This page was generated on 2018-04-12 13:37:08 -0400 (Thu, 12 Apr 2018).
cobindR 1.16.0 Manuela Benary
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
URL: https://git.bioconductor.org/packages/cobindR |
Branch: RELEASE_3_6 |
Last Commit: fcd8051 |
Last Changed Date: 2017-10-30 12:40:05 -0400 (Mon, 30 Oct 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
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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_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/cobindR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.16.0’
* 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 18.189 25.830 11.901
testCpG 18.036 4.477 13.036
search.gadem 16.602 3.366 8.132
search.pwm 12.737 3.454 10.662
rtfbs 11.933 3.031 8.967
write.sequences 10.258 2.053 8.004
sequences 9.598 1.430 3.212
bg_pairs 5.008 1.559 3.494
pairs_of_interest 4.117 1.318 2.923
bg_sequences 4.163 1.165 3.012
bg_binding_sites 4.469 0.842 4.461
binding_sites 3.917 1.084 2.980
* 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-3.6-bioc/meat/cobindR.Rcheck/00check.log’
for details.