segmentSeq 2.3.2
Thomas J. Hardcastle
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/segmentSeq | | Last Changed Rev: 107067 / Revision: 107696 | | Last Changed Date: 2015-08-04 03:46:22 -0700 (Tue, 04 Aug 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| oaxaca | 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-3.2-bioc/R/bin/R CMD check --no-vignettes --timings segmentSeq_2.3.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/segmentSeq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘2.3.2’
* 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 ‘segmentSeq’ can be installed ... [14s/14s] 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’
.constructMethNulls: no visible global function definition for
‘seqlevels’
.constructNullPriors: no visible global function definition for
‘seqlevels’
.constructNulls: no visible global function definition for ‘seqlevels’
.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: 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’
.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’
.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’
.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’
findChunks: no visible global function definition for ‘seqlevels’
plotGenome: no visible global function definition for ‘seqlevels’
plotGenome: no visible global function definition for ‘seqlevels<-’
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’
readGeneric: no visible global function definition for ‘Seqinfo’
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<-’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'plotMethDistribution':
plotMethDistribution
Code: function(meth, samples, bw = 0.001, subtract, chrs,
centromeres, add = FALSE, col, ylim = NULL, legend =
TRUE, ...)
Docs: function(meth, samples, bw = 0.001, subtract, chrs,
centromeres, add = FALSE, col, legend = TRUE, ...)
Argument names in code not in docs:
ylim
Mismatches in argument names:
Position: 9 Code: ylim Docs: legend
Position: 10 Code: legend Docs: ...
* 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 ... [90s/90s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
classifySeg 32.250 0.035 32.388
lociLikelihoods 10.256 0.000 10.268
readMeths 9.455 0.056 9.515
heuristicSeg 9.339 0.004 9.351
plotGenome 5.309 0.000 5.336
* 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-3.2-bioc/meat/segmentSeq.Rcheck/00check.log’
for details.