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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL genoCN
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘genoCN’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c tnorm_mle.c -o tnorm_mle.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c utility.c -o utility.o
utility.c: In function ‘readfile’:
utility.c:155:13: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  155 |             fscanf(file,"%s",temp);
      |             ^~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -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 -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o genoCN.so tnorm_mle.o utility.o xCNV.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-genoCN/00new/genoCN/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (genoCN)