segmentSeq 1.10.1
Thomas J. Hardcastle
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/segmentSeq | | Last Changed Rev: 71543 / Revision: 74773 | | Last Changed Date: 2012-11-29 02:27:10 -0800 (Thu, 29 Nov 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/segmentSeq.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.10.1’
* 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 whether package ‘segmentSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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
.stratifySample: no visible binding for global variable ‘sD’
.stratifySample: no visible binding for global variable ‘lensameFlag’
.stratifySample: no visible binding for global variable ‘seglens’
.zeroInMeth: no visible global function definition for ‘getMethCounts’
.zeroInMeth: no visible binding for global variable ‘cl’
* 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 examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
classifySeg 55.807 0.236 60.335
lociLikelihoods 29.258 0.092 32.048
heuristicSeg 27.774 0.100 29.229
segData-class 20.442 0.064 23.314
processAD 19.477 0.068 22.326
segmentSeq-package 19.149 0.060 21.350
plotGenome 14.805 0.016 16.606
alignmentData-class 8.501 0.052 10.380
getCounts 6.864 0.024 7.795
findChunks 6.697 0.024 7.730
getOverlaps 6.412 0.024 6.997
readMethods 6.016 0.016 6.331
* 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
‘/loc/home/biocbuild/bbs-2.11-bioc/meat/segmentSeq.Rcheck/00check.log’
for details.