Package: cobindR

Version: 1.18.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cobindR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings cobindR_1.18.0.tar.gz

StartedAt: 2018-10-17 01:15:52 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 01:25:04 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 552.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: cobindR.Rcheck

Warnings: 1

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cobindR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings cobindR_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/cobindR.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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 'C:/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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
testCpG          19.91   0.01   20.23
search.pwm       16.50   0.03   16.54
rtfbs            15.49   0.04   15.89
write.sequences  12.50   0.03   12.53
search.gadem     11.94   0.01   11.95
plot.gc           6.86   0.11    6.97
bg_binding_sites  4.75   1.58    6.49
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
testCpG          20.81   0.02   20.89
search.pwm       19.33   0.04   19.38
rtfbs            15.14   0.12   15.64
write.sequences  13.78   0.02   13.79
search.gadem     10.14   0.05   10.22
plot.gc           6.28   0.08    6.37
bg_binding_sites  5.49   0.45    5.94
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/cobindR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/cobindR_1.18.0.tar.gz && rm -rf cobindR.buildbin-libdir && mkdir cobindR.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cobindR.buildbin-libdir cobindR_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL cobindR_1.18.0.zip && rm cobindR_1.18.0.tar.gz cobindR_1.18.0.zip
###
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100  821k  100  821k    0     0  11.5M      0 --:--:-- --:--:-- --:--:-- 12.5M

install for i386

* 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
  converting help for package 'cobindR'
    finding HTML links ... done
    SeqObj-class                            html  
    bg_binding_sites                        html  
    finding level-2 HTML links ... done

    bg_pairs                                html  
    bg_sequence_origin                      html  
    bg_sequence_source                      html  
    bg_sequence_type                        html  
    bg_sequences                            html  
    binding_sites                           html  
    cobindRConfiguration                    html  
    cobindr-class                           html  
    cobindr-internal                        html  
    cobindr-package                         html  
    comment                                 html  
    configuration-class                     html  
    configuration                           html  
    downstream                              html  
    experiment_description                  html  
    fdrThreshold                            html  
    find.pairs                              html  
    get.bindingsite.ranges                  html  
    get.pairs                               html  
    get.significant.pairs                   html  
    id                                      html  
    location                                html  
    mart                                    html  
    max_distance                            html  
    name                                    html  
    pValue                                  html  
    pairs                                   html  
    pairs_of_interest                       html  
    path                                    html  
    pfm                                     html  
    pfm_path                                html  
    plot.detrending                         html  
    plot.gc                                 html  
    plot.pairdistance                       html  
    plot.pairdistribution                   html  
    plot.positionprofile                    html  
    plot.positions                          html  
    plot.positions.simple                   html  
    plot.tfbs.heatmap                       html  
    plot.tfbs.venndiagram                   html  
    plot.tfbslogo                           html  
    predicted2pwm                           html  
    pseudocount                             html  
    rtfbs                                   html  
    search.gadem                            html  
    search.pwm                              html  
    seqObj                                  html  
    sequence                                html  
    sequence_origin                         html  
    sequence_source                         html  
    sequence_type                           html  
    sequences                               html  
    species                                 html  
    testCpG                                 html  
    threshold                               html  
    uid                                     html  
    upstream                                html  
    write.bindingsites                      html  
    write.bindingsites.table                html  
    write.pairs                             html  
    write.sequences                         html  
** 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<-'
In R CMD INSTALL

install for x64

* installing *source* package 'cobindR' ...
** testing if installed package can be loaded
Warning: multiple methods tables found for 'path'
Warning: multiple methods tables found for 'path<-'
* MD5 sums
packaged installation of 'cobindR' as cobindR_1.18.0.zip
* DONE (cobindR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'cobindR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 17 01:24:44 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 
   8.32    0.75    9.06 

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 17 01:24:55 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 
   9.93    0.42   10.34