* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.6-bioc/meat/genoCN.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'genoCN/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genoCN' version '1.0.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'genoCN' can be installed ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
genoCNA: no visible binding for global variable 'init.Para.CNA'
genoCNV: no visible binding for global variable 'init.Para.CNV'
* 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 data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* install options are ' --no-html'
* installing *source* package 'genoCN' ...
** libs
making DLL ...
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c tnorm_mle.c -o tnorm_mle.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c utility.c -o utility.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c xCNV.c -o xCNV.o
xCNV.c: In function 'emiss':
xCNV.c:317: warning: unused variable 'k'
xCNV.c:317: warning: unused variable 'K'
xCNV.c: In function 'baum_welch':
xCNV.c:787: warning: unused variable 'sd_b_tmp'
xCNV.c:787: warning: unused variable 'mu_b_tmp'
xCNV.c:769: warning: 'pbf' may be used uninitialized in this function
xCNV.c:768: warning: 'nGtp' may be used uninitialized in this function
gcc -shared -s -static-libgcc -o genoCN.dll tmp.def tnorm_mle.o utility.o xCNV.o -LE:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to E:/biocbld/bbs-2.6-bioc/meat/genoCN.Rcheck/genoCN/libs
... done
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (genoCN)