segmentSeq 2.0.1
Thomas J. Hardcastle
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/segmentSeq | | Last Changed Rev: 96616 / Revision: 102249 | | Last Changed Date: 2014-11-07 13:48:56 -0800 (Fri, 07 Nov 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings segmentSeq_2.0.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/segmentSeq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-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 ‘2.0.1’
* 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 ‘segmentSeq’ can be installed ... [20s/21s] 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
‘parLapply’
.getLocLikelihoods: no visible global function definition for
‘clusterCall’
.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
‘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 ... 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 ... [107s/107s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
classifySeg 37.607 0.060 37.858
readMeths 12.889 0.076 13.028
lociLikelihoods 12.200 0.004 12.260
heuristicSeg 10.797 0.004 10.843
plotGenome 5.685 0.008 5.701
* 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
NOTE: There were 3 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/segmentSeq.Rcheck/00check.log’
for details.