segmentSeq 1.12.1 Thomas J. Hardcastle
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/segmentSeq | Last Changed Rev: 75473 / Revision: 81334 | Last Changed Date: 2013-04-09 11:52:21 -0700 (Tue, 09 Apr 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ OK ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/segmentSeq.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'segmentSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'segmentSeq' version '1.12.1'
* 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 ... [28s/29s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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
.partheuristicSeg: no visible global function definition for
'.methFunction'
.partheuristicSeg: no visible global function definition for
'.constructMethNulls'
.partheuristicSeg: no visible global function definition for
'getMethylatedCounts'
.squeezeAlign: no visible global function definition for
'findMethChunks'
.stratifySample: no visible binding for global variable 'sD'
.stratifySample: no visible binding for global variable 'lensameFlag'
.stratifySample: no visible binding for global variable 'seglens'
processAD : partCounts: no visible global function definition for
'getMethylatedCounts'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [292s/297s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
classifySeg 80.045 0.477 82.284
lociLikelihoods 38.379 0.151 38.918
heuristicSeg 37.234 0.187 38.181
processAD 24.481 0.146 24.915
segData-class 24.083 0.166 24.598
segmentSeq-package 23.770 0.204 24.189
plotGenome 18.975 0.070 19.232
alignmentData-class 6.863 0.118 7.059
getCounts 5.927 0.037 6.057
findChunks 5.859 0.036 6.010
getOverlaps 5.498 0.032 5.605
readMethods 5.087 0.055 5.187
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There was 1 note.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/segmentSeq.Rcheck/00check.log'
for details.