regioneR 1.8.1
Bernat Gel
| 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/regioneR | | Last Changed Rev: 131318 / Revision: 131943 | | Last Changed Date: 2017-07-18 08:48:04 -0400 (Tue, 18 Jul 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 regioneR_1.8.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/regioneR.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 ‘regioneR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘regioneR’ version ‘1.8.1’
* 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 ‘regioneR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘memoise’ ‘GenomicRanges’ ‘BSgenome’ ‘rtracklayer’ ‘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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
commonRegions: no visible global function definition for ‘hasArg’
createFunctionsList: no visible global function definition for ‘hasArg’
extendRegions: no visible global function definition for ‘hasArg’
joinRegions: no visible global function definition for ‘hasArg’
localZScore: no visible global function definition for ‘hasArg’
meanDistance: no visible global function definition for ‘hasArg’
meanInRegions: no visible global function definition for ‘hasArg’
mergeRegions: no visible global function definition for ‘hasArg’
numOverlaps: no visible global function definition for ‘hasArg’
overlapGraphicalSummary: no visible global function definition for
‘hasArg’
overlapPermTest: no visible global function definition for ‘hasArg’
overlapRegions: no visible global function definition for ‘hasArg’
overlapRegions: no visible global function definition for ‘queryHits’
overlapRegions: no visible global function definition for ‘subjectHits’
permTest: no visible global function definition for ‘hasArg’
plot.localZScoreResultsList: no visible global function definition for
‘is’
plot.permTestResultsList: no visible global function definition for
‘is’
plotRegions: no visible global function definition for ‘hasArg’
randomizeRegions: no visible global function definition for ‘hasArg’
removeOverlapping: no visible global function definition for
‘queryHits’
removeOverlapping: no visible global function definition for
‘subjectHits’
resampleRegions: no visible global function definition for ‘hasArg’
splitRegions: no visible global function definition for ‘hasArg’
subtractRegions: no visible global function definition for ‘hasArg’
toDataframe: no visible global function definition for ‘hasArg’
toDataframe: no visible global function definition for ‘is’
toGRanges: no visible global function definition for ‘hasArg’
toGRanges: no visible global function definition for ‘is’
toGRanges : <anonymous>: no visible global function definition for
‘read.delim’
toGRanges : <anonymous> : <anonymous>: no visible global function
definition for ‘read.csv’
uniqueRegions: no visible global function definition for ‘hasArg’
Undefined global functions or variables:
hasArg is queryHits read.csv read.delim subjectHits
Consider adding
importFrom("methods", "hasArg", "is")
importFrom("utils", "read.csv", "read.delim")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
circularRandomizeRegions 20.392 11.252 35.862
getMask 15.524 10.732 26.312
filterChromosomes 15.416 9.824 25.289
maskFromBSGenome 14.476 7.228 21.736
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/regioneR.Rcheck/00check.log’
for details.