downloading reverse dependencies ‘Familia’ trying URL 'file:///data/Repositories/CRAN/src/contrib/Familia_1.0.3.tar.gz' Content type 'unknown' length 641244 bytes (626 KB) ================================================== installing dependencies ‘BIGpopA’, ‘LEA’ begin installing package ‘BIGpopA’ begin installing package ‘LEA’ * installing *source* package ‘BIGpopA’ ... ** this is package ‘BIGpopA’ version ‘2.0.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (BIGpopA) * installing *source* package ‘LEA’ ... ** this is package ‘LEA’ version ‘3.24.0’ ** using staged installation ** libs using C compiler: ‘gcc-16 (Debian 16.2.0-1) 16.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpvlHjOc/R.INSTALL2a976a49eccd63/LEA/src' gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_LFMM.c -o R_LFMM.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_crossEntropy.c -o R_crossEntropy.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_createDataSet.c -o R_createDataSet.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_sNMF.c -o R_sNMF.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_ancestrymap2geno.c -o R_ancestrymap2geno.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_ancestrymap2lfmm.c -o R_ancestrymap2lfmm.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_geno2lfmm.c -o R_geno2lfmm.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_lfmm2geno.c -o R_lfmm2geno.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_pca.c -o R_pca.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_ped2geno.c -o R_ped2geno.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_ped2lfmm.c -o R_ped2lfmm.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_vcf2geno.c -o R_vcf2geno.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_tracyWidom.c -o R_tracyWidom.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_LEA.c -o R_init_LEA.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bituint/bituint.c -o bituint/bituint.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bituint/calc_bituint.c -o bituint/calc_bituint.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bituint/io_geno_bituint.c -o bituint/io_geno_bituint.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bituint/slice_bituint.c -o bituint/slice_bituint.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bituint/thread_bituint.c -o bituint/thread_bituint.o bituint/thread_bituint.c: In function ‘thread_fct_bituint’: bituint/thread_bituint.c:61:40: warning: ISO C forbids conversion of function pointer to object pointer type [-Wpedantic] 61 | (&thread[i], NULL, (void *)fct, (void *)Ma[i])) { | ^ bituint/thread_bituint.c:61:40: warning: ISO C forbids passing argument 3 of ‘pthread_create’ between function pointer and ‘void *’ [-Wpedantic] 61 | (&thread[i], NULL, (void *)fct, (void *)Ma[i])) { | ^~~~~~~~~~~ In file included from bituint/thread_bituint.c:22: /usr/include/pthread.h:204:36: note: expected ‘void * (*)(void *)’ but argument is of type ‘void *’ 204 | void *(*__start_routine) (void *), | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c convert/ancestrymap.c -o convert/ancestrymap.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c convert/geno.c -o convert/geno.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c convert/ped.c -o convert/ped.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c convert/vcf2geno.c -o convert/vcf2geno.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c convert/geno2lfmm.c -o convert/geno2lfmm.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c convert/lfmm2geno.c -o convert/lfmm2geno.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c convert/register_convert.c -o convert/register_convert.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c createDataSet/createDataSet.c -o createDataSet/createDataSet.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c createDataSet/error_cds.c -o createDataSet/error_cds.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c createDataSet/print_cds.c -o createDataSet/print_cds.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c createDataSet/register_cds.c -o createDataSet/register_cds.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c crossEntropy/crossEntropy.c -o crossEntropy/crossEntropy.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c crossEntropy/error_ce.c -o crossEntropy/error_ce.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c crossEntropy/print_ce.c -o crossEntropy/print_ce.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c crossEntropy/register_ce.c -o crossEntropy/register_ce.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io/io_data_double.c -o io/io_data_double.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io/io_data_float.c -o io/io_data_float.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io/io_data_int.c -o io/io_data_int.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io/io_error.c -o io/io_error.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io/io_tools.c -o io/io_tools.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io/print_bar.c -o io/print_bar.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LFMM/beta.c -o LFMM/beta.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LFMM/error_lfmm.c -o LFMM/error_lfmm.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LFMM/lfmm_k0.c -o LFMM/lfmm_k0.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LFMM/slice_lfmm.c -o LFMM/slice_lfmm.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LFMM/U.c -o LFMM/U.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LFMM/beta_k0.c -o LFMM/beta_k0.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LFMM/lfmm_algo.c -o LFMM/lfmm_algo.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LFMM/print_lfmm.c -o LFMM/print_lfmm.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LFMM/thread_lfmm.c -o LFMM/thread_lfmm.o LFMM/thread_lfmm.c: In function ‘thread_fct_lfmm’: LFMM/thread_lfmm.c:69:40: warning: ISO C forbids conversion of function pointer to object pointer type [-Wpedantic] 69 | (&thread[i], NULL, (void *)fct, (void *)Ma[i])) { | ^ LFMM/thread_lfmm.c:69:40: warning: ISO C forbids passing argument 3 of ‘pthread_create’ between function pointer and ‘void *’ [-Wpedantic] 69 | (&thread[i], NULL, (void *)fct, (void *)Ma[i])) { | ^~~~~~~~~~~ In file included from LFMM/thread_lfmm.c:22: /usr/include/pthread.h:204:36: note: expected ‘void * (*)(void *)’ but argument is of type ‘void *’ 204 | void *(*__start_routine) (void *), | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LFMM/V.c -o LFMM/V.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LFMM/data_lfmm.c -o LFMM/data_lfmm.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LFMM/LFMM.c -o LFMM/LFMM.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LFMM/register_lfmm.c -o LFMM/register_lfmm.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LFMM/thread_var.c -o LFMM/thread_var.o LFMM/thread_var.c: In function ‘thrd_var’: LFMM/thread_var.c:67:40: warning: ISO C forbids conversion of function pointer to object pointer type [-Wpedantic] 67 | (&thread[i], NULL, (void *)fct, (void *)Ma[i])) { | ^ LFMM/thread_var.c:67:40: warning: ISO C forbids passing argument 3 of ‘pthread_create’ between function pointer and ‘void *’ [-Wpedantic] 67 | (&thread[i], NULL, (void *)fct, (void *)Ma[i])) { | ^~~~~~~~~~~ In file included from LFMM/thread_var.c:22: /usr/include/pthread.h:204:36: note: expected ‘void * (*)(void *)’ but argument is of type ‘void *’ 204 | void *(*__start_routine) (void *), | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c matrix/cholesky.c -o matrix/cholesky.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c matrix/error_matrix.c -o matrix/error_matrix.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c matrix/normalize.c -o matrix/normalize.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c matrix/slice_matrix.c -o matrix/slice_matrix.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c matrix/data.c -o matrix/data.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c matrix/inverse.c -o matrix/inverse.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c matrix/rand.c -o matrix/rand.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c matrix/sylvester.c -o matrix/sylvester.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c matrix/diagonalize.c -o matrix/diagonalize.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c matrix/matrix.c -o matrix/matrix.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c matrix/random_projection.c -o matrix/random_projection.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c matrix/thread_matrix.c -o matrix/thread_matrix.o matrix/thread_matrix.c: In function ‘thread_fct_matrix’: matrix/thread_matrix.c:60:40: warning: ISO C forbids conversion of function pointer to object pointer type [-Wpedantic] 60 | (&thread[i], NULL, (void *)fct, (void *)Ma[i])) { | ^ matrix/thread_matrix.c:60:40: warning: ISO C forbids passing argument 3 of ‘pthread_create’ between function pointer and ‘void *’ [-Wpedantic] 60 | (&thread[i], NULL, (void *)fct, (void *)Ma[i])) { | ^~~~~~~~~~~ In file included from matrix/thread_matrix.c:22: /usr/include/pthread.h:204:36: note: expected ‘void * (*)(void *)’ but argument is of type ‘void *’ 204 | void *(*__start_routine) (void *), | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c nnlsm/blockpivot.c -o nnlsm/blockpivot.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c nnlsm/nnlsm.c -o nnlsm/nnlsm.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c nnlsm/solvenormaleqcomb.c -o nnlsm/solvenormaleqcomb.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c nnlsm/sort.c -o nnlsm/sort.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pca/calc_cov.c -o pca/calc_cov.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pca/error_pca.c -o pca/error_pca.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pca/pca.c -o pca/pca.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pca/print_pca.c -o pca/print_pca.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pca/register_pca.c -o pca/register_pca.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sNMF/als.c -o sNMF/als.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sNMF/als_k1.c -o sNMF/als_k1.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sNMF/criteria.c -o sNMF/criteria.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sNMF/print_snmf.c -o sNMF/print_snmf.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sNMF/sNMF.c -o sNMF/sNMF.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sNMF/thread_Q.c -o sNMF/thread_Q.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sNMF/als_F.c -o sNMF/als_F.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sNMF/als_Q.c -o sNMF/als_Q.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sNMF/error_snmf.c -o sNMF/error_snmf.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sNMF/register_snmf.c -o sNMF/register_snmf.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sNMF/thread_F.c -o sNMF/thread_F.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sNMF/thread_snmf.c -o sNMF/thread_snmf.o sNMF/thread_snmf.c: In function ‘thread_fct_snmf’: sNMF/thread_snmf.c:60:40: warning: ISO C forbids conversion of function pointer to object pointer type [-Wpedantic] 60 | (&thread[i], NULL, (void *)fct, (void *)Ma[i])) { | ^ sNMF/thread_snmf.c:60:40: warning: ISO C forbids passing argument 3 of ‘pthread_create’ between function pointer and ‘void *’ [-Wpedantic] 60 | (&thread[i], NULL, (void *)fct, (void *)Ma[i])) { | ^~~~~~~~~~~ In file included from sNMF/thread_snmf.c:22: /usr/include/pthread.h:204:36: note: expected ‘void * (*)(void *)’ but argument is of type ‘void *’ 204 | void *(*__start_routine) (void *), | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c stats/beta_distribution.c -o stats/beta_distribution.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c stats/gamma_density.c -o stats/gamma_density.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c stats/ln_beta_function.c -o stats/ln_beta_function.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c stats/beta_function.c -o stats/beta_function.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c stats/gamma_distribution.c -o stats/gamma_distribution.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c stats/ln_gamma_function.c -o stats/ln_gamma_function.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c stats/entire_incomplete_gamma_function.c -o stats/entire_incomplete_gamma_function.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c stats/gamma_dist_tables.c -o stats/gamma_dist_tables.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c stats/student_t_distribution.c -o stats/student_t_distribution.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c stats/factorial.c -o stats/factorial.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c stats/gamma_function.c -o stats/gamma_function.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c tracyWidom/error_tracyWidom.c -o tracyWidom/error_tracyWidom.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c tracyWidom/register_tracyWidom.c -o tracyWidom/register_tracyWidom.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c tracyWidom/print_tracyWidom.c -o tracyWidom/print_tracyWidom.o gcc-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c tracyWidom/tracyWidom.c -o tracyWidom/tracyWidom.o gcc-16 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o LEA.so R_LFMM.o R_crossEntropy.o R_createDataSet.o R_sNMF.o R_ancestrymap2geno.o R_ancestrymap2lfmm.o R_geno2lfmm.o R_lfmm2geno.o R_pca.o R_ped2geno.o R_ped2lfmm.o R_vcf2geno.o R_tracyWidom.o R_init_LEA.o bituint/bituint.o bituint/calc_bituint.o bituint/io_geno_bituint.o bituint/slice_bituint.o bituint/thread_bituint.o convert/ancestrymap.o convert/geno.o convert/ped.o convert/vcf2geno.o convert/geno2lfmm.o convert/lfmm2geno.o convert/register_convert.o createDataSet/createDataSet.o createDataSet/error_cds.o createDataSet/print_cds.o createDataSet/register_cds.o crossEntropy/crossEntropy.o crossEntropy/error_ce.o crossEntropy/print_ce.o crossEntropy/register_ce.o io/io_data_double.o io/io_data_float.o io/io_data_int.o io/io_error.o io/io_tools.o io/print_bar.o LFMM/beta.o LFMM/error_lfmm.o LFMM/lfmm_k0.o LFMM/slice_lfmm.o LFMM/U.o LFMM/beta_k0.o LFMM/lfmm_algo.o LFMM/print_lfmm.o LFMM/thread_lfmm.o LFMM/V.o LFMM/data_lfmm.o LFMM/LFMM.o LFMM/register_lfmm.o LFMM/thread_var.o matrix/cholesky.o matrix/error_matrix.o matrix/normalize.o matrix/slice_matrix.o matrix/data.o matrix/inverse.o matrix/rand.o matrix/sylvester.o matrix/diagonalize.o matrix/matrix.o matrix/random_projection.o matrix/thread_matrix.o nnlsm/blockpivot.o nnlsm/nnlsm.o nnlsm/solvenormaleqcomb.o nnlsm/sort.o pca/calc_cov.o pca/error_pca.o pca/pca.o pca/print_pca.o pca/register_pca.o sNMF/als.o sNMF/als_k1.o sNMF/criteria.o sNMF/print_snmf.o sNMF/sNMF.o sNMF/thread_Q.o sNMF/als_F.o sNMF/als_Q.o sNMF/error_snmf.o sNMF/register_snmf.o sNMF/thread_F.o sNMF/thread_snmf.o stats/beta_distribution.o stats/gamma_density.o stats/ln_beta_function.o stats/beta_function.o stats/gamma_distribution.o stats/ln_gamma_function.o stats/entire_incomplete_gamma_function.o stats/gamma_dist_tables.o stats/student_t_distribution.o stats/factorial.o stats/gamma_function.o tracyWidom/error_tracyWidom.o tracyWidom/register_tracyWidom.o tracyWidom/print_tracyWidom.o tracyWidom/tracyWidom.o -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -latomic_asneeded -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpvlHjOc/R.INSTALL2a976a49eccd63/LEA/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-LEA/00new/LEA/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 (LEA) checking BIGpopA_2.0.0.tar.gz ... checking Familia_1.0.3.tar.gz ... Depends: Package: BIGpopA Depends: R (>= 4.4.0) Imports: dplyr, janitor, quadprog, data.table, ggplot2 Timings: user system elapsed BIGpopA 50.724 6.322 58.314 Results: Check status summary: NOTE OK Source packages 1 0 Reverse depends 0 1 Check results summary: BIGpopA ... NOTE * checking CRAN incoming feasibility ... [5s/6s] NOTE rdepends_Familia ... OK