##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL genoCN
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'genoCN' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tnorm_mle.c -o tnorm_mle.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utility.c -o utility.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c xCNV.c -o xCNV.o
xCNV.c: In function 'emiss':
xCNV.c:317:25: warning: unused variable 'k' [-Wunused-variable]
  317 |   int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
      |                         ^
xCNV.c:317:16: warning: unused variable 'K' [-Wunused-variable]
  317 |   int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
      |                ^
xCNV.c: In function 'baum_welch':
xCNV.c:787:20: warning: unused variable 'sd_b_tmp' [-Wunused-variable]
  787 |   double mu_b_tmp, sd_b_tmp;
      |                    ^~~~~~~~
xCNV.c:787:10: warning: unused variable 'mu_b_tmp' [-Wunused-variable]
  787 |   double mu_b_tmp, sd_b_tmp;
      |          ^~~~~~~~
xCNV.c:762:10: warning: variable 'LL' set but not used [-Wunused-but-set-variable]
  762 |   int L, LL, N, NN, M, MM, S, LS, CNA = *RCNA,
      |          ^~
xCNV.c:1753:17: warning: 'pbf' may be used uninitialized [-Wmaybe-uninitialized]
 1753 |                 weights(ws, pbf, z, CNA, contam, nGtp, *geno_error);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
xCNV.c:769:18: note: 'pbf' was declared here
  769 |   double ws[10], pbf, baf;
      |                  ^~~
xCNV.c:1753:17: warning: 'nGtp' may be used uninitialized [-Wmaybe-uninitialized]
 1753 |                 weights(ws, pbf, z, CNA, contam, nGtp, *geno_error);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
xCNV.c:768:31: note: 'nGtp' was declared here
  768 |   int k1s[4], rid[4], cid[4], nGtp;
      |                               ^~~~
gcc -shared -s -static-libgcc -o genoCN.dll tmp.def tnorm_mle.o utility.o xCNV.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-genoCN/00new/genoCN/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (genoCN)