot.gc                10.163 41.084  34.770
rtfbs                  17.439  5.160   8.486
search.pwm             17.055  5.400  12.409
testCpG                16.698  4.589  13.233
search.gadem           11.627  3.217   9.507
write.sequences        10.192  2.376   7.887
bg_binding_sites        6.978  2.007   6.492
pfm                     3.881  1.669   3.911
sequences               3.637  1.677   3.691
bg_pairs                3.709  1.597   3.384
binding_sites           3.534  1.732   3.426
experiment_description  3.758  1.508   3.571
pairs_of_interest       3.655  1.490   3.603
configuration           3.435  1.672   3.385
bg_sequences            3.412  1.621   3.252
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/cobindR.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL cobindR
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 -- Wed Oct 16 00:46:35 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 
 10.838   0.420  11.263 

name	user	system	elapsed
SeqObj-class	0.001	0.000	0.001
bg_binding_sites	6.978	2.007	6.492
bg_pairs	3.709	1.597	3.384
bg_sequence_origin	0.003	0.000	0.003
bg_sequence_source	0.003	0.000	0.003
bg_sequence_type	0.002	0.000	0.002
bg_sequences	3.412	1.621	3.252
binding_sites	3.534	1.732	3.426
cobindRConfiguration	0.003	0.000	0.003
cobindr-class	0.001	0.000	0.001
comment	0.111	0.007	0.119
configuration-class	0.001	0.000	0.001
configuration	3.435	1.672	3.385
downstream	0.003	0.000	0.003
experiment_description	3.758	1.508	3.571
fdrThreshold	0.004	0.000	0.004
get.bindingsite.ranges	0	0	0
id	0.003	0.000	0.003
location	0.123	0.004	0.127
mart	0.003	0.000	0.004
max_distance	0.004	0.000	0.004
name	0.136	0.000	0.137
pValue	0.003	0.000	0.003
pairs	0.003	0.000	0.003
pairs_of_interest	3.655	1.490	3.603
path	0.003	0.000	0.003
pfm	3.881	1.669	3.911
pfm_path	0.004	0.000	0.003
plot.gc	10.163	41.084	34.770
pseudocount	0.004	0.000	0.004
rtfbs	17.439	5.160	8.486
search.gadem	11.627	3.217	9.507
search.pwm	17.055	5.400	12.409
seqObj	0.119	0.020	0.139
sequence	0.127	0.005	0.148
sequence_origin	0.003	0.000	0.003
sequence_source	0.004	0.000	0.004
sequence_type	0.003	0.000	0.003
sequences	3.637	1.677	3.691
species	0.003	0.000	0.003
testCpG	16.698	4.589	13.233
threshold	0.004	0.000	0.004
uid	0.141	0.009	0.150
upstream	0.003	0.000	0.004
write.sequences	10.192	2.376	7.887