Package: segmentSeq

Version: 1.10.1

Command: rm -rf segmentSeq.buildbin-libdir && mkdir segmentSeq.buildbin-libdir && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=segmentSeq.buildbin-libdir segmentSeq_1.10.1.tar.gz >segmentSeq-install.out 2>&1 && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD check --library=segmentSeq.buildbin-libdir --install="check:segmentSeq-install.out" --force-multiarch --no-vignettes --timings segmentSeq_1.10.1.tar.gz && mv segmentSeq.buildbin-libdir/* segmentSeq.Rcheck/ && rmdir segmentSeq.buildbin-libdir

StartedAt: 2013-03-25 03:04:03 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:13:36 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 572.9 seconds

RetCode: 0

Status:  OK

CheckDir: segmentSeq.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.11-bioc/meat/segmentSeq.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.10.1'
* 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 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' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
classifySeg        41.37   0.04   41.44
lociLikelihoods    21.61   0.00   21.61
heuristicSeg       21.17   0.02   21.18
segData-class      16.04   0.00   16.04
segmentSeq-package 15.27   0.01   15.28
processAD          15.07   0.00   15.09
plotGenome         12.27   0.00   12.27
readMethods         5.32   0.00    5.32
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
classifySeg         47.47   0.06   47.55
lociLikelihoods     27.67   0.00   27.67
heuristicSeg        23.87   0.02   23.89
processAD           19.42   0.00   19.42
segData-class       18.49   0.00   18.49
segmentSeq-package  17.70   0.03   17.73
plotGenome          13.79   0.01   14.10
alignmentData-class  6.23   0.02    6.24
readMethods          6.04   0.00    6.15
findChunks           5.83   0.00    5.83
getCounts            5.42   0.00    5.60
getOverlaps          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
  'D:/biocbld/bbs-2.11-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_1.10.1.zip

* DONE (segmentSeq)