Package: genoCN

Version: 1.5.0

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch genoCN_1.5.0.tar.gz

StartedAt: 2011-07-07 01:57:20 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 01:58:41 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 81.1 seconds

RetCode: 0

Status:  OK

CheckDir: genoCN.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/genoCN.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'genoCN/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genoCN' version '1.5.0'
* 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 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 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 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 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 'genoCN' ...
** libs
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c tnorm_mle.c -o tnorm_mle.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c utility.c -o utility.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c xCNV.c -o xCNV.o
xCNV.c: In function 'emiss':
xCNV.c:317:25: warning: unused variable 'k'
xCNV.c:317:16: warning: unused variable 'K'
xCNV.c: In function 'baum_welch':
xCNV.c:787:20: warning: unused variable 'sd_b_tmp'
xCNV.c:787:10: warning: unused variable 'mu_b_tmp'
xCNV.c:768:31: warning: 'nGtp' may be used uninitialized in this function
xCNV.c:769:18: warning: 'pbf' 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˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/genoCN.Rcheck/genoCN/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'genoCN.Rnw' 
** testing if installed package can be loaded

* DONE (genoCN)

name	user	system	elapsed
genoCNA	41.89	1.03	43.29
genoCNV	7.38	0.14	7.53
init.Para.CNA	0	0	0
init.Para.CNV	0	0	0
plotCN	0.36	0.00	0.36
snpData	0.33	0.00	0.33
snpInfo	0.31	0.00	0.31