Package: exomeCopy

Version: 1.0.1

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch exomeCopy_1.0.1.tar.gz

StartedAt: 2012-01-09 02:36:58 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 02:39:28 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 150.4 seconds

RetCode: 0

Status:  OK

CheckDir: exomeCopy.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/exomeCopy.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'exomeCopy/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'exomeCopy' version '1.0.1'
* 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 'exomeCopy' 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 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... OK
* 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

* installing *source* package 'exomeCopy' ...
** libs
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c exomeCopy.c -o exomeCopy.o
exomeCopy.c: In function 'viterbi':
exomeCopy.c:56:16: warning: 'running_max' may be used uninitialized in this function
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o exomeCopy.dll tmp.def exomeCopy.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/exomeCopy.Rcheck/exomeCopy/libs/x64
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'exomeCopy'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'exomeCopy.Rnw' 
** testing if installed package can be loaded

* DONE (exomeCopy)

name	user	system	elapsed
ExomeCopy-class	0	0	0
copyCountSegments	2.69	0.00	2.69
countBamInGRanges	0.5	0.0	0.5
exomeCopy	2.09	0.00	2.09
negLogLike	0.02	0.00	0.01
plot.exomeCopyObject	2.13	0.00	2.13
subdivideGRanges	0.07	0.00	0.08