segmentSeq 2.7.0
Thomas J. Hardcastle
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/segmentSeq | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings segmentSeq_2.7.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/segmentSeq.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘2.7.0’
* 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 ... NOTE
installed size is 10.0Mb
sub-directories of 1Mb or more:
extdata 9.2Mb
* 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 ... NOTE
'library' or 'require' call to ‘GenomicRanges’ which was already attached by Depends.
Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.chrProcessing: no visible global function definition for ‘seqlengths’
.chrProcessing: no visible global function definition for ‘seqlevels’
.classifyNulls : <anonymous>: no visible global function definition for
‘seqlengths’
.classifyNulls: no visible global function definition for ‘runif’
.constructMethNulls: no visible global function definition for
‘seqlevels’
.constructNullPriors: no visible global function definition for
‘seqlevels’
.constructNullPriors: no visible global function definition for ‘runif’
.constructNulls: no visible global function definition for ‘seqlevels’
.constructNulls: no visible global function definition for ‘runif’
.findMethChunks: no visible global function definition for ‘seqlevels’
.getCounts: no visible global function definition for ‘seqlevels’
.getCounts : <anonymous>: no visible global function definition for
‘clusterCall’
.getCounts : <anonymous>: no visible global function definition for
‘parLapplyLB’
.getLocLikelihoods : NBdens : PDgivenr.NB: no visible global function
definition for ‘dnbinom’
.getLocLikelihoods : BBdens : PDgivenr.BB : dbetabinom: no visible
global function definition for ‘dbinom’
.getLocLikelihoods: no visible global function definition for
‘clusterExport’
.getLocLikelihoods: no visible global function definition for
‘parRapply’
.getMethylatedCounts: no visible global function definition for
‘seqlevels’
.getMethylatedCounts: no visible global function definition for
‘clusterEvalQ’
.getOverlaps: no visible global function definition for ‘seqlevels’
.getOverlaps : <anonymous>: no visible global function definition for
‘clusterExport’
.getOverlaps : <anonymous>: no visible global function definition for
‘clusterCall’
.getOverlaps : <anonymous>: no visible global function definition for
‘parApply’
.getOverlaps: no visible global function definition for ‘clusterEvalQ’
.lociLikelihoods: no visible global function definition for ‘abind’
.massiveClassifyLoci: no visible global function definition for ‘runif’
.methFunction: no visible global function definition for ‘pbeta’
.partheuristicSeg: no visible global function definition for
‘seqlevels’
.partheuristicSeg : <anonymous>: no visible global function definition
for ‘seqlengths’
.partheuristicSeg : <anonymous>: no visible global function definition
for ‘seqlevels’
.plotSampleMeth: no visible global function definition for ‘seqlengths’
.plotSampleMeth: no visible global function definition for ‘lines’
.processPosts: no visible global function definition for ‘clusterEvalQ’
.processPosts: no visible global function definition for ‘seqlevels’
.processPosts : <anonymous>: no visible global function definition for
‘seqlengths’
.processPosts: no visible global function definition for ‘runif’
.processTags: no visible global function definition for ‘seqlevels’
.processTags: no visible global function definition for ‘seqlengths’
.processTags: no visible global function definition for ‘seqlengths<-’
.squeezeAlign: no visible global function definition for ‘seqlevels’
.subProfile: no visible global function definition for ‘seqlevels’
.subProfile : <anonymous> : summariseCoverage : <anonymous>: no visible
global function definition for ‘weighted.mean’
findChunks: no visible global function definition for ‘seqlevels’
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’
plotGenome: no visible global function definition for ‘seqlevels’
plotGenome: no visible global function definition for ‘seqlevels<-’
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’
processAD: no visible global function definition for ‘seqlevels’
readBAM: no visible global function definition for ‘Seqinfo’
readBAM : <anonymous>: no visible global function definition for
‘scanBam’
readBAM : <anonymous>: no visible global function definition for
‘ScanBamParam’
readBAM : <anonymous>: no visible global function definition for
‘seqlevels’
readBAM : <anonymous>: no visible global function definition for
‘write.table’
readGeneric: no visible global function definition for ‘Seqinfo’
readGeneric : <anonymous>: no visible global function definition for
‘read.table’
readGeneric : <anonymous>: no visible global function definition for
‘write.table’
readGeneric : <anonymous>: no visible global function definition for
‘seqlevels’
readMeths: no visible binding for global variable ‘seqlevels’
readMeths : <anonymous>: no visible global function definition for
‘seqlevels<-’
Undefined global functions or variables:
ScanBamParam Seqinfo abind abline clusterCall clusterEvalQ
clusterExport dbinom dev.cur dnbinom lines par parApply parLapplyLB
parRapply pbeta rainbow read.table runif scanBam seqlengths
seqlengths<- seqlevels seqlevels<- 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 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 25.532 0.012 25.562
lociLikelihoods 9.720 0.004 9.725
readMeths 8.932 0.040 9.012
heuristicSeg 8.780 0.004 8.786
* 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, 3 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/segmentSeq.Rcheck/00check.log’
for details.