[med-svn] [Git][med-team/phast][master] 6 commits: Add patch to fix tests on arm64 (Closes: #911983)
Nilesh Patra
gitlab at salsa.debian.org
Sat Oct 3 08:26:56 BST 2020
Nilesh Patra pushed to branch master at Debian Med / phast
Commits:
161e5a42 by Nilesh Patra at 2020-10-03T12:26:15+05:30
Add patch to fix tests on arm64 (Closes: #911983)
- - - - -
62a25a28 by Nilesh Patra at 2020-10-03T12:50:32+05:30
routine-update: Standards-Version: 4.5.0
- - - - -
b9174069 by Nilesh Patra at 2020-10-03T12:50:32+05:30
routine-update: debhelper-compat 13
- - - - -
703798e3 by Nilesh Patra at 2020-10-03T12:50:48+05:30
routine-update: Add salsa-ci file
- - - - -
9ef8cd7f by Nilesh Patra at 2020-10-03T12:50:48+05:30
routine-update: Rules-Requires-Root: no
- - - - -
1301a43b by Nilesh Patra at 2020-10-03T12:51:29+05:30
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
- - - - -
7 changed files:
- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/arm64.patch
- debian/patches/series
- + debian/salsa-ci.yml
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+phast (1.5+dfsg-2) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Standards-Version: 4.5.0 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+ Repository-Browse.
+
+ -- Nilesh Patra <npatra974 at gmail.com> Sat, 03 Oct 2020 12:50:32 +0530
+
phast (1.5+dfsg-1) unstable; urgency=medium
* New upstream version
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -3,16 +3,17 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 13),
liblapack-dev,
libblas-dev,
libtmglib-dev,
libpcre3-dev,
help2man
-Standards-Version: 4.2.1
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/phast
Vcs-Git: https://salsa.debian.org/med-team/phast.git
Homepage: http://compgen.cshl.edu/phast/
+Rules-Requires-Root: no
Package: phast
Architecture: any
=====================================
debian/patches/arm64.patch
=====================================
@@ -0,0 +1,752 @@
+Author: Nilesh Patra <npatra974 at gmail.com>
+Description: Make char signed wherever necessary to avoid invalid comparisions
+Last-Changed: October 3, 2020
+Forwarded: https://github.com/CshlSiepelLab/phast/pull/29 : isn't the exact same patch - there's a fuzz due to line numbers changes. However, it is mostly same.
+--- a/src/dless/dless.c
++++ b/src/dless/dless.c
+@@ -30,7 +30,7 @@
+ #define DEFAULT_NU 0.01
+
+ int main(int argc, char *argv[]) {
+- char c;
++ signed char c;
+ char *msa_fname = NULL;
+ int opt_idx, i, old_nnodes;
+ MSA *msa;
+@@ -70,7 +70,7 @@
+ char *seqname = NULL, *idpref = NULL;
+ IndelHistory *ih = NULL;
+
+- while ((c = (char)getopt_long(argc, argv, "R:t:p:E:C:r:M:i:N:P:I:H:h", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "R:t:p:E:C:r:M:i:N:P:I:H:h", long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 'R':
+ rho = get_arg_dbl_bounds(optarg, 0, 1);
+--- a/src/dless/dlessP.c
++++ b/src/dless/dlessP.c
+@@ -38,7 +38,7 @@
+ int write_header);
+
+ int main(int argc, char *argv[]) {
+- char c;
++ signed char c;
+ int i, opt_idx, old_nnodes;
+ FILE *msa_f;
+ TreeModel *mod;
+@@ -65,7 +65,7 @@
+ {0, 0, 0, 0}
+ };
+
+- while ((c = (char)getopt_long(argc, argv, "r:M:i:t:h", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "r:M:i:t:h", long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 'r':
+ refidx = get_arg_int_bounds(optarg, 0, INFTY);
+--- a/src/exoniphy/exoniphy.c
++++ b/src/exoniphy/exoniphy.c
+@@ -100,14 +100,14 @@
+ CategoryMap *cm = NULL;
+ GFF_Set *predictions;
+ String *data_path=NULL;
+- char c;
++ signed char c;
+ int i, j, ncats, trial, ntrials, opt_idx, gc_cat;
+ double gc;
+ char tmpstr[STR_LONG_LEN];
+ char *msa_fname = NULL;
+ String *fname_str = str_new(STR_LONG_LEN), *str;
+
+- while ((c = (char)getopt_long(argc, argv, "i:D:c:H:m:s:p:g:B:T:L:F:IW:N:n:b:e:A:xSYUhq",
++ while ((c = getopt_long(argc, argv, "i:D:c:H:m:s:p:g:B:T:L:F:IW:N:n:b:e:A:xSYUhq",
+ long_opts, &opt_idx)) != -1) {
+ switch(c) {
+ case 'i':
+--- a/src/phastCons/phastCons.c
++++ b/src/phastCons/phastCons.c
+@@ -70,7 +70,7 @@
+ /* other vars */
+ FILE *infile;
+ char *msa_fname;
+- char c;
++ signed char c;
+ int opt_idx, i, coding_potential=FALSE;
+ List *tmpl = NULL;
+ String *tmpstr;
+@@ -78,7 +78,7 @@
+ List *mod_fname_list;
+ msa_format_type msa_format = UNKNOWN_FORMAT;
+
+- while ((c = (char)getopt_long(argc, argv,
++ while ((c = getopt_long(argc, argv,
+ "S:H:V:ni:k:l:C:G:zt:E:R:T:O:r:xL:sN:P:g:U:c:e:IY:D:JM:F:pA:Xqh",
+ long_opts, &opt_idx)) != -1) {
+ switch (c) {
+--- a/src/phastMotif/phastMotif.c
++++ b/src/phastMotif/phastMotif.c
+@@ -144,10 +144,10 @@
+ String *output_prefix = str_new_charstr("phastm.");
+ double *has_motif = NULL;
+ double prior = PRIOR;
+- char c;
++ signed char c;
+ GFF_Set *bedfeats = NULL;
+
+- while ((c = (char)getopt(argc, argv, "t:i:b:sk:md:pn:I:R:P:w:c:SB:o:HDxh")) != -1) {
++ while ((c = getopt(argc, argv, "t:i:b:sk:md:pn:I:R:P:w:c:SB:o:HDxh")) != -1) {
+ switch (c) {
+ case 't':
+ tree = tr_new_from_file(phast_fopen(optarg, "r"));
+--- a/src/phastOdds/phastOdds.c
++++ b/src/phastOdds/phastOdds.c
+@@ -26,7 +26,7 @@
+ alignment */
+
+ int main(int argc, char *argv[]) {
+- char c;
++ signed char c;
+ List *l;
+ int i, j, strand, bed_output = 0, backgd_nmods = -1, feat_nmods = -1,
+ winsize = -1, verbose = 0, max_nmods, memblocksize, old_nleaves,
+@@ -61,7 +61,7 @@
+ {0, 0, 0, 0}
+ };
+
+- while ((c = (char)getopt_long(argc, argv, "B:b:F:f:r:g:w:W:i:ydvh", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "B:b:F:f:r:g:w:W:i:ydvh", long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 'B':
+ backgd_hmm = hmm_new_from_file(phast_fopen(optarg, "r"));
+--- a/src/phyloBoot/phyloBoot.c
++++ b/src/phyloBoot/phyloBoot.c
+@@ -121,7 +121,7 @@
+
+ /* other variables */
+ FILE *INF, *F;
+- char c;
++ signed char c;
+ int i, j, opt_idx, nparams = -1, seed = -1;
+ String *tmpstr;
+ List **estimates=NULL;
+@@ -167,7 +167,7 @@
+ {0, 0, 0, 0}
+ };
+
+- while ((c = (char)getopt_long(argc, argv, "L:n:i:d:a:m:o:xR:qht:s:k:Ep:M:S:w:l:P:F:D:r",
++ while ((c = getopt_long(argc, argv, "L:n:i:d:a:m:o:xR:qht:s:k:Ep:M:S:w:l:P:F:D:r",
+ long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 'L':
+--- a/src/phyloFit/phyloFit.c
++++ b/src/phyloFit/phyloFit.c
+@@ -33,7 +33,7 @@
+ int main(int argc, char *argv[]) {
+ char *msa_fname = NULL, *alph = "ACGT";
+ msa_format_type input_format = UNKNOWN_FORMAT;
+- char c;
++ signed char c;
+ int opt_idx, seed=-1;
+ String *optstr;
+ List *tmplist = NULL;
+@@ -99,7 +99,7 @@
+
+ pf = phyloFit_struct_new(0);
+
+- while ((c = (char)getopt_long(argc, argv, "m:t:s:g:c:C:i:o:k:a:l:w:v:M:p:A:I:K:S:b:d:O:u:Y:e:D:GVENRqLPXZUBFfnrzhWyJ", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "m:t:s:g:c:C:i:o:k:a:l:w:v:M:p:A:I:K:S:b:d:O:u:Y:e:D:GVENRqLPXZUBFfnrzhWyJ", long_opts, &opt_idx)) != -1) {
+ switch(c) {
+ case 'm':
+ msa_fname = optarg;
+--- a/src/phyloP/phyloP.c
++++ b/src/phyloP/phyloP.c
+@@ -14,7 +14,7 @@
+
+ int main(int argc, char *argv[]) {
+ struct phyloP_struct *p = phyloP_struct_new(0);
+- char c;
++ signed char c;
+ FILE *msa_f = NULL;
+ msa_format_type msa_format = UNKNOWN_FORMAT;
+
+@@ -56,7 +56,7 @@
+ srandom((unsigned int)now.tv_usec);
+ #endif
+
+- while ((c = (char)getopt_long(argc, argv, "m:o:i:n:pc:s:f:Fe:l:r:B:d:qwgbPN:h",
++ while ((c = getopt_long(argc, argv, "m:o:i:n:pc:s:f:Fe:l:r:B:d:qwgbPN:h",
+ long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 'm':
+--- a/src/prequel/pbsDecode.c
++++ b/src/prequel/pbsDecode.c
+@@ -16,7 +16,7 @@
+
+ int main(int argc, char *argv[]) {
+ FILE *prob_f;
+- char c;
++ signed char c;
+ int opt_idx, i, nvals = 0, ngaps = 0, pos = 0;
+ unsigned int idx;
+ PbsCode *code;
+@@ -32,7 +32,7 @@
+ /* options and defaults */
+ int start = -1, end = -1, discard_gaps = FALSE;
+
+- while ((c = (char)getopt_long(argc, argv, "s:e:Gh", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "s:e:Gh", long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 's':
+ start = get_arg_int_bounds(optarg, 1, INFTY);
+--- a/src/prequel/pbsEncode.c
++++ b/src/prequel/pbsEncode.c
+@@ -16,7 +16,7 @@
+
+ int main(int argc, char *argv[]) {
+ FILE *prob_f;
+- char c;
++ signed char c;
+ int opt_idx, i, nlines = 0, ngaps = 0;
+ unsigned idx;
+ PbsCode *code;
+@@ -36,7 +36,7 @@
+
+ set_seed(-1);
+
+- while ((c = (char)getopt_long(argc, argv, "Gh", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "Gh", long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 'G':
+ discard_gaps = TRUE;
+--- a/src/prequel/pbsScoreMatrix.c
++++ b/src/prequel/pbsScoreMatrix.c
+@@ -16,7 +16,7 @@
+ #include <tree_model.h>
+
+ int main(int argc, char *argv[]) {
+- char c;
++ signed char c;
+ int opt_idx, bl, i, j, k, l, alph_size;
+ PbsCode *code = NULL;
+ TreeModel *mod;
+@@ -35,7 +35,7 @@
+ /* argument variables and defaults */
+ enum {FULL, HALF, NONE} pbs_mode = FULL;
+
+- while ((c = (char)getopt_long(argc, argv, "a:b:h", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "a:b:h", long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 't':
+ lst_push_dbl(branchlens, get_arg_dbl_bounds(optarg, 0, INFTY));
+--- a/src/prequel/pbsTrain.c
++++ b/src/prequel/pbsTrain.c
+@@ -20,7 +20,7 @@
+
+ int main(int argc, char *argv[]) {
+ FILE *STATSF;
+- char c;
++ signed char c;
+ int opt_idx, i, max_nrows;
+ String *line = str_new(STR_MED_LEN), *args = str_new(STR_MED_LEN);
+ List *fields = lst_new_ptr(5), *vectors = lst_new_ptr(1000),
+@@ -55,7 +55,7 @@
+ if (i < argc - 1) str_append_char(args, ' ');
+ }
+
+- while ((c = (char)getopt_long(argc, argv, "n:b:l:Gxh", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "n:b:l:Gxh", long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 'n':
+ nrows = get_arg_int_bounds(optarg, 1, INFTY);
+--- a/src/prequel/prequel.c
++++ b/src/prequel/prequel.c
+@@ -20,7 +20,7 @@
+ void do_indels(MSA *msa, TreeModel *mod);
+
+ int main(int argc, char *argv[]) {
+- char c;
++ signed char c;
+ int opt_idx, node;
+ FILE *out_f = NULL, *msa_f, *mod_f;
+ char *out_root;
+@@ -50,7 +50,7 @@
+ PbsCode *code = NULL;
+ int gibbs_nsamples = -1;
+
+- while ((c = (char)getopt_long(argc, argv, "r:i:s:e:knxSh", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "r:i:s:e:knxSh", long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 'r':
+ refseq_f = phast_fopen(optarg, "r");
+--- a/src/util/all_dists.c
++++ b/src/util/all_dists.c
+@@ -41,7 +41,7 @@
+ }
+
+ int main(int argc, char *argv[]) {
+- char c;
++ signed char c;
+ int i, j, t, opt_idx, ntrees, nleaves = -1;
+ TreeNode *n, *node_i, *node_j, *lca, *nametree = NULL;
+ TreeNode **tree;
+@@ -58,7 +58,7 @@
+ {0, 0, 0, 0}
+ };
+
+- while ((c = (char)getopt_long(argc, argv, "mt:h", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "mt:h", long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 'm':
+ mod = TRUE;
+--- a/src/util/base_evolve.c
++++ b/src/util/base_evolve.c
+@@ -32,7 +32,7 @@
+ MSA *msa;
+ int *labels = NULL, *path_to_cat, *reverse_compl;
+ GFF_Set *feats;
+- char c;
++ signed char c;
+ int opt_idx, i, j, seed = -1;
+ List *l;
+
+@@ -47,7 +47,7 @@
+ {0, 0, 0, 0}
+ };
+
+- while ((c = (char)getopt_long(argc, argv, "n:o:f:c:e:s:h", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "n:o:f:c:e:s:h", long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 'n':
+ nsites = get_arg_int_bounds(optarg, 1, INFTY);
+--- a/src/util/chooseLines.c
++++ b/src/util/chooseLines.c
+@@ -31,9 +31,9 @@
+ int i, n, k = -1;
+ String *line = str_new(STR_MED_LEN);
+ int *chosen;
+- char c;
++ signed char c;
+
+- while ((c = (char)getopt(argc, argv, "k:rh")) != -1) {
++ while ((c = getopt(argc, argv, "k:rh")) != -1) {
+ switch (c) {
+ case 'k':
+ k = atoi(optarg);
+--- a/src/util/clean_genes.c
++++ b/src/util/clean_genes.c
+@@ -971,7 +971,7 @@
+ int ncons_tested, nkept, nconserved_exons;
+ int nce_gap_type[NGAP_TYPES], nconsid[NTYPES], nfail[NTYPES];
+ double Nfrac = 0.05;
+- char c;
++ signed char c;
+ MSA *msa;
+ GFF_Set *gff;
+ msa_format_type msa_format = UNKNOWN_FORMAT;
+@@ -1012,7 +1012,7 @@
+ {0, 0, 0, 0}
+ };
+
+- while ((c = (char)getopt_long(argc, argv, "N:i:r:L:M:S:g:d:stlnfceICxh",
++ while ((c = getopt_long(argc, argv, "N:i:r:L:M:S:g:d:stlnfceICxh",
+ long_opts, &opt_idx)) != -1) {
+ switch(c) {
+ case 's':
+--- a/src/util/consEntropy.c
++++ b/src/util/consEntropy.c
+@@ -43,7 +43,7 @@
+ }
+
+ int main(int argc, char *argv[]) {
+- char c;
++ signed char c;
+ int i, j, opt_idx, nleaves, alph_size, nlabels;
+ TreeModel *cons_mod, *noncons_mod;
+ MSA *msa;
+@@ -60,7 +60,7 @@
+ {0, 0, 0, 0}
+ };
+
+- while ((c = (char)getopt_long(argc, argv, "H:N::h", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "H:N::h", long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 'H':
+ H = get_arg_dbl_bounds(optarg, 0, INFTY);
+--- a/src/util/convert_coords.c
++++ b/src/util/convert_coords.c
+@@ -56,9 +56,9 @@
+ int src_ref = -1, dest_ref = 0, offset = 0;
+ char *msa_fname = NULL, *feat_fname = NULL;
+ GFF_Set *gff;
+- char c;
++ signed char c;
+
+- while ((c = (char)getopt(argc, argv, "hm:f:s:d:i:p:n:")) != -1) {
++ while ((c = getopt(argc, argv, "hm:f:s:d:i:p:n:")) != -1) {
+ switch(c) {
+ case 'm':
+ msa_fname = optarg;
+--- a/src/util/display_rate_matrix.c
++++ b/src/util/display_rate_matrix.c
+@@ -383,14 +383,14 @@
+ cpg_tv = 0, non_cpg_ti = 0, non_cpg_tv = 0, cpg_eqfreq = 0;
+ char *rate_format_string = "%8.6f";
+ MarkovMatrix *M;
+- char c;
++ signed char c;
+ char tuple[5], tuple2[5]; /* , aa_alph[50]; */
+ char *subst_mat_fname = NULL, *subst_score_fname = NULL,
+ *subst_mat_fname_paml = NULL, *order1_mod_fname = NULL;
+ Matrix *subst_mat = NULL;
+ List *matrix_list = lst_new_ptr(20), *traversal = NULL;
+
+- while ((c = (char)getopt(argc, argv, "t:fedlLiM:N:A:B:aszSECh")) != -1) {
++ while ((c = getopt(argc, argv, "t:fedlLiM:N:A:B:aszSECh")) != -1) {
+ switch(c) {
+ case 't':
+ if (optarg[0] == 'A') all_branches = 1;
+--- a/src/util/draw_tree.c
++++ b/src/util/draw_tree.c
+@@ -40,10 +40,10 @@
+ int draw_to_scale = 1;
+
+ TreeNode *tree;
+- char c;
++ signed char c;
+ String *suffix;
+
+- while ((c = (char)getopt(argc, argv, "dbvsh")) != -1) {
++ while ((c = getopt(argc, argv, "dbvsh")) != -1) {
+ switch(c) {
+ case 'd':
+ square_branches = 0;
+--- a/src/util/eval_predictions.c
++++ b/src/util/eval_predictions.c
+@@ -218,7 +218,7 @@
+ int main(int argc, char* argv[]) {
+ FILE* F;
+ GFF_Set *gff_real=NULL, *gff_pred=NULL;
+- char c;
++ signed char c;
+ List *real_fname_list = NULL, *pred_fname_list = NULL,
+ *feat_list = NULL, *seq_len_list = NULL, *l = NULL;
+ int nfile, i, j;
+@@ -229,7 +229,7 @@
+ tot_nexons_pred = 0, dump_exons = 0, nnc = -1, tot_nnc = -1,
+ nc_threshold = 0;
+
+- while ((c = (char)getopt(argc, argv, "r:p:f:l:d:n:h")) != -1) {
++ while ((c = getopt(argc, argv, "r:p:f:l:d:n:h")) != -1) {
+ switch(c) {
+ case 'r':
+ real_fname_list = get_arg_list(optarg);
+--- a/src/util/hmm_train.c
++++ b/src/util/hmm_train.c
+@@ -118,12 +118,12 @@
+ Matrix *traincounts = NULL;
+ Vector *begcounts = NULL, *statecounts = NULL;
+ CategoryMap *cm = NULL;
+- char c;
++ signed char c;
+ GapPatternMap *gpm = NULL;
+ GFF_Set *gff;
+ char *reverse_groups_tag = NULL;
+
+- while ((c = (char)getopt(argc, argv, "i:g:c:m:M:R:I:n:t:P:G:qh")) != -1) {
++ while ((c = getopt(argc, argv, "i:g:c:m:M:R:I:n:t:P:G:qh")) != -1) {
+ switch(c) {
+ case 'i':
+ input_format = msa_str_to_format(optarg);
+--- a/src/util/hmm_tweak.c
++++ b/src/util/hmm_tweak.c
+@@ -87,13 +87,13 @@
+ CategoryMap *cm;
+ int *tcat, *fcat, *tpat=NULL, *fpat=NULL, *isolated;
+ GapPatternMap *gpm = NULL;
+- char c;
++ signed char c;
+ double sum = 0;
+ int count = 0, npasses = 1, pass;
+ double gp_sum[5] = {0, 0, 0, 0, 0};
+ int gp_count[5] = {0, 0, 0, 0, 0};
+
+- while ((c = (char)getopt(argc, argv, "m:a:e:f:t:i:u:F:T:zyRh")) != -1) {
++ while ((c = getopt(argc, argv, "m:a:e:f:t:i:u:F:T:zyRh")) != -1) {
+ switch (c) {
+ case 'm':
+ mult_fact = get_arg_dbl(optarg);
+--- a/src/util/hmm_view.c
++++ b/src/util/hmm_view.c
+@@ -48,10 +48,10 @@
+ int *new_to_old=NULL, *show_cat;
+ TreeNode *tree = NULL;
+ double t;
+- char c;
++ signed char c;
+ String *source, *sink;
+
+- while ((c = (char)getopt(argc, argv, "k:i:t:C:xh")) != -1) {
++ while ((c = getopt(argc, argv, "k:i:t:C:xh")) != -1) {
+ switch(c) {
+ case 'k':
+ nratecats = get_arg_int(optarg);
+--- a/src/util/indelFit.c
++++ b/src/util/indelFit.c
+@@ -22,7 +22,7 @@
+ char *reference);
+
+ int main(int argc, char *argv[]) {
+- char c;
++ signed char c;
+ int opt_idx, i, cat;
+ TreeNode *tree;
+ IndelHistory *ih;
+@@ -53,7 +53,7 @@
+ {0, 0, 0, 0}
+ };
+
+- while ((c = (char)getopt_long(argc, argv, "a:b:t:Lcf:r:l:h", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "a:b:t:Lcf:r:l:h", long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 'a':
+ alpha = get_arg_dbl_bounds(optarg, 0, 1);
+--- a/src/util/indelHistory.c
++++ b/src/util/indelHistory.c
+@@ -26,7 +26,7 @@
+ MSA *msa = NULL, *out_msa;
+ IndelHistory *ih;
+ char *read_hist_fname = NULL;
+- char c;
++ signed char c;
+ int opt_idx, old_nnodes, i;
+
+ msa_format_type msa_format = UNKNOWN_FORMAT;
+@@ -41,7 +41,7 @@
+ {0, 0, 0, 0}
+ };
+
+- while ((c = (char)getopt_long(argc, argv, "i:H:AIh", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "i:H:AIh", long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 'i':
+ msa_format = msa_str_to_format(optarg);
+--- a/src/util/maf_parse.c
++++ b/src/util/maf_parse.c
+@@ -266,7 +266,8 @@
+ char *maf_fname = NULL, *out_root_fname = "maf_parse", *masked_fn = NULL;
+ String *refseq = NULL, *currRefseq;
+ int opt_idx, startcol = 1, endcol = -1, include = 1, splitInterval = -1;
+- char c, outfilename[1000], splitFormat[100]="%s%.1i.maf", *group_tag = NULL;
++ signed char c;
++ char outfilename[1000], splitFormat[100]="%s%.1i.maf", *group_tag = NULL;
+ List *order_list = NULL, *seqlist_str = NULL, *cats_to_do_str=NULL, *cats_to_do=NULL;
+ MafBlock *block;
+ FILE *mfile, *outfile=NULL, *masked_file=NULL;
+@@ -310,7 +311,7 @@
+ };
+
+
+- while ((c = (char)getopt_long(argc, argv, "s:e:l:O:r:S:d:g:c:P:b:o:m:M:pLnxEIh", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "s:e:l:O:r:S:d:g:c:P:b:o:m:M:pLnxEIh", long_opts, &opt_idx)) != -1) {
+ switch(c) {
+ case 's':
+ startcol = get_arg_int(optarg);
+--- a/src/util/makeHKY.c
++++ b/src/util/makeHKY.c
+@@ -19,7 +19,7 @@
+ #define ALPHABET "ACGT"
+
+ int main(int argc, char *argv[]) {
+- char c;
++ signed char c;
+ int opt_idx;
+
+ double gc = 0.4, t = 1, kappa;
+@@ -39,7 +39,7 @@
+ {0, 0, 0, 0}
+ };
+
+- while ((c = (char)getopt_long(argc, argv, "g:p:t:T:h", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "g:p:t:T:h", long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 'g':
+ gc = get_arg_dbl_bounds(optarg, 0, 1);
+--- a/src/util/modFreqs.c
++++ b/src/util/modFreqs.c
+@@ -16,7 +16,7 @@
+ #include "modFreqs.help"
+
+ int main(int argc, char *argv[]) {
+- char c;
++ signed char c;
+ int opt_idx;
+ Vector *newfreqs = vec_new(4);
+ TreeModel *mod;
+@@ -26,7 +26,7 @@
+ {0, 0, 0, 0}
+ };
+
+- while ((c = (char)getopt_long(argc, argv, "h", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "h", long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 'h':
+ printf("%s", HELP);
+--- a/src/util/msa_diff.c
++++ b/src/util/msa_diff.c
+@@ -16,7 +16,7 @@
+ #include "msa_diff.help"
+
+ int main(int argc, char *argv[]) {
+- char c;
++ signed char c;
+ int opt_idx;
+ MSA *msa1, *msa2;
+ int i, j, ncommon, len, ndiffs, lastsame, same, diffstart, col;
+@@ -38,7 +38,7 @@
+ {0, 0, 0, 0}
+ };
+
+- while ((c = (char)getopt_long(argc, argv, "bga:i:j:h", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "bga:i:j:h", long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 'b':
+ ignore_base_id = TRUE;
+--- a/src/util/msa_split.c
++++ b/src/util/msa_split.c
+@@ -411,7 +411,7 @@
+ *cats_to_do = NULL;
+ String *sum_fname = NULL;
+ FILE *SUM_F = NULL;
+- char c;
++ signed char c;
+ int nallgaps, nallgaps_strip, nanygaps, nanygaps_strip,
+ length_strip, i;
+ Vector *freqs, *freqs_strip;
+@@ -450,7 +450,7 @@
+ {0, 0, 0, 0}
+ };
+
+- while ((c = (char)getopt_long(argc, argv, "i:M:g:c:p:d:n:sfG:r:o:L:C:T:w:I:O:B:P:F:l:xSzqh", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "i:M:g:c:p:d:n:sfG:r:o:L:C:T:w:I:O:B:P:F:l:xSzqh", long_opts, &opt_idx)) != -1) {
+ switch(c) {
+ case 'i':
+ input_format = msa_str_to_format(optarg);
+--- a/src/util/msa_view.c
++++ b/src/util/msa_view.c
+@@ -411,7 +411,8 @@
+ cycle_size = -1, maf_keep_overlapping = FALSE, collapse_missing = FALSE,
+ fourD = FALSE, mark_missing_maxsize = -1, missing_as_indels = FALSE,
+ unmask = FALSE, split_all = FALSE;
+- char c, *out_root=NULL, out_fname[STR_MED_LEN];
++ signed char c;
++ char *out_root=NULL, out_fname[STR_MED_LEN];
+ List *cats_to_do = NULL, *aggregate_list = NULL, *msa_fname_list = NULL,
+ *order_list = NULL, *fill_N_list = NULL;
+ msa_coord_map *map = NULL;
+@@ -461,7 +462,7 @@
+ {0, 0, 0, 0}
+ };
+
+- while ((c = (char)getopt_long(argc, argv, "i:o:s:e:l:G:r:T:a:g:c:C:L:I:A:M:O:w:N:Y:X:fuDVxPzRSk4mh", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "i:o:s:e:l:G:r:T:a:g:c:C:L:I:A:M:O:w:N:Y:X:fuDVxPzRSk4mh", long_opts, &opt_idx)) != -1) {
+ switch(c) {
+ case 'i':
+ input_format = msa_str_to_format(optarg);
+--- a/src/util/phastBias.c
++++ b/src/util/phastBias.c
+@@ -44,7 +44,7 @@
+
+ int main(int argc, char *argv[]) {
+ FILE *infile;
+- char c;
++ signed char c;
+ int opt_idx;
+ msa_format_type msa_format;
+ struct bgchmm_struct *b = bgchmm_struct_new(0);
+@@ -70,7 +70,7 @@
+ {"help", 0, 0, 'h'},
+ {0,0,0,0}};
+
+- while ((c = (char)getopt_long(argc, argv, "B:b:L:l:C:c:R:E:T:S:s:f:g:p:m:i:oWh", long_opts, &opt_idx))
++ while ((c = getopt_long(argc, argv, "B:b:L:l:C:c:R:E:T:S:s:f:g:p:m:i:oWh", long_opts, &opt_idx))
+ != -1) {
+ switch (c) {
+ case 'B':
+--- a/src/util/refeature.c
++++ b/src/util/refeature.c
+@@ -111,7 +111,7 @@
+ }
+
+ int main(int argc, char *argv[]) {
+- char c;
++ signed char c;
+ int opt_idx;
+ GFF_Set *gff;
+ List *include = NULL;
+@@ -139,7 +139,7 @@
+ {0, 0, 0, 0}
+ };
+
+- while ((c = (char)getopt_long(argc, argv, "o:i:l:g:e:d:UISfusbh", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "o:i:l:g:e:d:UISfusbh", long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 'o':
+ if (!strcmp("bed", optarg)) output_format = BED;
+--- a/src/util/stringiphy.c
++++ b/src/util/stringiphy.c
+@@ -62,7 +62,7 @@
+
+ int main(int argc, char *argv[]) {
+ GFF_Set *exons;
+- char c;
++ signed char c;
+ int i, j, opt_idx;
+ List *group_data;
+
+@@ -71,7 +71,7 @@
+ {0, 0, 0, 0}
+ };
+
+- while ((c = (char)getopt_long(argc, argv, "h", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "h", long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 'h':
+ usage(argv[0]);
+--- a/src/util/treeGen.c
++++ b/src/util/treeGen.c
+@@ -21,7 +21,7 @@
+
+
+ int main(int argc, char *argv[]) {
+- char c;
++ signed char c;
+ int opt_idx, i, j, k, N, nleaves;
+ List *names, *treelist, *newlist, *tmpl, *groups = NULL;
+ TreeNode *t, *tnew;
+@@ -32,7 +32,7 @@
+ {0, 0, 0, 0}
+ };
+
+- while ((c = (char)getopt_long(argc, argv, "h", long_opts, &opt_idx)) != -1) {
++ while ((c = getopt_long(argc, argv, "h", long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 'h':
+ printf("%s", HELP);
+--- a/src/util/tree_doctor.c
++++ b/src/util/tree_doctor.c
+@@ -162,7 +162,7 @@
+
+ /* other variables */
+ String *suffix, *optstr;
+- char c;
++ signed char c;
+ int i, opt_idx;
+ TreeNode *n;
+
+@@ -189,7 +189,7 @@
+ {0, 0, 0, 0}
+ };
+
+- while ((c = (char)getopt_long(argc, argv, "s:p:P:g:m:r:R:B:S:D:l:L:adtNbnh",
++ while ((c = getopt_long(argc, argv, "s:p:P:g:m:r:R:B:S:D:l:L:adtNbnh",
+ long_opts, &opt_idx)) != -1) {
+ switch (c) {
+ case 's':
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ use_debian_packaged_libpcre.patch
use_debian_packaged_help2man.patch
hardening.patch
fix_test_makefile.patch
+arm64.patch
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/CshlSiepelLab/phast/issues
+Bug-Submit: https://github.com/CshlSiepelLab/phast/issues/new
Reference:
Author: Melissa J. Hubisz and Katherine S. Pollard and Adam Siepel
Title: "PHAST and RPHAST: phylogenetic analysis with space/time models"
@@ -19,3 +21,5 @@ Registry:
Entry: SCR_003204
- Name: conda:bioconda
Entry: phast
+Repository: https://github.com/CshlSiepelLab/phast.git
+Repository-Browse: https://github.com/CshlSiepelLab/phast
View it on GitLab: https://salsa.debian.org/med-team/phast/-/compare/38add8cf999f21dc48f80f5aeac6e878b7291065...1301a43bbc755cff0e69c8591d76a4a331fe17ab
--
View it on GitLab: https://salsa.debian.org/med-team/phast/-/compare/38add8cf999f21dc48f80f5aeac6e878b7291065...1301a43bbc755cff0e69c8591d76a4a331fe17ab
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