segmentSeq 1.11.0 Thomas J. Hardcastle
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/segmentSeq | Last Changed Rev: 70052 / Revision: 74774 | Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012) |
| 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 Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/segmentSeq.Rcheck'
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'segmentSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'segmentSeq' version '1.11.0'
* 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 whether package 'segmentSeq' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... [174s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
classifySeg 41.59 0.05 41.64
lociLikelihoods 21.98 0.00 21.98
heuristicSeg 20.59 0.00 20.59
segData-class 14.38 0.02 14.41
processAD 14.01 0.02 14.04
segmentSeq-package 13.97 0.01 13.98
plotGenome 13.93 0.01 13.94
getCounts 5.99 0.00 5.99
alignmentData-class 5.15 0.00 5.15
** running examples for arch 'x64' ... [190s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
classifySeg 41.79 0.02 41.80
heuristicSeg 27.30 0.00 27.30
lociLikelihoods 23.51 0.02 23.52
processAD 17.05 0.00 17.05
segData-class 15.73 0.00 15.72
segmentSeq-package 15.29 0.00 15.29
plotGenome 13.32 0.01 13.34
readMethods 5.54 0.00 5.54
getOverlaps 5.51 0.00 5.52
getCounts 5.32 0.00 5.32
alignmentData-class 5.27 0.01 5.29
findChunks 5.27 0.00 5.27
* 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
'E:/biocbld/bbs-2.12-bioc/meat/segmentSeq.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'segmentSeq' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'segmentSeq.Rnw'
** testing if installed package can be loaded
install for x64
* installing *source* package 'segmentSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'segmentSeq' as segmentSeq_1.11.0.zip
* DONE (segmentSeq)