############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL LEA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘LEA’ ... ** this is package ‘LEA’ version ‘3.19.4’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c R_LFMM.c -o R_LFMM.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c R_crossEntropy.c -o R_crossEntropy.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c R_createDataSet.c -o R_createDataSet.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c R_sNMF.c -o R_sNMF.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c R_ancestrymap2geno.c -o R_ancestrymap2geno.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c R_ancestrymap2lfmm.c -o R_ancestrymap2lfmm.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c R_geno2lfmm.c -o R_geno2lfmm.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c R_lfmm2geno.c -o R_lfmm2geno.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c R_pca.c -o R_pca.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c R_ped2geno.c -o R_ped2geno.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c R_ped2lfmm.c -o R_ped2lfmm.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c R_vcf2geno.c -o R_vcf2geno.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c R_tracyWidom.c -o R_tracyWidom.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c R_init_LEA.c -o R_init_LEA.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c bituint/bituint.c -o bituint/bituint.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c bituint/calc_bituint.c -o bituint/calc_bituint.o bituint/calc_bituint.c: In function ‘tBtX’: bituint/calc_bituint.c:49:69: warning: passing argument 9 of ‘thread_fct_bituint’ from incompatible pointer type [-Wincompatible-pointer-types] 49 | thread_fct_bituint(X, A, B, K, Mc, Mp, N, num_thrd, slice_tBtX); | ^~~~~~~~~~ | | | void (*)(void *) In file included from bituint/calc_bituint.c:26: bituint/thread_bituint.h:52:61: note: expected ‘void (*)(void)’ but argument is of type ‘void (*)(void *)’ 52 | int Mp, int N, int num_thrd, void (*fct) ()); | ~~~~~~~^~~~~~~ bituint/calc_bituint.c: In function ‘BX’: bituint/calc_bituint.c:101:69: warning: passing argument 9 of ‘thread_fct_bituint’ from incompatible pointer type [-Wincompatible-pointer-types] 101 | thread_fct_bituint(X, A, B, K, Mc, Mp, N, num_thrd, slice_BX); | ^~~~~~~~ | | | void (*)(void *) bituint/thread_bituint.h:52:61: note: expected ‘void (*)(void)’ but argument is of type ‘void (*)(void *)’ 52 | int Mp, int N, int num_thrd, void (*fct) ()); | ~~~~~~~^~~~~~~ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c bituint/io_geno_bituint.c -o bituint/io_geno_bituint.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c bituint/slice_bituint.c -o bituint/slice_bituint.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c bituint/thread_bituint.c -o bituint/thread_bituint.o bituint/thread_bituint.c:34:6: error: conflicting types for ‘thread_fct_bituint’; have ‘void(bituint *, double *, double *, int, int, int, int, int, void (*)(struct _multithreading_bituint *))’ {aka ‘void(long unsigned int *, double *, double *, int, int, int, int, int, void (*)(struct _multithreading_bituint *))’} 34 | void thread_fct_bituint(bituint * X, double *A, double *B, int K, int Mc, | ^~~~~~~~~~~~~~~~~~ In file included from bituint/thread_bituint.c:25: bituint/thread_bituint.h:51:6: note: previous declaration of ‘thread_fct_bituint’ with type ‘void(bituint *, double *, double *, int, int, int, int, int, void (*)(void))’ {aka ‘void(long unsigned int *, double *, double *, int, int, int, int, int, void (*)(void))’} 51 | void thread_fct_bituint(bituint * X, double *A, double *B, int K, int Mc, | ^~~~~~~~~~~~~~~~~~ make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:201: bituint/thread_bituint.o] Error 1 ERROR: compilation failed for package ‘LEA’ * removing ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/LEA’