############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL genoCN ### ############################################################################## ############################################################################## * 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 13.2.0-23ubuntu4) 13.2.0’ 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’