* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘rphast’ ...
** package ‘rphast’ successfully unpacked and MD5 sums checked
** using staged installation
checking for CFLAGS...  -g
checking for gcc... gcc-8
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc-8 accepts -g... yes
checking for gcc-8 option to accept ISO C89... none needed
 -g
checking how to run the C preprocessor... gcc-8 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for size_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking for ANSI C header files... (cached) yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking pcre.h usability... yes
checking pcre.h presence... yes
checking for pcre.h... yes
checking for an ANSI C-conforming const... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for size_t... (cached) yes
checking whether time.h and sys/time.h may both be included... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for working strtod... yes
checking for vprintf... yes
checking for _doprnt... no
checking for atexit... yes
checking for bzero... yes
checking for floor... no
checking for gethostname... yes
checking for gettimeofday... yes
checking for memset... yes
checking for pow... no
checking for re_comp... yes
checking for regcomp... yes
checking for rint... no
checking for sqrt... no
checking for strcasecmp... yes
checking for strdup... yes
checking for strstr... yes
checking for strtol... yes
checking for library containing pcre_compile... -lpcre
checking for vecLib... no
checking for R's Lapack... yes
checking for -fno-strict-aliasing... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars

- configuration summary:

    C preprocessor .................. : gcc-8 -E
    C compiler ...................... : gcc-8
    C compiler flags ................ : -fno-strict-aliasing
    Extra libraries ................. : -lpcre 
    Lapack flag ..................... : -DR_LAPACK
    Lapack libs ..................... : ${LAPACK_LIBS} ${BLAS_LIBS} ${FLIBS}
    BLAS libs ....................... : -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas
    FLIBS ........................... : -lgfortran -lm -lquadmath

** libs
make[1]: Entering directory '/tmp/RtmpbfpIfc/R.INSTALL13e23f84909c/rphast/src'
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c complex_matrix.c -o complex_matrix.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c complex_vector.c -o complex_vector.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c eigen.c -o eigen.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c hashtable.c -o hashtable.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c list_of_lists.c -o list_of_lists.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c lists.c -o lists.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c markov_matrix.c -o markov_matrix.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c matrix.c -o matrix.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c memory_handler.c -o memory_handler.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c misc.c -o misc.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c numerical_opt.c -o numerical_opt.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c prob_matrix.c -o prob_matrix.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c prob_vector.c -o prob_vector.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c stringsplus.c -o stringsplus.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c vector.c -o vector.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c bed.c -o bed.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c category_map.c -o category_map.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c genepred.c -o genepred.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c gff.c -o gff.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c wig.c -o wig.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c em.c -o em.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c hmm.c -o hmm.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c motif.c -o motif.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c tfbs.c -o tfbs.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c local_alignment.c -o local_alignment.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c maf.c -o maf.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c maf_block.c -o maf_block.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c msa.c -o msa.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c multi_msa.c -o multi_msa.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c sufficient_stats.c -o sufficient_stats.o
sufficient_stats.c: In function ‘ss_from_msas’:
sufficient_stats.c:140:4: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation]
    else
    ^~~~
sufficient_stats.c:142:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’
       max_tuples = pow_bounded(strlen(msa->alphabet) + (int)strlen(msa->missing) + 1,
       ^~~~~~~~~~
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c bgc_hmm.c -o bgc_hmm.o
bgc_hmm.c: In function ‘bgcHmm’:
bgc_hmm.c:241:15: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
       sprintf(warning_str, "%s, %s", warning_str, ((String*)lst_get_ptr(pruned_names, j))->chars);
               ^~~~~~~~~~~            ~~~~~~~~~~~
bgc_hmm.c:242:13: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
     sprintf(warning_str, "%s)\n", warning_str);
             ^~~~~~~~~~~           ~~~~~~~~~~~
bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
       sprintf(warning_str, "%s, %s", warning_str, ((String*)lst_get_ptr(pruned_names, j))->chars);
                               ^~
bgc_hmm.c:241:7: note: ‘sprintf’ output 3 or more bytes (assuming 10002) into a destination of size 10000
       sprintf(warning_str, "%s, %s", warning_str, ((String*)lst_get_ptr(pruned_names, j))->chars);
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bgc_hmm.c:242:29: warning: ‘)
   ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
     sprintf(warning_str, "%s)\n", warning_str);
                             ^~~
bgc_hmm.c:242:5: note: ‘sprintf’ output between 3 and 10002 bytes into a destination of size 10000
     sprintf(warning_str, "%s)\n", warning_str);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c dgamma.c -o dgamma.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c fit_column.c -o fit_column.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c fit_em.c -o fit_em.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c fit_feature.c -o fit_feature.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c indel_history.c -o indel_history.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c indel_mod.c -o indel_mod.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c phast_cons.c -o phast_cons.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c phylo_fit.c -o phylo_fit.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c phylo_p.c -o phylo_p.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c phylo_p_print.c -o phylo_p_print.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c subst_distrib.c -o subst_distrib.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c subst_mods.c -o subst_mods.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c tree_likelihoods.c -o tree_likelihoods.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c tree_model.c -o tree_model.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c trees.c -o trees.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c gap_patterns.c -o gap_patterns.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c phylo_hmm.c -o phylo_hmm.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c rph_bgc_hmm.c -o rph_bgc_hmm.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c rph_category_map.c -o rph_category_map.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c rph_gff.c -o rph_gff.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c rph_hmm.c -o rph_hmm.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c rph_list_of_lists.c -o rph_list_of_lists.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c rph_msa.c -o rph_msa.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c rph_phastCons.c -o rph_phastCons.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c rph_phyloFit.c -o rph_phyloFit.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c rph_phyloP.c -o rph_phyloP.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c rph_phylo_hmm.c -o rph_phylo_hmm.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c rph_subst_mods.c -o rph_subst_mods.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c rph_tfbs.c -o rph_tfbs.o
rph_tfbs.c: In function ‘rph_ms_split_size’:
rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
           strncpy(outputMS->names[outputSeqNum], inputMS->names[inputSeqNum], strlen(inputMS->names[inputSeqNum]));
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
           strncpy(outputMS->names[outputSeqNum], inputMS->names[inputSeqNum], strlen(inputMS->names[inputSeqNum]));
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rph_tfbs.c: In function ‘rph_ms_simulate’:
rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
     strncpy(outputMS->names[i], name, strlen(name));
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c rph_tree_model.c -o rph_tree_model.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c rph_trees.c -o rph_trees.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c rph_util.c -o rph_util.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c rph_wig.c -o rph_wig.o
gcc-8 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.4"' -DRPHAST -DUSE_PHAST_MEMORY_HANDLER -DR_LAPACK -fno-strict-aliasing -fpic  -g -O2 -Wall -pedantic -mtune=native  -c rph_init.c -o rph_init.o
gcc-8 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o rphast.so complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o bed.o category_map.o genepred.o gff.o wig.o em.o hmm.o motif.o tfbs.o local_alignment.o maf.o maf_block.o msa.o multi_msa.o sufficient_stats.o bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o gap_patterns.o phylo_hmm.o rph_bgc_hmm.o rph_category_map.o rph_gff.o rph_hmm.o rph_list_of_lists.o rph_msa.o rph_phastCons.o rph_phyloFit.o rph_phyloP.o rph_phylo_hmm.o rph_subst_mods.o rph_tfbs.o rph_tree_model.o rph_trees.o rph_util.o rph_wig.o rph_init.o -lpcre -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRlapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpbfpIfc/R.INSTALL13e23f84909c/rphast/src'
make[1]: Entering directory '/tmp/RtmpbfpIfc/R.INSTALL13e23f84909c/rphast/src'
make[1]: Leaving directory '/tmp/RtmpbfpIfc/R.INSTALL13e23f84909c/rphast/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-rphast/00new/rphast/libs
** R
** 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 (rphast)