MethylSeekR 1.16.0
Lukas Burger
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/MethylSeekR | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings MethylSeekR_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/MethylSeekR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MethylSeekR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethylSeekR’ version ‘1.16.0’
* 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 ‘MethylSeekR’ 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.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘parallel’
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
Namespace in Imports field not imported from: ‘geneplotter’
All declared Imports should be used.
Package in Depends field not imported from: ‘rtracklayer’
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
PMDviterbiSegmentation : <anonymous>: no visible global function
definition for ‘predict’
PMDviterbiSegmentation : <anonymous>: no visible global function
definition for ‘Rle’
PMDviterbiSegmentation : <anonymous>: no visible global function
definition for ‘runValue’
calculateAlphaDistr : <anonymous>: no visible global function
definition for ‘Rle’
calculateFDRs: no visible global function definition for ‘queryHits’
calculateFDRs : <anonymous>: no visible global function definition for
‘Rle’
calculateFDRs : <anonymous>: no visible global function definition for
‘runValue’
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
function definition for ‘Rle’
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
function definition for ‘nrun’
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
function definition for ‘runValue’
plotFinalSegmentation: no visible global function definition for ‘Rle’
removeSNPs: no visible global function definition for ‘queryHits’
segmentUMRsLMRs : <anonymous>: no visible global function definition
for ‘Rle’
segmentUMRsLMRs : <anonymous>: no visible global function definition
for ‘runValue’
segmentUMRsLMRs: no visible global function definition for ‘queryHits’
segmentUMRsLMRs: no visible global function definition for
‘subjectHits’
segmentUMRsLMRs: no visible global function definition for ‘Rle’
segmentUMRsLMRs: no visible global function definition for ‘DataFrame’
segmentUMRsLMRs: no visible global function definition for
‘colorRampPalette’
Undefined global functions or variables:
DataFrame Rle colorRampPalette nrun predict queryHits runValue
subjectHits
Consider adding
importFrom("grDevices", "colorRampPalette")
importFrom("stats", "predict")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
MethylSeekR-package 44.540 0.952 67.620
plotPMDSegmentation 26.392 0.352 26.772
savePMDSegments 25.616 0.292 25.935
segmentPMDs 24.252 0.208 24.479
calculateFDRs 6.792 0.028 25.660
plotAlphaDistributionOneChr 5.728 0.064 5.800
* 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
‘/home/biocbuild/bbs-3.5-bioc/meat/MethylSeekR.Rcheck/00check.log’
for details.