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Berner" Date: Sat, 29 Aug 2020 08:34:28 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r546884 - head/biology/phyml/files X-SVN-Group: ports-head X-SVN-Commit-Author: tcberner X-SVN-Commit-Paths: head/biology/phyml/files X-SVN-Commit-Revision: 546884 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.33 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 29 Aug 2020 08:34:29 -0000 Author: tcberner Date: Sat Aug 29 08:34:27 2020 New Revision: 546884 URL: https://svnweb.freebsd.org/changeset/ports/546884 Log: biology/phyml: fix build on recent current mostly backport of: https://github.com/stephaneguindon/phyml/commit/3574fb82d54438518d50d5ba8f74423d5395a96a Obtained from: https://github.com/stephaneguindon/phyml/commit/3574fb82d54438518d50d5ba8f74423d5395a96a Added: head/biology/phyml/files/ head/biology/phyml/files/patch-src_io.c (contents, props changed) head/biology/phyml/files/patch-src_phyrex.c (contents, props changed) head/biology/phyml/files/patch-src_utilities.c (contents, props changed) head/biology/phyml/files/patch-src_utilities.h (contents, props changed) Added: head/biology/phyml/files/patch-src_io.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phyml/files/patch-src_io.c Sat Aug 29 08:34:27 2020 (r546884) @@ -0,0 +1,20 @@ +--- src/io.c.orig 2020-07-09 11:49:16 UTC ++++ src/io.c +@@ -39,8 +39,6 @@ t_tree *Read_Tree(char **s_tree) + if((*s_tree)[i] == ',') n_otu++; + } + n_otu+=1; +- +- + + tree = Make_Tree_From_Scratch(n_otu,NULL); + subs = Sub_Trees((*s_tree),°ree); +@@ -2312,7 +2310,7 @@ void Print_Fp_Out(FILE *fp_out, time_t t_beg, time_t t + div_t hour,min; + int i, j; + +- if (precision > 0) snprintf (format, 8, "%%.%df", precision); ++ if (precision > 0) snprintf(format,8,"%%.%huf",(unsigned short)precision); + + if(n_data_set == 1) + { Added: head/biology/phyml/files/patch-src_phyrex.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phyml/files/patch-src_phyrex.c Sat Aug 29 08:34:27 2020 (r546884) @@ -0,0 +1,11 @@ +--- src/phyrex.c.orig 2020-07-09 11:49:16 UTC ++++ src/phyrex.c +@@ -958,7 +958,7 @@ phydbl *PHYREX_MCMC(t_tree *tree) + PHYREX_Label_Nodes_With_Locations(tree); + PHYREX_Label_Edges(tree); + char *s = Write_Tree(tree); +- PhyML_Fprintf(fp_tree,"\ntree %d [&lnP=%f,precision={1.e-1,1e-02,1e-01}] = [&R] %s",tree->mcmc->sample_num,tree->c_lnL,s); ++ PhyML_Fprintf(fp_tree,"\ntree %d [&lnP=%f,precision={1.e-1,1e-02,1e-01}] = [&R] %s",tree->mcmc->run,tree->c_lnL,s); + PhyML_Fprintf(fp_tree,"\nend;"); + fseek(fp_tree,-5,SEEK_END); + tree->write_tax_names = YES; Added: head/biology/phyml/files/patch-src_utilities.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phyml/files/patch-src_utilities.c Sat Aug 29 08:34:27 2020 (r546884) @@ -0,0 +1,30 @@ +--- src/utilities.c.orig 2020-07-09 11:49:16 UTC ++++ src/utilities.c +@@ -17,6 +17,9 @@ the GNU public licence. See http://www.opensource.org + #include "beagle_utils.h" + #endif + ++int CALL; ++int TIME; ++ + ////////////////////////////////////////////////////////////// + ////////////////////////////////////////////////////////////// + +@@ -3066,7 +3069,7 @@ int Assign_State_With_Ambiguity(char *c, int datatype, + if(Is_Ambigu(c,GENERIC,stepsize)) state[0] = T_MAX_ALPHABET-1; + else + { +- char format[6]; ++ char format[20]; + sprintf(format,"%%%dd",stepsize); + if(!sscanf(c,format,state)) + { +@@ -4891,7 +4894,7 @@ int Are_Compatible(char *statea, char *stateb, int ste + else + { + int a,b; +- char format[6]; ++ char format[20]; + + sprintf(format,"%%%dd",stepsize); + Added: head/biology/phyml/files/patch-src_utilities.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phyml/files/patch-src_utilities.h Sat Aug 29 08:34:27 2020 (r546884) @@ -0,0 +1,13 @@ +--- src/utilities.h.orig 2020-08-29 08:31:23 UTC ++++ src/utilities.h +@@ -94,8 +94,8 @@ static inline int isinf_ld (long double x) { return is + #endif + + +-int CALL; +-int TIME; ++extern int CALL; ++extern int TIME; + + #define SLFV_GAUSSIAN 0 /* Spatial Lambda-Fleming-Viot model (Gaussian) */ + #define SLFV_UNIFORM 1 /* Spatial Lambda-Fleming-Viot model (Uniform) */