* installing *source* package ‘rtfbs’ ... ** package ‘rtfbs’ successfully unpacked and MD5 sums checked checking for CFLAGS... -g checking for gcc... clang -mtune=native 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 clang -mtune=native accepts -g... yes checking for clang -mtune=native option to accept ISO C89... none needed -g checking how to run the C preprocessor... clang -mtune=native -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... rm: conftest.dSYM: is a directory rm: conftest.dSYM: is a directory 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 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 for an ANSI C-conforming const... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for size_t... 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... yes checking for gethostname... yes checking for gettimeofday... yes checking for memset... yes checking for pow... yes checking for re_comp... no checking for regcomp... yes checking for rint... yes checking for sqrt... yes checking for strcasecmp... yes checking for strdup... yes checking for strstr... yes checking for strtol... yes checking for -fno-strict-aliasing... yes checking for inline... inline checking for int64_t... yes checking for an ANSI C-conforming const... (cached) yes checking for bcopy... yes checking for memmove... yes checking for strerror... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for gzopen in -lz... yes checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes checking for libbz2... yes checking readline/readline.h usability... yes checking readline/readline.h presence... yes checking for readline/readline.h... yes checking readline/history.h usability... yes checking readline/history.h presence... yes checking for readline/history.h... yes checking for readline in -lreadline... yes configure: creating ./config.status config.status: creating src/pcre/pcre.h config.status: creating src/pcre/config.h config.status: src/pcre/config.h is unchanged configure: creating ./config.status config.status: creating src/pcre/pcre.h config.status: creating src/Makevars config.status: creating src/pcre/config.h config.status: src/pcre/config.h is unchanged - configuration summary: C preprocessor .................. : clang -mtune=native -E C compiler ...................... : clang -mtune=native C compiler flags ................ : -g -fno-strict-aliasing Extra libraries ................. : ** libs clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c fit_em.c -o fit_em.o fit_em.c:685:53: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] int nrc = mod->nratecats > 1 ? mod->nratecats : -mod->alpha; ~~~ ^~~~~~~~~~~ fit_em.c:412:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fit_em.c:1120:53: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] int nrc = mod->nratecats > 1 ? mod->nratecats : -mod->alpha; ~~~ ^~~~~~~~~~~ 3 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c rph_phyloP.c -o rph_phyloP.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c msa.c -o msa.o msa.c:170:29: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion] base = do_toupper ? toupper(line[k]) : line[k]; ~ ^~~~~~~~~~~~~~~~ msa.c:118:7: warning: variable 'len' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if (format == PHYLIP || format == MPM) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ msa.c:127:36: note: uninitialized use occurs here msa = msa_new(NULL, NULL, nseqs, len, alphabet); ^~~ msa.c:118:3: note: remove the 'if' if its condition is always true if (format == PHYLIP || format == MPM) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ msa.c:104:29: note: initialize the variable 'len' to silence this warning int i, j, k=-1, nseqs, len, do_toupper; ^ = 0 msa.c:118:7: warning: variable 'nseqs' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if (format == PHYLIP || format == MPM) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ msa.c:127:29: note: uninitialized use occurs here msa = msa_new(NULL, NULL, nseqs, len, alphabet); ^~~~~ msa.c:118:3: note: remove the 'if' if its condition is always true if (format == PHYLIP || format == MPM) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ msa.c:104:24: note: initialize the variable 'nseqs' to silence this warning int i, j, k=-1, nseqs, len, do_toupper; ^ = 0 msa.c:324:38: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion] msa->seqs[i][j] = do_toupper ? toupper(s->chars[j]) : s->chars[j]; ~ ^~~~~~~~~~~~~~~~~~~~ msa.c:554:40: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32] if (msa->seqs != NULL) msa->length = strlen(msa->seqs[0]); ~ ^~~~~~~~~~~~~~~~~~~~ msa.c:1475:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int i, j, size = strlen(msa->alphabet); ~~~~ ^~~~~~~~~~~~~~~~~~~~~ msa.c:1576:39: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] int thiscount = (cat >= 0 ? msa->ss->cat_counts[cat][i] : ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ msa.c:1577:28: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] msa->ss->counts[i]); ^~~~~~~~~~~~~~~~~~ msa.c:1552:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(msa->alphabet); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~ msa.c:1622:55: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int i, j, spec, numcodon=msa->length/3, alph_size = strlen(msa->alphabet); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~ msa.c:2766:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int i, nchars = strlen(newalph); ~~~~~~ ^~~~~~~~~~~~~~~ msa.c:2797:34: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] int char_idx = 4.0 * unif_rand(); ~~~~~~~~ ~~~~^~~~~~~~~~~~~ msa.c:2816:32: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] int char_idx = 4.0 * unif_rand(); ~~~~~~~~ ~~~~^~~~~~~~~~~~~ msa.c:2846:19: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion] char newc = toupper(msa->alphabet[i]); ~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~ msa.c:2869:34: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion] toupper(ss_get_char_tuple(msa, i, j, -k))); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ msa.c:2876:27: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion] msa->seqs[i][j] = toupper(msa->seqs[i][j]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~ msa.c:2985:23: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion] cod[codpos++] = toupper(c); ~ ^~~~~~~~~~ 17 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c fit_column.c -o fit_column.o fit_column.c:1469:18: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] g->ngrid1 = 1.0/GRIDSIZE1; ~ ~~~^~~~~~~~~~ fit_column.c:1470:46: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] g->ngrid2 = (1.0 * GRIDMAXLOG / GRIDSIZE2) + 1; ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ fit_column.c:1536:11: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] idx = floor(scale / GRIDSIZE1); ~ ^~~~~~~~~~~~~~~~~~~~~~~~ fit_column.c:1538:21: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] idx = g->ngrid1 + floor(log(scale) / GRIDSIZE2); ~ ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c indel_mod.c -o indel_mod.o 4 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c rph_tfbs.c -o rph_tfbs.o rph_tfbs.c:220:16: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] resultP[0] = totalSeqLengths; ~ ^~~~~~~~~~~~~~~ rph_tfbs.c:375:25: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] inputSeqLen = strlen(inputMS->seqs[inputSeqNum]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rph_tfbs.c:600:23: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] strlen(inputMS->seqs[currentSequence]), inputMS->idx_offsets[currentSequence], ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rph_tfbs.c:601:23: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] strlen(inputMS->alphabet), MarkovMatrices, pwm, reverseCompPWM, ^~~~~~~~~~~~~~~~~~~~~~~~~ rph_tfbs.c:752:18: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] resultP[i] = strlen(ms->seqs[i]); ~ ^~~~~~~~~~~~~~~~~~~ 5 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c motif.c -o motif.o motif.c:99:26: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] alph_size = multiseq ? strlen(pmsa->pooled_msa->alphabet) : ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ motif.c:100:5: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] strlen(seqset->set->alphabet); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ motif.c:300:42: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] if (sample < 0 || position < 0) return strlen(set->alphabet); ~~~~~~ ^~~~~~~~~~~~~~~~~~~~~ motif.c:883:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(s->set->alphabet); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~ motif.c:943:7: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] n = ceil(1.0 * number/s->set->nseqs); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ motif.c:946:19: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] int start = rint(1.0 * (s->lens[i] - tuple_size) * unif_rand()); ~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ motif.c:1009:30: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = multiseq ? strlen(pmsa->pooled_msa->alphabet) : ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ motif.c:1010:5: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] strlen(ss->set->alphabet); ^~~~~~~~~~~~~~~~~~~~~~~~~ motif.c:1247:18: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] m->alph_size = strlen(m->alphabet); ~ ^~~~~~~~~~~~~~~~~~~ 9 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c tfbs.c -o tfbs.o tfbs.c:110:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] seqLen = strlen(ms->seqs[i]); ~ ^~~~~~~~~~~~~~~~~~~ tfbs.c:285:37: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion] ms->seqs[i][j] = do_toupper ? toupper(s->chars[j]) : s->chars[j]; ~ ^~~~~~~~~~~~~~~~~~~~ tfbs.c:324:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] alph_size = strlen(inputMS->alphabet); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~ tfbs.c:331:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] seqLen = strlen(inputMS->seqs[j]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~ tfbs.c:360:18: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] for (i = strlen(inputMS->seqs[j]); i >= 0 ; i--) { ~ ^~~~~~~~~~~~~~~~~~~~~~~~ 5 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c phylo_p_print.c -o phylo_p_print.o phylo_p_print.c:332:38: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] cond = pm_x_given_tot(prior_joint, post_min_tot); ~~~~~~~~~~~~~~ ^~~~~~~~~~~~ phylo_p_print.c:336:38: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] cond = pm_x_given_tot(prior_joint, post_max_tot); ~~~~~~~~~~~~~~ ^~~~~~~~~~~~ 2 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c rph_msa.c -o rph_msa.o rph_msa.c:129:22: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int i, alph_size = strlen(msa->alphabet); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~ rph_msa.c:367:18: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] cmStrLen = strlen(cmStr); ~ ^~~~~~~~~~~~~ rph_msa.c:1192:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] nstate = int_pow(strlen(msa->alphabet), mod->order+1); ~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~ 3 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c indel_history.c -o indel_history.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c em.c -o em.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c gap_patterns.c -o gap_patterns.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c trees.c -o trees.o trees.c:63:53: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int i, in_distance = FALSE, in_label=FALSE, len = strlen(treestr), nopen_parens = 0, ~~~ ^~~~~~~~~~~~~~~ trees.c:291:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] len = strlen(root->name); ~ ^~~~~~~~~~~~~~~~~~ trees.c:730:28: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] y[n->parent->id] - n->dparent*scale; ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ trees.c:733:28: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] x[n->parent->id] + n->dparent*scale; ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ trees.c:788:22: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32] xoffset = -3 * (n->name != NULL ? strlen(n->name) : 0); ~ ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c sufficient_stats.c -o sufficient_stats.o sufficient_stats.c:120:22: warning: implicit conversion turns floating-point number into integer: 'double' to 'long' [-Wconversion] max_tuples = min(pow(strlen(msa->alphabet)+ strlen(msa->missing) + 1, ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./misc.h:58:33: note: expanded from macro 'min' #define min(x, y) ((x) < (y) ? (x) : (y)) ^ sufficient_stats.c:139:22: warning: implicit conversion turns floating-point number into integer: 'double' to 'long' [-Wconversion] max_tuples = min(pow(strlen(msa->alphabet) + strlen(msa->missing) + 1, ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./misc.h:58:33: note: expanded from macro 'min' #define min(x, y) ((x) < (y) ? (x) : (y)) ^ sufficient_stats.c:123:29: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] ss_new(msa, tuple_size, max_tuples, do_cats, store_order); ~~~~~~ ^~~~~~~~~~ sufficient_stats.c:142:33: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] ss_realloc(msa, tuple_size, max_tuples, do_cats, store_order); ~~~~~~~~~~ ^~~~~~~~~~ sufficient_stats.c:147:74: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] tuple_hash = existing_hash != NULL ? existing_hash : hsh_new(max_tuples/3); ~~~~~~~ ~~~~~~~~~~^~ sufficient_stats.c:1064:11: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] midpt = ceil(ss->tuple_size/2.0); ~ ^~~~~~~~~~~~~~~~~~~~~~~~ sufficient_stats.c:1089:11: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] midpt = ceil(msa->length/2.0); ~ ^~~~~~~~~~~~~~~~~~~~~ 7 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c lists.c -o lists.o lists.c:38:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] l->step = ceil(l->elementsz * 1.0/sizeof(void*)); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ lists.c:229:32: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] lower_val = lst_get_dbl(l, lower_idx); ~~~~~~~~~~~ ^~~~~~~~~ lists.c:230:32: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] upper_val = lst_get_dbl(l, upper_idx); ~~~~~~~~~~~ ^~~~~~~~~ 3 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c matrix.c -o matrix.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c subst_distrib.c -o subst_distrib.o subst_distrib.c:73:12: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] for (j = mean; ; j++) ~ ^~~~ subst_distrib.c:394:19: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] counts[tup] = msa->ss->counts[tup]; /* have to convert to int */ ~ ^~~~~~~~~~~~~~~~~~~~ subst_distrib.c:572:48: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] cond = pm_x_given_tot(prior, msub[tup] + msup[tup]); ~~~~~~~~~~~~~~ ~~~~~~~~~~^~~~~~~~~~~ subst_distrib.c:812:19: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] counts[tup] = msa->ss->counts[tup]; /* have to convert to int */ ~ ^~~~~~~~~~~~~~~~~~~~ subst_distrib.c:964:27: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] stats[idx].post_min = floor(this_min); ~ ^~~~~~~~~~~~~~~ subst_distrib.c:965:27: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] stats[idx].post_max = ceil(this_max); ~ ^~~~~~~~~~~~~~ subst_distrib.c:994:11: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] int l = sqrt(max_convolve_size / ~ ^~~~~~~~~~~~~~~~~~~~~~~~ subst_distrib.c:1157:23: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] max_nrows = ceil(len * prior_site_mean_left + ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_distrib.c:1159:23: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] max_ncols = ceil(len * prior_site_mean_right + ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_distrib.c:1232:32: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] stats[idx].post_min_left = floor(this_min_left); ~ ^~~~~~~~~~~~~~~~~~~~ subst_distrib.c:1233:32: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] stats[idx].post_max_left = ceil(this_max_left); ~ ^~~~~~~~~~~~~~~~~~~ subst_distrib.c:1234:33: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] stats[idx].post_min_right = floor(this_min_right); ~ ^~~~~~~~~~~~~~~~~~~~~ subst_distrib.c:1235:33: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] stats[idx].post_max_right = ceil(this_max_right); ~ ^~~~~~~~~~~~~~~~~~~~ subst_distrib.c:1236:31: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] stats[idx].post_min_tot = floor(this_min_tot); ~ ^~~~~~~~~~~~~~~~~~~ subst_distrib.c:1237:31: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] stats[idx].post_max_tot = ceil(this_max_tot); ~ ^~~~~~~~~~~~~~~~~~ 15 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c rph_phylo_hmm.c -o rph_phylo_hmm.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c memory_handler.c -o memory_handler.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c bed.c -o bed.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c eigen.c -o eigen.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c rph_phyloFit.c -o rph_phyloFit.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c rph_util.c -o rph_util.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c rph_phastCons.c -o rph_phastCons.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c rph_list_of_lists.c -o rph_list_of_lists.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c genepred.c -o genepred.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c phast_cons.c -o phast_cons.o phast_cons.c:837:23: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] if (mu < 0 && abs(mu) < TM_IMAG_EPS) /* consider close enough to 0 */ ~~~ ^~ 1 warning generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c tree_model.c -o tree_model.o tree_model.c:78:22: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] nstate = int_pow(strlen(alphabet), tm->order+1); ~~~~~~~ ^~~~~~~~~~~~~~~~ tree_model.c:2196:6: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion] c = tolower(mod->rate_matrix->states[i]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree_model.c:2375:26: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] currparam->length = strlen(currparam->chars); ~ ^~~~~~~~~~~~~~~~~~~~~~~~ tree_model.c:3014:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int numstate=strlen(msa->alphabet), **minState, *numMinState; ~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~ tree_model.c:3374:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] return -mod->alpha; /* (here, nratecats is stored as -alpha) */ ~~~~~~ ^~~~~~~~~~~ 5 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c misc.c -o misc.o misc.c:53:19: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] int randidx = rint(1.0 * (lst_size(eligible)-1) * unif_rand()); ~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ misc.c:95:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] randidx = rint(1.0 * (lst_size(eligible)-1) * unif_rand()); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ misc.c:118:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(alphabet); ~~~~~~~~~ ^~~~~~~~~~~~~~~~ misc.c:164:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int tuple_size = strlen(tuple); ~~~~~~~~~~ ^~~~~~~~~~~~~ misc.c:179:33: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int k, remainder, alph_size = strlen(alphabet); ~~~~~~~~~ ^~~~~~~~~~~~~~~~ misc.c:225:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] file_size = strlen(file_alph); ~ ^~~~~~~~~~~~~~~~~ misc.c:226:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size = strlen(alph); ~ ^~~~~~~~~~~~ misc.c:455:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int len = strlen(word); ~~~ ^~~~~~~~~~~~ misc.c:464:8: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion] b1 = toupper(b1); b2 = toupper(b2); ~ ^~~~~~~~~~~ misc.c:464:26: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion] b1 = toupper(b1); b2 = toupper(b2); ~ ^~~~~~~~~~~ misc.c:586:10: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] return bn1; ~~~~~~ ^~~ misc.c:634:35: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] counts[data[i].idx] = data[i].count; ~ ~~~~~~~~^~~~~ 12 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c local_alignment.c -o local_alignment.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c prob_vector.c -o prob_vector.o prob_vector.c:162:17: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] max_x = max(ceil(n * mean + max_nsd * sqrt(n * var)), p->size); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./misc.h:56:33: note: expanded from macro 'max' #define max(x, y) ((x) > (y) ? (x) : (y)) ^ prob_vector.c:222:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] max_x = ceil(n * mean + max_nsd * sqrt(n * var)); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prob_vector.c:284:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] max_x = ceil(tot_mean + max_nsd * sqrt(tot_var)); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prob_vector.c:328:33: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] Vector *pois = vec_new(max(10 * lambda, 50)); ~~~~~~~ ~~~^~~~~~~~ ./misc.h:56:33: note: expanded from macro 'max' #define max(x, y) ((x) > (y) ? (x) : (y)) ^ 4 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c complex_matrix.c -o complex_matrix.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c subst_mods.c -o subst_mods.o subst_mods.c:249:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] n = strlen(mod->rate_matrix->states); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:252:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] n = strlen(mod->rate_matrix->states); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:699:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion] c = toupper(mod->rate_matrix->states[i]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:891:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:937:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:1032:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:1070:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:1152:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:1202:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:1306:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:1348:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:1441:28: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int i, j, k, alph_size = strlen(mod->rate_matrix->states), codi[3], codj[3], ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:1524:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] alph_size = strlen(states); ~ ^~~~~~~~~~~~~~ subst_mods.c:1595:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] alph_size = strlen(states); ~ ^~~~~~~~~~~~~~ subst_mods.c:1788:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:1815:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:1874:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:1904:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:1967:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:1999:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:2070:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:2106:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:2168:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:2251:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:2278:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:2300:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:2356:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:2407:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:2438:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:2506:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:2533:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subst_mods.c:2590:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] nstate = strlen(states); ~ ^~~~~~~~~~~~~~ subst_mods.c:2611:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] nstate = strlen(states); ~ ^~~~~~~~~~~~~~ subst_mods.c:2726:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion] c = toupper(states[i]); ~ ^~~~~~~~~~~~~~~~~~ subst_mods.c:2723:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int i, nstate = strlen(states); ~~~~~~ ^~~~~~~~~~~~~~ subst_mods.c:2741:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] alph_size = strlen(mm->states), chartype[5]; ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ 36 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c list_of_lists.c -o list_of_lists.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c maf.c -o maf.o maf.c:142:32: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] max_tuples = max(1000000, pow(strlen(msa->alphabet)+strlen(msa->missing)+1, ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./misc.h:56:39: note: expanded from macro 'max' #define max(x, y) ((x) > (y) ? (x) : (y)) ^ maf.c:149:8: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] pow(strlen(msa->alphabet)+strlen(msa->missing)+1, 2 * msa->nseqs * tuple_size)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./misc.h:58:39: note: expanded from macro 'min' #define min(x, y) ((x) < (y) ? (x) : (y)) ^ maf.c:390:28: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion] refseq->chars[i] = toupper(refseq->chars[i]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~ maf.c:331:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(msa->alphabet), nreftuples = int_pow(alph_size, tuple_size); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~ maf.c:599:22: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] pow(strlen(msa->alphabet)+strlen(msa->missing)+1, msa->nseqs * tuple_size)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./misc.h:58:39: note: expanded from macro 'min' #define min(x, y) ((x) < (y) ? (x) : (y)) ^ maf.c:605:22: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] pow(strlen(msa->alphabet)+strlen(msa->missing)+1, msa->nseqs * tuple_size)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./misc.h:58:39: note: expanded from macro 'min' #define min(x, y) ((x) < (y) ? (x) : (y)) ^ maf.c:746:28: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion] refseq->chars[i] = toupper(refseq->chars[i]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~ maf.c:698:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(msa->alphabet), nreftuples = int_pow(alph_size, tuple_size); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~ maf.c:932:48: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion] mini_msa->seqs[seqidx][i] = do_toupper ? toupper(this_seq->chars[i]) : ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ maf.c:1053:48: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion] mini_msa->seqs[seqidx][i] = do_toupper ? toupper(this_seq->chars[i]) : ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 10 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c maf_block.c -o maf_block.o maf_block.c:120:16: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] sub->start = atol(((String*)lst_get_ptr(l, 2))->chars); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ maf_block.c:134:18: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] sub->srcSize = atol(((String*)lst_get_ptr(l, 5))->chars); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ maf_block.c:439:22: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] fieldSize[2] = strlen(tempstr); ~ ^~~~~~~~~~~~~~~ maf_block.c:444:22: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] fieldSize[3] = strlen(tempstr); ~ ^~~~~~~~~~~~~~~ maf_block.c:451:22: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] fieldSize[5] = strlen(tempstr); ~ ^~~~~~~~~~~~~~~ 5 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c rph_category_map.c -o rph_category_map.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c complex_vector.c -o complex_vector.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c dgamma.c -o dgamma.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c gff.c -o gff.o gff.c:673:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int i, taglen = strlen(tag); ~~~~~~ ^~~~~~~~~~~ 1 warning generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c hmm.c -o hmm.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c rph_init.c -o rph_init.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c category_map.c -o category_map.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c rph_hmm.c -o rph_hmm.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c tree_likelihoods.c -o tree_likelihoods.o tree_likelihoods.c:210:35: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion] char thischar = (int)ss_get_char_tuple(msa, tupleidx, ~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree_likelihoods.c:47:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(mod->rate_matrix->states); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree_likelihoods.c:478:32: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int i, seq, idx, alph_size = strlen(msa->alphabet); ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~ tree_likelihoods.c:838:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int alph_size = strlen(alphabet); ~~~~~~~~~ ^~~~~~~~~~~~~~~~ tree_likelihoods.c:883:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int tuple_size = strlen(tuple); ~~~~~~~~~~ ^~~~~~~~~~~~~ 5 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c stringsplus.c -o stringsplus.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c multi_msa.c -o multi_msa.o stringsplus.c:30:23: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] String *s = str_new(strlen(str)); ~~~~~~~ ^~~~~~~~~~~ stringsplus.c:85:35: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] str_nappend_charstr(s, charstr, strlen(charstr)); ~~~~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~ stringsplus.c:448:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int len = strlen(substr); ~~~ ^~~~~~~~~~~~~~ stringsplus.c:460:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] int len = strlen(substr); ~~~ ^~~~~~~~~~~~~~ stringsplus.c:669:19: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion] s->chars[i] = toupper(s->chars[i]); ~ ^~~~~~~~~~~~~~~~~~~~ stringsplus.c:675:19: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion] s->chars[i] = tolower(s->chars[i]); ~ ^~~~~~~~~~~~~~~~~~~~ 6 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c rph_tree_model.c -o rph_tree_model.o rph_tree_model.c:439:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] dim = int_pow(strlen(alphabet), tm_order(subst_mod)+1); ~~~~~~~ ^~~~~~~~~~~~~~~~ 1 warning generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c markov_matrix.c -o markov_matrix.o markov_matrix.c:40:39: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] alph_size = states == NULL ? size : strlen(states); ~ ^~~~~~~~~~~~~~ markov_matrix.c:160:24: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] if (abs(sum + diag - targetval) > SUM_EPSILON) { ~~~ ~~~~~~~~~~~^~~~~~~~~~~ 2 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c hashtable.c -o hashtable.o hashtable.c:28:18: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] ht->nbuckets = ceil(est_capacity*1.0/LOADING_FACTOR); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c phylo_p.c -o phylo_p.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c rph_gff.c -o rph_gff.o rph_gff.c:535:11: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] overlappingFragments, overlapping_gff); ^~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c rph_subst_mods.c -o rph_subst_mods.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c rph_trees.c -o rph_trees.o rph_trees.c:52:20: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion] while (';'!=(c=fgetc(infile))) { ~^~~~~~~~~~~~~ 1 warning generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c vector.c -o vector.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c fit_feature.c -o fit_feature.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c phylo_hmm.c -o phylo_hmm.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c pcre/pcre_newline.c -o pcre/pcre_newline.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c pcre/pcre_study.c -o pcre/pcre_study.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c pcre/pcre_compile.c -o pcre/pcre_compile.o pcre/pcre_compile.c:2186:7: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT(hc, 0, offset + adjust); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:2197:43: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] if (cd->start_code + offset >= group) PUT(ptr, 1, offset + adjust); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:2226:1: warning: implicit conversion loses integer precision: 'long' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT(code, 0, ptr - cd->start_pattern); /* Pattern offset */ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:2253:1: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT(previous_callout, 2 + LINK_SIZE, length); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:2252:38: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] int length = ptr - cd->start_pattern - GET(previous_callout, 2); ~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_compile.c:3706:19: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = class_lastchar; ~ ^~~~~~~~~~~~~~ pcre/pcre_compile.c:3719:23: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] mcbuffer[0] = class_lastchar; ~ ^~~~~~~~~~~~~~ pcre/pcre_compile.c:3982:49: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] if (repeat_max == -1) *code++ = OP_STAR + repeat_type; ~ ~~~~~~~~^~~~~~~~~~~~~ pcre/pcre_compile.c:3983:56: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] else if (repeat_max == 1) *code++ = OP_QUERY + repeat_type; ~ ~~~~~~~~~^~~~~~~~~~~~~ pcre/pcre_compile.c:3986:29: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = OP_UPTO + repeat_type; ~ ~~~~~~~~^~~~~~~~~~~~~ pcre/pcre_compile.c:3987:11: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT2INC(code, 0, repeat_max); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:406:25: note: expanded from macro 'PUT2INC' #define PUT2INC(a,n,d) PUT2(a,n,d), a += 2 ^~~~~~~~~~~ pcre/pcre_internal.h:400:14: note: expanded from macro 'PUT2' a[n] = (d) >> 8; \ ~ ~~~~^~~~ pcre/pcre_compile.c:3999:29: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = OP_PLUS + repeat_type; ~ ~~~~~~~~^~~~~~~~~~~~~ pcre/pcre_compile.c:4004:29: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = OP_UPTO + repeat_type; ~ ~~~~~~~~^~~~~~~~~~~~~ pcre/pcre_compile.c:4005:11: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT2INC(code, 0, repeat_max - 1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:406:25: note: expanded from macro 'PUT2INC' #define PUT2INC(a,n,d) PUT2(a,n,d), a += 2 ^~~~~~~~~~~ pcre/pcre_internal.h:400:14: note: expanded from macro 'PUT2' a[n] = (d) >> 8; \ ~ ~~~~^~~~ pcre/pcre_compile.c:4014:28: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = OP_EXACT + op_type; /* NB EXACT doesn't have repeat_type */ ~ ~~~~~~~~~^~~~~~~~~ pcre/pcre_compile.c:4015:9: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT2INC(code, 0, repeat_min); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:406:25: note: expanded from macro 'PUT2INC' #define PUT2INC(a,n,d) PUT2(a,n,d), a += 2 ^~~~~~~~~~~ pcre/pcre_internal.h:400:14: note: expanded from macro 'PUT2' a[n] = (d) >> 8; \ ~ ~~~~^~~~ pcre/pcre_compile.c:4034:23: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = c; ~ ^ pcre/pcre_compile.c:4037:25: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = prop_type; ~ ^~~~~~~~~ pcre/pcre_compile.c:4038:25: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = prop_value; ~ ^~~~~~~~~~ pcre/pcre_compile.c:4041:29: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = OP_STAR + repeat_type; ~ ~~~~~~~~^~~~~~~~~~~~~ pcre/pcre_compile.c:4058:21: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = c; ~ ^ pcre/pcre_compile.c:4061:23: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = prop_type; ~ ^~~~~~~~~ pcre/pcre_compile.c:4062:23: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = prop_value; ~ ^~~~~~~~~~ pcre/pcre_compile.c:4068:32: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = OP_QUERY + repeat_type; ~ ~~~~~~~~~^~~~~~~~~~~~~ pcre/pcre_compile.c:4072:31: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = OP_UPTO + repeat_type; ~ ~~~~~~~~^~~~~~~~~~~~~ pcre/pcre_compile.c:4073:13: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT2INC(code, 0, repeat_max); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:406:25: note: expanded from macro 'PUT2INC' #define PUT2INC(a,n,d) PUT2(a,n,d), a += 2 ^~~~~~~~~~~ pcre/pcre_internal.h:400:14: note: expanded from macro 'PUT2' a[n] = (d) >> 8; \ ~ ~~~~^~~~ pcre/pcre_compile.c:4088:17: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = c; ~ ^ pcre/pcre_compile.c:4129:29: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = OP_CRSTAR + repeat_type; ~ ~~~~~~~~~~^~~~~~~~~~~~~ pcre/pcre_compile.c:4131:29: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = OP_CRPLUS + repeat_type; ~ ~~~~~~~~~~^~~~~~~~~~~~~ pcre/pcre_compile.c:4133:30: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = OP_CRQUERY + repeat_type; ~ ~~~~~~~~~~~^~~~~~~~~~~~~ pcre/pcre_compile.c:4136:30: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = OP_CRRANGE + repeat_type; ~ ~~~~~~~~~~~^~~~~~~~~~~~~ pcre/pcre_compile.c:4137:9: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT2INC(code, 0, repeat_min); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:406:25: note: expanded from macro 'PUT2INC' #define PUT2INC(a,n,d) PUT2(a,n,d), a += 2 ^~~~~~~~~~~ pcre/pcre_internal.h:400:14: note: expanded from macro 'PUT2' a[n] = (d) >> 8; \ ~ ~~~~^~~~ pcre/pcre_compile.c:4139:9: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT2INC(code, 0, repeat_max); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:406:25: note: expanded from macro 'PUT2INC' #define PUT2INC(a,n,d) PUT2(a,n,d), a += 2 ^~~~~~~~~~~ pcre/pcre_internal.h:400:14: note: expanded from macro 'PUT2' a[n] = (d) >> 8; \ ~ ~~~~^~~~ pcre/pcre_compile.c:4216:36: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *previous++ = OP_BRAZERO + repeat_type; ~ ~~~~~~~~~~~^~~~~~~~~~~~~ pcre/pcre_compile.c:4234:36: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *previous++ = OP_BRAZERO + repeat_type; ~ ~~~~~~~~~~~^~~~~~~~~~~~~ pcre/pcre_compile.c:4242:11: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUTINC(previous, 0, offset); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:392:25: note: expanded from macro 'PUTINC' #define PUTINC(a,n,d) PUT(a,n,d), a += LINK_SIZE ^~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:4290:17: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT(cd->hwm, 0, GET(hc, 0) + len); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:4340:32: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = OP_BRAZERO + repeat_type; ~ ~~~~~~~~~~~^~~~~~~~~~~~~ pcre/pcre_compile.c:4351:13: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUTINC(code, 0, offset); ^~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:392:25: note: expanded from macro 'PUTINC' #define PUTINC(a,n,d) PUT(a,n,d), a += LINK_SIZE ^~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:4357:13: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT(cd->hwm, 0, GET(hc, 0) + len + ((i != 0)? 2+LINK_SIZE : 1)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:4375:11: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUTINC(code, 0, offset); ^~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:392:25: note: expanded from macro 'PUTINC' #define PUTINC(a,n,d) PUT(a,n,d), a += LINK_SIZE ^~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:4376:11: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT(bra, 1, offset); ^~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:4395:31: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *ketcode = OP_KETRMAX + repeat_type; ~ ~~~~~~~~~~~^~~~~~~~~~~~~ pcre/pcre_compile.c:4487:9: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUTINC(code, 0, len); ^~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:392:25: note: expanded from macro 'PUTINC' #define PUTINC(a,n,d) PUT(a,n,d), a += LINK_SIZE ^~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:4488:9: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT(tempcode, 1, len); ^~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:4552:30: warning: implicit conversion loses integer precision: 'const int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = verbs[i].op; ~ ~~~~~~~~~^~ pcre/pcre_compile.c:4709:11: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT2(code, 2+LINK_SIZE, recno); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:400:14: note: expanded from macro 'PUT2' a[n] = (d) >> 8; \ ~ ~~~~^~~~ pcre/pcre_compile.c:4731:11: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT2(code, 2+LINK_SIZE, recno); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:400:14: note: expanded from macro 'PUT2' a[n] = (d) >> 8; \ ~ ~~~~^~~~ pcre/pcre_compile.c:4740:11: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT2(code, 2+LINK_SIZE, i); ^~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:400:14: note: expanded from macro 'PUT2' a[n] = (d) >> 8; \ ~ ~~~~^~~~ pcre/pcre_compile.c:4773:11: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT2(code, 2+LINK_SIZE, recno); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:400:14: note: expanded from macro 'PUT2' a[n] = (d) >> 8; \ ~ ~~~~^~~~ pcre/pcre_compile.c:4790:11: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT2(code, 2+LINK_SIZE, recno); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:400:14: note: expanded from macro 'PUT2' a[n] = (d) >> 8; \ ~ ~~~~^~~~ pcre/pcre_compile.c:4872:21: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = n; ~ ^ pcre/pcre_compile.c:4873:11: warning: implicit conversion loses integer precision: 'long' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT(code, 0, ptr - cd->start_pattern + 1); /* Pattern offset */ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:5008:13: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT2(slot, 0, cd->bracount + 1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:400:14: note: expanded from macro 'PUT2' a[n] = (d) >> 8; \ ~ ~~~~^~~~ pcre/pcre_compile.c:5206:15: warning: implicit conversion loses integer precision: 'long' to 'uschar' (aka 'unsigned char') [-Wconversion] PUTINC(cd->hwm, 0, code + 2 + LINK_SIZE - cd->start_code); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:392:25: note: expanded from macro 'PUTINC' #define PUTINC(a,n,d) PUT(a,n,d), a += LINK_SIZE ^~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:5230:11: warning: implicit conversion loses integer precision: 'long' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT(code, 1, called - cd->start_code); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:5356:7: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT2(code, 1+LINK_SIZE, cd->bracount); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:400:14: note: expanded from macro 'PUT2' a[n] = (d) >> 8; \ ~ ~~~~^~~~ pcre/pcre_compile.c:5367:13: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code = bravalue; ~ ^~~~~~~~ pcre/pcre_compile.c:5653:9: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT2INC(code, 0, recno); ^~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:406:25: note: expanded from macro 'PUT2INC' #define PUT2INC(a,n,d) PUT2(a,n,d), a += 2 ^~~~~~~~~~~ pcre/pcre_internal.h:400:14: note: expanded from macro 'PUT2' a[n] = (d) >> 8; \ ~ ~~~~^~~~ pcre/pcre_compile.c:5703:19: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = -c; ~ ^~ pcre/pcre_compile.c:5719:20: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] mcbuffer[0] = c; ~ ^ pcre/pcre_compile.c:5733:19: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] mcbuffer[0] = c; ~ ^ pcre/pcre_compile.c:3113:53: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] posix_class = check_posix_name(ptr, tempptr - ptr); ~~~~~~~~~~~~~~~~ ~~~~~~~~^~~~~ pcre/pcre_compile.c:4151:22: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] int len = code - previous; ~~~ ~~~~~^~~~~~~~~~ pcre/pcre_compile.c:4172:26: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] ketoffset = code - ket; ~ ~~~~~^~~~~ pcre/pcre_compile.c:4240:52: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] offset = (bralink == NULL)? 0 : previous - bralink; ~ ~~~~~~~~~^~~~~~~~~ pcre/pcre_compile.c:4349:50: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] offset = (bralink == NULL)? 0 : code - bralink; ~ ~~~~~^~~~~~~~~ pcre/pcre_compile.c:4370:39: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] int offset = code - bralink + 1; ~~~~~~ ~~~~~~~~~~~~~~~^~~ pcre/pcre_compile.c:4458:18: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] len = code - tempcode; ~ ~~~~~^~~~~~~~~~ pcre/pcre_compile.c:4534:21: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] namelen = ptr - name; ~ ~~~~^~~~~~ pcre/pcre_compile.c:4677:23: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] namelen = ptr - name; ~ ~~~~^~~~~~ pcre/pcre_compile.c:4907:25: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] namelen = ptr - name; ~ ~~~~^~~~~~ pcre/pcre_compile.c:5037:23: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] namelen = ptr - name; ~ ~~~~^~~~~~ pcre/pcre_compile.c:5887:20: warning: implicit conversion loses integer precision: 'int' to 'pcre_uint16' (aka 'unsigned short') [-Wconversion] capitem.number = capnumber; ~ ^~~~~~~~~ pcre/pcre_compile.c:6018:14: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] else { PUT(reverse_count, 0, fixed_length); } ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:6039:9: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT(last_branch, 1, branch_length); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:6049:5: warning: implicit conversion loses integer precision: 'long' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT(code, 1, code - start_bracket); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:6064:9: warning: implicit conversion loses integer precision: 'long' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT(start_bracket, 1, code - start_bracket); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:6066:9: warning: implicit conversion loses integer precision: 'long' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT(code, 1, code - start_bracket); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:6078:17: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *code++ = oldims; ~ ^~~~~~ pcre/pcre_compile.c:6121:5: warning: implicit conversion loses integer precision: 'long' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT(code, 1, code - last_branch); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:6035:32: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] int branch_length = code - last_branch; ~~~~~~~~~~~~~ ~~~~~^~~~~~~~~~~~~ pcre/pcre_compile.c:6598:17: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] cd->nl[0] = newline; ~ ^~~~~~~ pcre/pcre_compile.c:6681:17: warning: implicit conversion loses integer precision: 'int' to 'pcre_uint16' (aka 'unsigned short') [-Wconversion] re->flags = cd->external_flags; ~ ~~~~^~~~~~~~~~~~~~ pcre/pcre_compile.c:6686:27: warning: implicit conversion loses integer precision: 'int' to 'pcre_uint16' (aka 'unsigned short') [-Wconversion] re->name_entry_size = cd->name_entry_size; ~ ~~~~^~~~~~~~~~~~~~~ pcre/pcre_compile.c:6687:22: warning: implicit conversion loses integer precision: 'int' to 'pcre_uint16' (aka 'unsigned short') [-Wconversion] re->name_count = cd->names_found; ~ ~~~~^~~~~~~~~~~ pcre/pcre_compile.c:6720:23: warning: implicit conversion loses integer precision: 'int' to 'pcre_uint16' (aka 'unsigned short') [-Wconversion] re->top_bracket = cd->bracount; ~ ~~~~^~~~~~~~ pcre/pcre_compile.c:6721:23: warning: implicit conversion loses integer precision: 'int' to 'pcre_uint16' (aka 'unsigned short') [-Wconversion] re->top_backref = cd->top_backref; ~ ~~~~^~~~~~~~~~~ pcre/pcre_compile.c:6722:17: warning: implicit conversion loses integer precision: 'int' to 'pcre_uint16' (aka 'unsigned short') [-Wconversion] re->flags = cd->external_flags; ~ ~~~~^~~~~~~~~~~~~~ pcre/pcre_compile.c:6750:10: warning: implicit conversion loses integer precision: 'long' to 'uschar' (aka 'unsigned char') [-Wconversion] else PUT(((uschar *)codestart), offset, groupptr - codestart); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:6786:13: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] *be = end_op; ~ ^~~~~~ pcre/pcre_compile.c:6793:7: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] PUT(cc, 1, fixed_length); ^~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_internal.h:349:15: note: expanded from macro 'PUT' (a[n] = (d) >> 8), \ ~ ~~~~^~~~ pcre/pcre_compile.c:6835:30: warning: implicit conversion loses integer precision: 'int' to 'pcre_uint16' (aka 'unsigned short') [-Wconversion] cd->fcc[ch] == ch)? ch : firstbyte; ^~ pcre/pcre_compile.c:6835:35: warning: implicit conversion loses integer precision: 'int' to 'pcre_uint16' (aka 'unsigned short') [-Wconversion] cd->fcc[ch] == ch)? ch : firstbyte; ^~~~~~~~~ pcre/pcre_compile.c:6852:53: warning: implicit conversion loses integer precision: 'int' to 'pcre_uint16' (aka 'unsigned short') [-Wconversion] cd->fcc[ch] == ch)? (reqbyte & ~REQ_CASELESS) : reqbyte; ^~~~~~~ pcre/pcre_compile.c:6679:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'pcre_uint32' (aka 'unsigned int') [-Wshorten-64-to-32] re->size = size; ~ ^~~~ pcre/pcre_compile.c:6805:22: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] *erroroffset = ptr - (const uschar *)pattern; ~ ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 97 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c pcre/pcre_valid_utf8.c -o pcre/pcre_valid_utf8.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c pcre/pcre_globals.c -o pcre/pcre_globals.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c pcre/pcre_get.c -o pcre/pcre_get.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c pcre/pcre_fullinfo.c -o pcre/pcre_fullinfo.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c pcre/pcre_tables.c -o pcre/pcre_tables.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c pcre/pcre_chartables.c -o pcre/pcre_chartables.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c pcre/pcre_try_flipped.c -o pcre/pcre_try_flipped.o pcre/pcre_try_flipped.c:109:21: warning: implicit conversion loses integer precision: 'unsigned long' to 'pcre_uint32' (aka 'unsigned int') [-Wshorten-64-to-32] internal_re->size = byteflip(re->size, sizeof(re->size)); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_try_flipped.c:110:24: warning: implicit conversion loses integer precision: 'unsigned long' to 'pcre_uint32' (aka 'unsigned int') [-Wshorten-64-to-32] internal_re->options = byteflip(re->options, sizeof(re->options)); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_try_flipped.c:130:26: warning: implicit conversion loses integer precision: 'unsigned long' to 'pcre_uint32' (aka 'unsigned int') [-Wshorten-64-to-32] internal_study->size = byteflip(study->size, sizeof(study->size)); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_try_flipped.c:131:27: warning: implicit conversion loses integer precision: 'unsigned long' to 'pcre_uint32' (aka 'unsigned int') [-Wshorten-64-to-32] internal_study->flags = byteflip(study->flags, sizeof(study->flags)); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_try_flipped.c:132:31: warning: implicit conversion loses integer precision: 'unsigned long' to 'pcre_uint32' (aka 'unsigned int') [-Wshorten-64-to-32] internal_study->minlength = byteflip(study->minlength, ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ 5 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c pcre/pcre_exec.c -o pcre/pcre_exec.o pcre/pcre_exec.c:736:57: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] md->offset_vector[md->offset_end - number] = eptr - md->start_subject; ~ ~~~~~^~~~~~~~~~~~~~~~~~~ pcre/pcre_exec.c:829:47: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] cb.subject_length = md->end_subject - md->start_subject; ~ ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ pcre/pcre_exec.c:830:38: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] cb.start_match = mstart - md->start_subject; ~ ~~~~~~~^~~~~~~~~~~~~~~~~~~ pcre/pcre_exec.c:831:36: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] cb.current_position = eptr - md->start_subject; ~ ~~~~~^~~~~~~~~~~~~~~~~~~ pcre/pcre_exec.c:1057:42: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] md->offset_vector[offset+1] = eptr - md->start_subject; ~ ~~~~~^~~~~~~~~~~~~~~~~~~ pcre/pcre_exec.c:1215:45: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] cb.subject_length = md->end_subject - md->start_subject; ~ ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ pcre/pcre_exec.c:1216:36: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] cb.start_match = mstart - md->start_subject; ~ ~~~~~~~^~~~~~~~~~~~~~~~~~~ pcre/pcre_exec.c:1217:34: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] cb.current_position = eptr - md->start_subject; ~ ~~~~~^~~~~~~~~~~~~~~~~~~ pcre/pcre_exec.c:1494:44: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] md->offset_vector[offset+1] = eptr - md->start_subject; ~ ~~~~~^~~~~~~~~~~~~~~~~~~ pcre/pcre_exec.c:2078:67: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] length = (md->jscript_compat)? 0 : md->end_subject - eptr + 1; ~ ~~~~~~~~~~~~~~~~~~~~~~~^~~ pcre/pcre_exec.c:5360:17: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] md->nl[0] = newline; ~ ^~~~~~~ pcre/pcre_exec.c:5235:45: warning: implicit conversion loses integer precision: 'const unsigned long' to 'unsigned int' [-Wshorten-64-to-32] register unsigned int flags = extra_data->flags; ~~~~~ ~~~~~~~~~~~~^~~~~ pcre/pcre_exec.c:5787:38: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] offsets[0] = md->start_match_ptr - md->start_subject; ~ ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ pcre/pcre_exec.c:5788:36: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] offsets[1] = md->end_match_ptr - md->start_subject; ~ ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ pcre/pcre_exec.c:5814:32: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] offsets[0] = start_partial - (USPTR)subject; ~ ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ pcre/pcre_exec.c:5815:30: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] offsets[1] = end_subject - (USPTR)subject; ~ ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 16 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c pcre/pcre_xclass.c -o pcre/pcre_xclass.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c pcre/pcre_ord2utf8.c -o pcre/pcre_ord2utf8.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c pcre/pcre_info.c -o pcre/pcre_info.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c pcre/pcre_config.c -o pcre/pcre_config.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c pcre/pcre_refcount.c -o pcre/pcre_refcount.o pcre/pcre_refcount.c:78:31: warning: implicit conversion loses integer precision: 'int' to 'pcre_uint16' (aka 'unsigned short') [-Wconversion] re->ref_count + adjust; ~~~~~~~~~~~~~~^~~~~~~~ 1 warning generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c pcre/pcre_version.c -o pcre/pcre_version.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c pcre/pcre_maketables.c -o pcre/pcre_maketables.o pcre/pcre_maketables.c:86:34: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion] for (i = 0; i < 256; i++) *p++ = tolower(i); ~ ^~~~~~~~~~ pcre/pcre_maketables.c:90:46: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion] for (i = 0; i < 256; i++) *p++ = islower(i)? toupper(i) : tolower(i); ~ ^~~~~~~~~~ pcre/pcre_maketables.c:90:59: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion] for (i = 0; i < 256; i++) *p++ = islower(i)? toupper(i) : tolower(i); ~ ^~~~~~~~~~ pcre/pcre_maketables.c:137:10: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion] *p++ = x; ~ ^ 4 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c pcre/pcre_ucd.c -o pcre/pcre_ucd.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c pcre/pcre_dfa_exec.c -o pcre/pcre_dfa_exec.o pcre/pcre_dfa_exec.c:476:23: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] current_subject - start_subject : max_back; ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:493:46: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] int bstate = end_code - start_code + 2 + 2*LINK_SIZE; ~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:529:37: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] ADD_NEW(end_code - start_code + length, 0); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ pcre/pcre_dfa_exec.c:347:31: note: expanded from macro 'ADD_NEW' next_new_state->offset = (x); \ ^ pcre/pcre_dfa_exec.c:756:42: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] offsets[0] = current_subject - start_subject; ~ ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:757:30: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] offsets[1] = ptr - start_subject; ~ ~~~~^~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:779:23: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] ADD_ACTIVE(code - start_code, 0); ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:324:34: note: expanded from macro 'ADD_ACTIVE' next_active_state->offset = (x); \ ^ pcre/pcre_dfa_exec.c:787:42: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] ADD_ACTIVE(code - start_code + 1 + LINK_SIZE, 0); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:324:34: note: expanded from macro 'ADD_ACTIVE' next_active_state->offset = (x); \ ^ pcre/pcre_dfa_exec.c:796:40: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] ADD_ACTIVE(code - start_code + 3 + LINK_SIZE, 0); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:324:34: note: expanded from macro 'ADD_ACTIVE' next_active_state->offset = (x); \ ^ pcre/pcre_dfa_exec.c:800:42: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] ADD_ACTIVE(code - start_code + 1 + LINK_SIZE, 0); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:324:34: note: expanded from macro 'ADD_ACTIVE' next_active_state->offset = (x); \ ^ pcre/pcre_dfa_exec.c:811:40: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] ADD_ACTIVE(code - start_code + 1 + LINK_SIZE, 0); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:324:34: note: expanded from macro 'ADD_ACTIVE' next_active_state->offset = (x); \ ^ pcre/pcre_dfa_exec.c:818:40: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] ADD_ACTIVE(code - start_code + 1 + LINK_SIZE, 0); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:324:34: note: expanded from macro 'ADD_ACTIVE' next_active_state->offset = (x); \ ^ pcre/pcre_dfa_exec.c:2236:35: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] next_state_offset = ecode - start_code; ~ ~~~~~~^~~~~~~~~~~~ pcre/pcre_dfa_exec.c:2307:15: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] ptr - start_subject, /* start offset */ ~~~~^~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:2318:53: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] { ADD_ACTIVE(endasscode + LINK_SIZE + 1 - start_code, 0); } ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:324:34: note: expanded from macro 'ADD_ACTIVE' next_active_state->offset = (x); \ ^ pcre/pcre_dfa_exec.c:2345:47: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] cb.subject_length = end_subject - start_subject; ~ ~~~~~~~~~~~~^~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:2346:51: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] cb.start_match = current_subject - start_subject; ~ ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:2347:39: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] cb.current_position = ptr - start_subject; ~ ~~~~^~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:2398:17: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] ptr - start_subject, /* start offset */ ~~~~^~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:2410:53: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] { ADD_ACTIVE(endasscode + LINK_SIZE + 1 - start_code, 0); } ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:324:34: note: expanded from macro 'ADD_ACTIVE' next_active_state->offset = (x); \ ^ pcre/pcre_dfa_exec.c:2431:15: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] ptr - start_subject, /* start offset */ ~~~~^~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:2483:15: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] ptr - start_subject, /* start offset */ ~~~~^~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:2500:71: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] next_state_offset = end_subpattern - start_code + LINK_SIZE + 1; ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ pcre/pcre_dfa_exec.c:2508:41: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] end_subpattern - start_code - GET(end_subpattern, 1) : -1; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:2572:43: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] cb.subject_length = end_subject - start_subject; ~ ~~~~~~~~~~~~^~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:2573:47: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] cb.start_match = current_subject - start_subject; ~ ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:2574:35: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] cb.current_position = ptr - start_subject; ~ ~~~~^~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:2625:41: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] offsets[0] = md->start_used_ptr - start_subject; ~ ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:2626:34: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] offsets[1] = end_subject - start_subject; ~ ~~~~~~~~~~~~^~~~~~~~~~~~~~~ pcre/pcre_dfa_exec.c:2819:17: warning: implicit conversion loses integer precision: 'int' to 'uschar' (aka 'unsigned char') [-Wconversion] md->nl[0] = newline; ~ ^~~~~~~ pcre/pcre_dfa_exec.c:2722:36: warning: implicit conversion loses integer precision: 'const unsigned long' to 'unsigned int' [-Wshorten-64-to-32] unsigned int flags = extra_data->flags; ~~~~~ ~~~~~~~~~~~~^~~~~ 30 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c prob_matrix.c -o prob_matrix.o prob_matrix.c:135:58: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] max_nrows = ceil(n * mean + max_nsd * sqrt(n * var)) + 1; ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ prob_matrix.c:137:58: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] max_ncols = ceil(n * mean + max_nsd * sqrt(n * var)) + 1; ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ prob_matrix.c:206:24: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] max_nrows = max(1, ceil(n * mean + max_nsd * sqrt(n * var))); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./misc.h:56:39: note: expanded from macro 'max' #define max(x, y) ((x) > (y) ? (x) : (y)) ^ prob_matrix.c:208:24: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] max_ncols = max(1, ceil(n * mean + max_nsd * sqrt(n * var))); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./misc.h:56:39: note: expanded from macro 'max' #define max(x, y) ((x) > (y) ? (x) : (y)) ^ prob_matrix.c:287:62: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] max_nrows = ceil(tot_mean_x + max_nsd * sqrt(tot_var_x)) + 1; ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ prob_matrix.c:288:62: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] max_ncols = ceil(tot_mean_y + max_nsd * sqrt(tot_var_y)) + 1; ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ prob_matrix.c:403:58: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] max_nrows = ceil(n * mean + max_nsd * sqrt(n * var)) + 1; ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ prob_matrix.c:405:58: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] max_ncols = ceil(n * mean + max_nsd * sqrt(n * var)) + 1; ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 8 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c phylo_fit.c -o phylo_fit.o phylo_fit.c:164:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] else prefixlen = strlen(prefix); ~ ^~~~~~~~~~~~~~ clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -I. -Ipcre -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.2.1"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER -g -fno-strict-aliasing -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c numerical_opt.c -o numerical_opt.o numerical_opt.c:1361:11: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] tv1 = floor(val1); tv2 = floor(val2); ~ ^~~~~~~~~~~ numerical_opt.c:1361:30: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] tv1 = floor(val1); tv2 = floor(val2); ~ ^~~~~~~~~~~ 2 warnings generated. 1 warning generated. clang -mtune=native -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o rtfbs.so fit_em.o rph_phyloP.o msa.o fit_column.o indel_mod.o rph_tfbs.o motif.o tfbs.o phylo_p_print.o rph_msa.o indel_history.o em.o gap_patterns.o trees.o sufficient_stats.o lists.o matrix.o subst_distrib.o rph_phylo_hmm.o memory_handler.o bed.o eigen.o rph_phyloFit.o rph_util.o rph_phastCons.o rph_list_of_lists.o genepred.o phast_cons.o tree_model.o misc.o local_alignment.o prob_vector.o complex_matrix.o subst_mods.o list_of_lists.o maf.o maf_block.o rph_category_map.o complex_vector.o dgamma.o gff.o hmm.o rph_init.o category_map.o rph_hmm.o tree_likelihoods.o stringsplus.o multi_msa.o rph_tree_model.o markov_matrix.o hashtable.o phylo_p.o rph_gff.o rph_subst_mods.o rph_trees.o vector.o fit_feature.o phylo_hmm.o pcre/pcre_newline.o pcre/pcre_study.o pcre/pcre_compile.o pcre/pcre_valid_utf8.o pcre/pcre_globals.o pcre/pcre_get.o pcre/pcre_fullinfo.o pcre/pcre_tables.o pcre/pcre_chartables.o pcre/pcre_try_flipped.o pcre/pcre_exec.o pcre/pcre_xclass.o pcre/pcre_ord2utf8.o pcre/pcre_info.o pcre/pcre_config.o pcre/pcre_refcount.o pcre/pcre_version.o pcre/pcre_maketables.o pcre/pcre_ucd.o pcre/pcre_dfa_exec.o prob_matrix.o phylo_fit.o numerical_opt.o -L/Users/ripley/R/R-clang/lib -lR -dylib_file libRblas.dylib:/Users/ripley/R/R-clang/lib/libRblas.dylib -Wl,-framework -Wl,CoreFoundation installing to /Users/ripley/R/packages/tests-clang/rtfbs.Rcheck/rtfbs/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘vignette.Rnw’ ** testing if installed package can be loaded * DONE (rtfbs)