motifRG 1.21.0
Zizhen Yao
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/motifRG | | Last Changed Rev: 129129 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings motifRG_1.21.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/motifRG.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifRG/DESCRIPTION’ ... OK
* this is package ‘motifRG’ version ‘1.21.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘Biostrings’ ‘IRanges’ ‘seqLogo’ ‘parallel’ ‘grid’ ‘BSgenome’
‘XVector’ ‘BSgenome.Hsapiens.UCSC.hg19’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘motifRG’ 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.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘Biostrings’ ‘IRanges’ ‘seqLogo’ ‘parallel’ ‘methods’ ‘grid’ ‘graphics’ ‘XVector’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘parallel’ which was already attached by Depends.
Please remove these calls from your code.
Namespaces in Imports field not imported from:
‘graphics’ ‘methods’
All declared Imports should be used.
Packages in Depends field not imported from:
‘BSgenome.Hsapiens.UCSC.hg19’ ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bestPWMMatch: no visible global function definition for ‘Rle’
discretize.glm: no visible global function definition for ‘glm.fit’
findMotif : refinePattern: no visible global function definition for
‘t.test’
findMotif : refinePattern: no visible global function definition for
‘new’
findPatternView: no visible global function definition for ‘as’
getScore: no visible global function definition for ‘binomial’
getScore : <anonymous>: no visible global function definition for
‘glm.fit’
getScore : <anonymous>: no visible global function definition for
‘summary.glm’
matchPWMCoor: no visible global function definition for ‘as’
matchPWMCoor: no visible global function definition for ‘GRanges’
motifHtmlTable: no visible global function definition for ‘png’
motifHtmlTable: no visible global function definition for ‘par’
motifHtmlTable: no visible global function definition for ‘dev.off’
motifLatexTable: no visible global function definition for ‘pdf’
motifLatexTable: no visible global function definition for ‘par’
motifLatexTable: no visible global function definition for ‘dev.off’
plotPWM: no visible global function definition for ‘axis’
plotPWM: no visible global function definition for ‘par’
plotPWM: no visible global function definition for ‘col2rgb’
plotPWM: no visible global function definition for ‘rgb’
plotPWM: no visible global function definition for ‘points’
plotPair: no visible global function definition for ‘rgb’
plotPair: no visible global function definition for ‘lines’
Undefined global functions or variables:
GRanges Rle as axis binomial col2rgb dev.off glm.fit lines new par
pdf png points rgb summary.glm t.test
Consider adding
importFrom("grDevices", "col2rgb", "dev.off", "pdf", "png", "rgb")
importFrom("graphics", "axis", "lines", "par", "points")
importFrom("methods", "as", "new")
importFrom("stats", "binomial", "glm.fit", "summary.glm", "t.test")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: YY1.control.Rd:8-9: Dropping empty section \details
prepare_Rd: YY1.peak.Rd:8-9: Dropping empty section \details
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
findMotif 157.687 87.64 95.727
* 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: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/motifRG.Rcheck/00check.log’
for details.