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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL genoCN
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘genoCN’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c tnorm_mle.c -o tnorm_mle.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -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-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -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 ‘viterbi’:
xCNV.c:449:25: warning: implicit declaration of function ‘Calloc’; did you mean ‘calloc’? [-Wimplicit-function-declaration]
449 | trans1 = (double**) Calloc(N, double*);
| ^~~~~~
| calloc
xCNV.c:449:35: error: expected expression before ‘double’
449 | trans1 = (double**) Calloc(N, double*);
| ^~~~~~
xCNV.c:450:39: error: expected expression before ‘double’
450 | trans1[0] = (double*) Calloc(N*N, double);
| ^~~~~~
xCNV.c:455:33: error: expected expression before ‘double’
455 | v_old = (double *)Calloc(N, double);
| ^~~~~~
xCNV.c:456:33: error: expected expression before ‘double’
456 | v_new = (double *)Calloc(N, double);
| ^~~~~~
xCNV.c:458:32: error: expected expression before ‘int’
458 | path_m = (int**) Calloc(L, int*);
| ^~~
xCNV.c:459:36: error: expected expression before ‘int’
459 | path_m[0] = (int*) Calloc(L*N, int);
| ^~~
xCNV.c:464:31: error: expected expression before ‘double’
464 | tmp = (double *)Calloc(N, double);
| ^~~~~~
xCNV.c:532:5: warning: implicit declaration of function ‘Free’; did you mean ‘free’? [-Wimplicit-function-declaration]
532 | Free(v_old);
| ^~~~
| free
xCNV.c: In function ‘forward’:
xCNV.c:579:29: error: expected expression before ‘double’
579 | v = (double *)Calloc(N, double);
| ^~~~~~
xCNV.c:581:35: error: expected expression before ‘double’
581 | trans1 = (double**) Calloc(N, double*);
| ^~~~~~
xCNV.c:582:39: error: expected expression before ‘double’
582 | trans1[0] = (double*) Calloc(N*N, double);
| ^~~~~~
xCNV.c: In function ‘backward’:
xCNV.c:652:29: error: expected expression before ‘double’
652 | v = (double *)Calloc(N, double);
| ^~~~~~
xCNV.c:654:35: error: expected expression before ‘double’
654 | trans1 = (double**) Calloc(N, double*);
| ^~~~~~
xCNV.c:655:39: error: expected expression before ‘double’
655 | trans1[0] = (double*) Calloc(N*N, double);
| ^~~~~~
xCNV.c: In function ‘baum_welch’:
xCNV.c:878:34: error: expected expression before ‘double’
878 | dis = (double *)Calloc(L-1, double);
| ^~~~~~
xCNV.c:879:34: error: expected expression before ‘double’
879 | vjk = (double *)Calloc(L-1, double);
| ^~~~~~
xCNV.c:880:33: error: expected expression before ‘double’
880 | vjk0 = (double *)Calloc(LS, double);
| ^~~~~~
xCNV.c:881:32: error: expected expression before ‘double’
881 | lvjk = (double *)Calloc(N, double);
| ^~~~~~
xCNV.c:882:34: error: expected expression before ‘double’
882 | lvjk_j = (double *)Calloc(N-1, double);
| ^~~~~~
xCNV.c:883:32: error: expected expression before ‘double’
883 | ps = (double *)Calloc(L, double);
| ^~~~~~
xCNV.c:886:30: error: expected expression before ‘double’
886 | rUS = (double *)Calloc(N, double);
| ^~~~~~
xCNV.c:887:30: error: expected expression before ‘double’
887 | pPS = (double *)Calloc(N, double);
| ^~~~~~
xCNV.c:888:30: error: expected expression before ‘double’
888 | rNcb = (double *)Calloc(L, double);
| ^~~~~~
xCNV.c:891:33: error: expected expression before ‘double’
891 | rUS_cn = (double *)Calloc(N, double);
| ^~~~~~
xCNV.c:892:33: error: expected expression before ‘double’
892 | pPS_cn = (double *)Calloc(N, double);
| ^~~~~~
xCNV.c:895:31: error: expected expression before ‘double’
895 | bUS = (double *)Calloc(N, double);
| ^~~~~~
xCNV.c:896:28: error: expected expression before ‘int’
896 | Omiga = (int *)Calloc(L, int);
| ^~~
xCNV.c:897:31: error: expected expression before ‘double’
897 | BAF01 = (double *)Calloc(L, double);
| ^~~~~~
xCNV.c:898:31: error: expected expression before ‘double’
898 | bNcb = (double *)Calloc(L, double);
| ^~~~~~
xCNV.c:904:30: error: expected expression before ‘double’
904 | rU = (double**) Calloc(L, double*);
| ^~~~~~
xCNV.c:905:33: error: expected expression before ‘double’
905 | rU[0] = (double*) Calloc(L*N, double);
| ^~~~~~
xCNV.c:914:30: error: expected expression before ‘double’
914 | rN = (double**) Calloc(L, double*);
| ^~~~~~
xCNV.c:915:33: error: expected expression before ‘double’
915 | rN[0] = (double*) Calloc(L*N, double);
| ^~~~~~
xCNV.c:922:30: error: expected expression before ‘double’
922 | bU = (double**) Calloc(L, double*);
| ^~~~~~
xCNV.c:923:33: error: expected expression before ‘double’
923 | bU[0] = (double*) Calloc(L*N, double);
| ^~~~~~
xCNV.c:930:30: error: expected expression before ‘double’
930 | bN = (double**) Calloc(L, double*);
| ^~~~~~
xCNV.c:931:34: error: expected expression before ‘double’
931 | bN[0] = (double*) Calloc(L*MM, double);
| ^~~~~~
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,
| ^~
make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:195: xCNV.o] Error 1
ERROR: compilation failed for package ‘genoCN’
* removing ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/genoCN’
* restoring previous ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/genoCN’
