commit: d4d7228930146c4626f8da2c0fb68c788329eb6a Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sat Nov 19 04:45:55 2022 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat Nov 19 04:45:55 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d4d72289
sci-biology/tree-puzzle: regenerate configure script for clang 16 Closes: https://bugs.gentoo.org/879751 Signed-off-by: David Seifert <soap <AT> gentoo.org> .../files/tree-puzzle-5.2-C99-decls.patch | 360 +++++++++++++++++++++ .../tree-puzzle/files/tree-puzzle-impl-dec.patch | 14 - sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild | 9 +- 3 files changed, 368 insertions(+), 15 deletions(-) diff --git a/sci-biology/tree-puzzle/files/tree-puzzle-5.2-C99-decls.patch b/sci-biology/tree-puzzle/files/tree-puzzle-5.2-C99-decls.patch new file mode 100644 index 000000000000..98456c0dacc1 --- /dev/null +++ b/sci-biology/tree-puzzle/files/tree-puzzle-5.2-C99-decls.patch @@ -0,0 +1,360 @@ +--- a/src/consensus.c ++++ b/src/consensus.c +@@ -32,7 +32,7 @@ + /******************************************************************************/ + + /* prepare for consensus tree analysis */ +-void initconsensus() ++void initconsensus(void) + { + # if ! PARALLEL + biparts = new_cmatrix(Maxspc-3, Maxspc); +--- a/src/consensus.h ++++ b/src/consensus.h +@@ -65,7 +65,7 @@ + /******************************************************************************/ + + /* prepare for consensus tree analysis */ +-void initconsensus(); ++void initconsensus(void); + + /* recursive function to get bipartitions */ + /* traversal should be optimazable (HAS) */ +--- a/src/ml1.c ++++ b/src/ml1.c +@@ -244,7 +244,7 @@ + /***************************** exported functions *****************************/ + + +-void evaluateseqs() ++void evaluateseqs(void) + { + ivector ali; + +@@ -1018,7 +1018,7 @@ + + + /* compute 1 PAM rate matrix, its eigensystem, and the inverse matrix thereof */ +-void tranprobmat() ++void tranprobmat(void) + { + eigensystem(Eval, Evec); /* eigensystem of 1 PAM rate matrix */ + luinverse(Evec, Ievc, tpmradix); /* inverse eigenvectors are in Ievc */ +@@ -1324,7 +1324,7 @@ + + + /* initialize distance matrix */ +-void initdistan() ++void initdistan(void) + { + int i, j, k, diff, x, y; + double obs, temp; +@@ -1478,7 +1478,7 @@ + + #else /* not PARALLEL */ + +-void computedistan() ++void computedistan(void) + { + int i, j; + +--- a/src/ml2.c ++++ b/src/ml2.c +@@ -1036,7 +1036,7 @@ + + + /* preparation for ML analysis */ +-void mlstart() ++void mlstart(void) + { + /* number of states and code length */ + tpmradix = gettpmradix(); +@@ -1098,7 +1098,7 @@ + + + /* cleanup after ML analysis */ +-void mlfinish() ++void mlfinish(void) + { + if (Ctree != NULL) + free_tree(Ctree, Numspc); +@@ -1566,7 +1566,7 @@ + int bestratefound, + int ncats) /* numcats */ + #endif +-void findbestratecombination() ++void findbestratecombination(void) + { + int k, u; + double bestvalue, fv2; +@@ -2147,7 +2147,7 @@ + } /* clock_lklhd */ + + /* find out the edge containing the root */ +-int findrootedge() ++int findrootedge(void) + { + int e, ebest; + double logbest, logtest; +--- a/src/mlparam.c ++++ b/src/mlparam.c +@@ -70,7 +70,7 @@ + } + + /* compute rates of each category when rates are Gamma-distributed */ +-void updaterates() ++void updaterates(void) + { + int i; + double alpha; +@@ -190,7 +190,7 @@ + } + + /* estimate substitution process parameters - random quartets */ +-void optimseqevolparamsquart() ++void optimseqevolparamsquart(void) + { + double tsmeanold, yrmeanold; + dvector tslist, yrlist; +@@ -320,7 +320,7 @@ + + + /* optimize substitution process parameters - tree */ +-void optimseqevolparamstree() ++void optimseqevolparamstree(void) + { + twodimenmin(EPSILON_SUBSTPARAM, + (SH_optn || nuc_optn) && optim_optn && (data_optn == 0), +@@ -379,7 +379,7 @@ + + + /* optimize rate heterogeneity parameters */ +-void optimrateparams() ++void optimrateparams(void) + { + twodimenmin(EPSILON_RATEPARAM, + fracinv_optim, +@@ -396,7 +396,7 @@ + + /* estimate parameters of substitution process and rate heterogeneity - no tree + n-taxon tree is not needed because of quartet method or NJ tree topology */ +-void estimateparametersnotree() ++void estimateparametersnotree(void) + { + int it, nump, change; + double TSold, YRold, FIold, GEold; +@@ -495,7 +495,7 @@ + + /* estimate parameters of substitution process and rate heterogeneity - tree + same as above but here the n-taxon tree is already in memory */ +-void estimateparameterstree() ++void estimateparameterstree(void) + { + int it, nump, change; + double TSold, YRold, FIold, GEold; +--- a/src/model1.c ++++ b/src/model1.c +@@ -31,7 +31,7 @@ + #include "ml.h" + + /* number of states of the selected model */ +-int gettpmradix() ++int gettpmradix(void) + { + if (data_optn == 0) { /* nucleotides */ + if (nuc_optn) return 4; +--- a/src/puzzle1.c ++++ b/src/puzzle1.c +@@ -345,7 +345,7 @@ + /******************************************************************************/ + + /* compute TN parameters according to F84 Ts/Tv ratio */ +-void makeF84model() ++void makeF84model(void) + { + double rho, piA, piC, piG, piT, piR, piY, ts, yr; + +@@ -390,7 +390,7 @@ + } /* makeF84model */ + + /* compute number of quartets used in LM analysis */ +-void compnumqts() ++void compnumqts(void) + { + if (lmqts == 0) { + if (numclust == 4) +@@ -407,7 +407,7 @@ + } /* compnumqts */ + + /* set options interactively */ +-void setoptions() ++void setoptions(void) + { + int i, valid; + double sumfreq; +@@ -1718,7 +1718,7 @@ + } /* closefile */ + + /* symmetrize doublet frequencies */ +-void symdoublets() ++void symdoublets(void) + { + int i, imean; + double mean; +@@ -1769,7 +1769,7 @@ + } /* symdoublets */ + + /* show Ts/Tv ratio and Ts Y/R ratio */ +-void computeexpectations() ++void computeexpectations(void) + { + double AlphaYBeta, AlphaRBeta, piR, piY, num, denom, pyr, pur; + +@@ -4604,7 +4604,7 @@ + /* Reconstruct a tree with QP */ + /* (parameter estimation already done) */ + +-void recon_tree() ++void recon_tree(void) + { + int i; + unsigned char tmpweight; +@@ -4848,7 +4848,7 @@ + + /***************************************************************/ + +-void map_lklhd() ++void map_lklhd(void) + { + int i, a, a1, a2, b, b1, b2, c, c1, c2, d; + uli nq; +@@ -5101,7 +5101,7 @@ + + /***************************************************************/ + +-void setdefaults() { ++void setdefaults(void) { + + strcpy(INFILE, INFILEDEFAULT); + strcpy(OUTFILE, OUTFILEDEFAULT); +@@ -6027,7 +6027,7 @@ + + /***************************************************************/ + +-void memcleanup() { ++void memcleanup(void) { + if (puzzlemode == QUARTPUZ && typ_optn == TREERECON_OPTN) { + free(splitfreqs); + free(splitpatterns); +--- a/src/puzzle2.c ++++ b/src/puzzle2.c +@@ -860,7 +860,7 @@ + + + /* estimate mean base frequencies from translated data set */ +-void estimatebasefreqs() ++void estimatebasefreqs(void) + { + int tpmradix, i, j; + uli all, *gene; +@@ -903,7 +903,7 @@ + + + /* guess model of substitution */ +-void guessmodel() ++void guessmodel(void) + { + double c1, c2, c3, c4, c5, c6; + dvector f; +@@ -1160,7 +1160,7 @@ + } /* callocquartets */ + + /* free quartet memory */ +-void freequartets() ++void freequartets(void) + { + free(quartetinfo); + } /* freequartets */ +@@ -1357,7 +1357,7 @@ + /*************************/ + + /* checks out all possible quartets */ +-void computeallquartets() ++void computeallquartets(void) + { + double onethird; + uli nq; +--- a/src/sprng/makeseed.c ++++ b/src/sprng/makeseed.c +@@ -1,10 +1,6 @@ + #include <time.h> + +-#ifdef __STDC__ +-int make_new_seed() +-#else +-int make_new_seed() +-#endif ++int make_new_seed(void) + { + time_t tp; + struct tm *temp; +--- a/src/sprng/primes-lcg64.c ++++ b/src/sprng/primes-lcg64.c +@@ -1,5 +1,6 @@ + #include <stdio.h> + #include <stdlib.h> ++#include <string.h> + #include "primes-lcg64.h" + #include "primelist-lcg64.h" + +--- a/src/treesort.c ++++ b/src/treesort.c +@@ -487,7 +487,7 @@ + /**********/ + + /* malloc new tree list item */ +-treelistitemtype *gettreelistitem() ++treelistitemtype *gettreelistitem(void) + { + treelistitemtype *tmpptr; + tmpptr = (treelistitemtype *)calloc((size_t) 1, sizeof(treelistitemtype)); +--- a/src/treesort.h ++++ b/src/treesort.h +@@ -84,7 +84,7 @@ + /**********/ + + /* allocate memory for ctree 3 ints pointer plus 1 check byte */ +-int *initctree(); ++int *initctree(void); + + /**********/ + +@@ -174,7 +174,7 @@ + /**********/ + + /* malloc new tree list item */ +-treelistitemtype *gettreelistitem(); ++treelistitemtype *gettreelistitem(void); + + /**********/ + +--- a/src/util.c ++++ b/src/util.c +@@ -507,7 +507,7 @@ + #define EPS 1.2e-7 + #define RNMX (1.0-EPS) + +-double randomunitintervall() ++double randomunitintervall(void) + /* Long period (> 2e18) random number generator. Returns a uniform random + deviate between 0.0 and 1.0 (exclusive of endpoint values). + +@@ -734,7 +734,7 @@ + /* Reads characters from stdin until a newline character or EOF + is received. The newline is not made part of the string. + If an error occurs a null string \0 is returned */ +-cvector mygets() ++cvector mygets(void) + { + int c, n; + cvector str; diff --git a/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch b/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch deleted file mode 100644 index 93b960f5c2b4..000000000000 --- a/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch +++ /dev/null @@ -1,14 +0,0 @@ - src/sprng/primes-lcg64.c | 1 + - 1 files changed, 1 insertions(+), 0 deletions(-) - -diff --git a/src/sprng/primes-lcg64.c b/src/sprng/primes-lcg64.c -index 8e5a7c9..fb04373 100644 ---- a/src/sprng/primes-lcg64.c -+++ b/src/sprng/primes-lcg64.c -@@ -1,5 +1,6 @@ - #include <stdio.h> - #include <stdlib.h> -+#include <string.h> - #include "primes-lcg64.h" - #include "primelist-lcg64.h" - diff --git a/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild index e5093420d6a8..b5e8e3931220 100644 --- a/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild +++ b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild @@ -3,6 +3,8 @@ EAPI=8 +inherit autotools + DESCRIPTION="Maximum likelihood analysis for nucleotide, amino acid, and two-state data" HOMEPAGE="http://www.tree-puzzle.de"; SRC_URI="http://www.tree-puzzle.de/${P}.tar.gz"; @@ -17,10 +19,15 @@ DEPEND="mpi? ( virtual/mpi )" RDEPEND="${DEPEND}" PATCHES=( - "${FILESDIR}"/${PN}-impl-dec.patch + "${FILESDIR}"/${P}-C99-decls.patch "${FILESDIR}"/${P}-MPI-3.0.patch ) +src_prepare() { + default + eautoreconf +} + src_configure() { default
