segmentSeq 1.16.0
Thomas J. Hardcastle
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/segmentSeq | | Last Changed Rev: 88838 / Revision: 95116 | | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings segmentSeq_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/segmentSeq.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.16.0’
* 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 ... [18s/18s] 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 ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘baySeq’ ‘IRanges’ ‘methods’ ‘GenomicRanges’
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 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.
Package in Depends field not imported from: ‘ShortRead’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.partheuristicSeg : <anonymous>: warning in Rle(-Inf, length =
length(emptyPD@coordinates)): partial argument match of 'length' to
'lengths'
.constructNulls: no visible binding for global variable ‘cl’
.getMethylatedCounts : <anonymous> : createIntervals: no visible
binding for global variable ‘dupTags’
.methLikelihoods : <anonymous>: possible error in getLikelihoods.BB(cD
= repD, bootStraps = bootStraps, nullData = TRUE, verbose = FALSE, cl
= cl): unused argument (nullData = TRUE)
.stratifySample: no visible binding for global variable ‘sD’
.stratifySample: no visible binding for global variable ‘lensameFlag’
.stratifySample: no visible binding for global variable ‘seglens’
plotAverageProfile: no visible binding for global variable
‘profCHH.DMR’
* checking Rd files ... NOTE
prepare_Rd: averageMethylationRegions.Rd:104-105: Dropping empty section \examples
prepare_Rd: summariseLoci.Rd:22-24: Dropping empty section \details
* 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 ... [164s/168s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
classifySeg 50.519 0.072 51.465
lociLikelihoods 21.774 0.028 22.150
heuristicSeg 20.329 0.012 20.516
plotGenome 13.820 0.036 14.186
readMeths 13.801 0.040 14.019
segData-class 7.320 0.028 7.646
segmentSeq-package 7.289 0.004 7.452
processAD 7.089 0.016 7.306
* 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
NOTE: There were 5 notes.
See
‘/home/biocbuild/bbs-2.14-bioc/meat/segmentSeq.Rcheck/00check.log’
for details.