PWMEnrich 4.8.2
Robert Stojnic
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/PWMEnrich | | Last Changed Rev: 117513 / Revision: 122332 | | Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / 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 PWMEnrich_4.8.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/PWMEnrich.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PWMEnrich/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PWMEnrich’ version ‘4.8.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘PWMEnrich’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
doc 1.4Mb
extdata 3.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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' calls in package code:
‘PWMEnrich.Dmelanogaster.background’ ‘PWMEnrich.Hsapiens.background’
‘PWMEnrich.Mmusculus.background’ ‘parallel’
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
colMedians: no visible binding for global variable ‘median’
colSds: no visible binding for global variable ‘sd’
getPromoters: no visible global function definition for
‘providerVersion’
getPromoters: no visible global function definition for ‘data’
gevPerSequence: no visible global function definition for ‘predict.lm’
logNormPval: no visible global function definition for ‘plnorm’
makePWMGEVBackground : <anonymous>: no visible global function
definition for ‘lm’
makePWMLognBackground : dlnorm.lcen: no visible global function
definition for ‘dlnorm’
makePWMLognBackground : dlnorm.lcen: no visible global function
definition for ‘plnorm’
makePWMLognBackground: no visible binding for global variable ‘sd’
makePWMLognBackground: no visible global function definition for
‘quantile’
makePWMLognBackground: no visible global function definition for
‘median’
makePWMLognBackground: no visible global function definition for
‘optimize’
makePWMPvalCutoffBackground: no visible global function definition for
‘quantile’
makePWMPvalCutoffBackground: no visible global function definition for
‘ecdf’
makePWMPvalCutoffBackgroundFromSeq: no visible global function
definition for ‘na.omit’
makePWMPvalCutoffBackgroundFromSeq: no visible global function
definition for ‘quantile’
makePWMPvalCutoffBackgroundFromSeq: no visible global function
definition for ‘ecdf’
matrixShuffleZscorePerSequence: no visible binding for global variable
‘sd’
motifEcdf : <anonymous>: no visible global function definition for
‘na.omit’
motifEcdf: no visible binding for global variable ‘ecdf’
motifEnrichment: no visible binding for global variable ‘qlnorm’
motifEnrichment : <anonymous>: no visible global function definition
for ‘pchisq’
motifScores: no visible global function definition for ‘mclapply’
motifScoresBigMemory: no visible global function definition for
‘mclapply’
motifSimilarity: no visible binding for global variable ‘sd’
plotMotifScores: no visible global function definition for ‘palette’
plotMotifScores: no visible global function definition for ‘col2rgb’
plotMotifScores: no visible global function definition for ‘rgb’
plotMotifScores: no visible global function definition for ‘par’
plotMotifScores: no visible global function definition for ‘lines’
plotMotifScores: no visible global function definition for ‘polygon’
plotMotifScores: no visible global function definition for ‘rect’
plotMotifScores: no visible global function definition for ‘text’
registerCoresPWMEnrich: no visible global function definition for
‘detectCores’
tryAllMotifAlignments : <anonymous>: no visible global function
definition for ‘cor’
Undefined global functions or variables:
col2rgb cor data detectCores dlnorm ecdf lines lm mclapply median
na.omit optimize palette par pchisq plnorm polygon predict.lm
providerVersion qlnorm quantile rect rgb sd text
Consider adding
importFrom("grDevices", "col2rgb", "palette", "rgb")
importFrom("graphics", "lines", "par", "polygon", "rect", "text")
importFrom("stats", "cor", "dlnorm", "ecdf", "lm", "median", "na.omit",
"optimize", "pchisq", "plnorm", "predict.lm", "qlnorm",
"quantile", "sd")
importFrom("utils", "data")
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
motifScores 5.126 0.033 5.161
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/PWMEnrich.Rcheck/00check.log’
for details.