segmentSeq 2.8.0
Thomas J. Hardcastle
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/segmentSeq | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings segmentSeq_2.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/segmentSeq.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘segmentSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘segmentSeq’ version ‘2.8.0’
* 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 ‘segmentSeq’ can be installed ... OK
* checking installed package size ... OK
* 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 loading without being on the library search path ... 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
.classifyNulls: no visible global function definition for ‘runif’
.constructNullPriors: no visible global function definition for ‘runif’
.constructNulls: no visible global function definition for ‘runif’
.getLocLikelihoods : NBdens : PDgivenr.NB: no visible global function
definition for ‘dnbinom’
.getLocLikelihoods : BBdens : PDgivenr.BB : dbetabinom: no visible
global function definition for ‘dbinom’
.massiveClassifyLoci: no visible global function definition for ‘runif’
.methFunction: no visible global function definition for ‘pbeta’
.plotSampleMeth: no visible global function definition for ‘lines’
.processPosts: no visible global function definition for ‘runif’
.subProfile : <anonymous> : summariseCoverage : <anonymous>: no visible
global function definition for ‘weighted.mean’
plotAverageProfile: no visible global function definition for ‘rainbow’
plotAverageProfile : <anonymous>: no visible global function definition
for ‘lines’
plotAverageProfile: no visible global function definition for ‘abline’
plotAverageProfile: no visible global function definition for ‘dev.cur’
plotAverageProfile: no visible global function definition for ‘par’
plotAverageProfile : <anonymous>: no visible global function definition
for ‘rainbow’
plotAverageProfile: no visible global function definition for ‘title’
plotAverageProfile: no visible global function definition for ‘lines’
plotAverageProfile: no visible global function definition for
‘weighted.mean’
plotMeth: no visible global function definition for ‘par’
plotMeth : <anonymous>: no visible global function definition for
‘abline’
plotMethDistribution: no visible global function definition for
‘rainbow’
readBAM : <anonymous>: no visible global function definition for
‘write.table’
readGeneric : <anonymous>: no visible global function definition for
‘read.table’
readGeneric : <anonymous>: no visible global function definition for
‘write.table’
Undefined global functions or variables:
abline dbinom dev.cur dnbinom lines par pbeta rainbow read.table
runif title weighted.mean write.table
Consider adding
importFrom("grDevices", "dev.cur", "rainbow")
importFrom("graphics", "abline", "lines", "par", "title")
importFrom("stats", "dbinom", "dnbinom", "pbeta", "runif",
"weighted.mean")
importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘normaliseNC’
Undocumented S4 methods:
generic '[' and siglist 'alignmentClass,ANY,ANY,ANY'
generic '[' and siglist 'alignmentData,ANY,ANY,ANY'
generic '[' and siglist 'alignmentMeth,ANY,ANY,ANY'
generic '[' and siglist 'lociData,ANY,ANY,ANY'
generic '[' and siglist 'methData,ANY,ANY,ANY'
generic '[' and siglist 'segClass,ANY,ANY,ANY'
generic '[' and siglist 'segData,ANY,ANY,ANY'
generic '[' and siglist 'segMeth,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
classifySeg 34.199 0.245 34.515
lociLikelihoods 13.792 0.069 13.886
heuristicSeg 12.103 0.040 12.151
readMeths 8.870 0.457 9.332
plotGenome 6.249 0.035 6.292
* 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: 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.4-bioc/meat/segmentSeq.Rcheck/00check.log’
for details.