[gentoo-commits] repo/gentoo:master commit in: sci-biology/tree-puzzle/files/, sci-biology/tree-puzzle/
commit: d4d7228930146c4626f8da2c0fb68c788329eb6a
Author: David Seifert gentoo org>
AuthorDate: Sat Nov 19 04:45:55 2022 +
Commit: David Seifert gentoo org>
CommitDate: Sat Nov 19 04:45:55 2022 +
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 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 ..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
[gentoo-commits] repo/gentoo:master commit in: sci-biology/tree-puzzle/files/, sci-biology/tree-puzzle/
commit: 8fe21c3fd5b5e7be60a75a09ba4b3ec4bad417bd
Author: David Seifert gentoo org>
AuthorDate: Sat Jan 29 00:00:14 2022 +
Commit: David Seifert gentoo org>
CommitDate: Sat Jan 29 00:00:14 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8fe21c3f
sci-biology/tree-puzzle: fix build system and MPI
Closes: https://bugs.gentoo.org/690900
Closes: https://bugs.gentoo.org/810502
Closes: https://bugs.gentoo.org/814185
Signed-off-by: David Seifert gentoo.org>
.../files/tree-puzzle-5.2-MPI-3.0.patch| 362 +
sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild | 25 +-
2 files changed, 375 insertions(+), 12 deletions(-)
diff --git a/sci-biology/tree-puzzle/files/tree-puzzle-5.2-MPI-3.0.patch
b/sci-biology/tree-puzzle/files/tree-puzzle-5.2-MPI-3.0.patch
new file mode 100644
index ..66e3e6482338
--- /dev/null
+++ b/sci-biology/tree-puzzle/files/tree-puzzle-5.2-MPI-3.0.patch
@@ -0,0 +1,362 @@
+https://bugs.gentoo.org/690900
+rename MPI 1.0 to 3.0+ functions:
+- MPI_Address -> MPI_Get_address
+- MPI_Type_struct -> MPI_Type_create_struct
+
+--- a/src/ppuzzle.c
b/src/ppuzzle.c
+@@ -297,13 +297,13 @@
+ elseMPI_Recv(, 0, MPI_INT, PP_MyMaster, PP_UPDATEEEI,
PP_Comm, );
+
+ Dtypes[0] = MPI_DOUBLE; Dtypelens[0] = tpmradix;
+- MPI_Address(&(Eval[0]), &(Dtypeaddr[0]));
++ MPI_Get_address(&(Eval[0]), &(Dtypeaddr[0]));
+ Dtypes[1] = MPI_DOUBLE; Dtypelens[1] = tpmradix * tpmradix;
+- MPI_Address(&(Evec[0][0]), &(Dtypeaddr[1]));
++ MPI_Get_address(&(Evec[0][0]), &(Dtypeaddr[1]));
+ Dtypes[2] = MPI_DOUBLE; Dtypelens[2] = tpmradix * tpmradix;
+- MPI_Address(&(Ievc[0][0]), &(Dtypeaddr[2]));
++ MPI_Get_address(&(Ievc[0][0]), &(Dtypeaddr[2]));
+
+- MPI_Type_struct(3, Dtypelens, Dtypeaddr, Dtypes, _Data);
++ MPI_Type_create_struct(3, Dtypelens, Dtypeaddr, Dtypes, _Data);
+ MPI_Type_commit(_Data);
+
+ MPI_Bcast (MPI_BOTTOM, 1, PP_Data, PP_MyMaster, PP_Comm);
+@@ -341,19 +341,19 @@
+ double* DMVector = new_dvector(jobs);
+
+ Dtypes[0] = MPI_DOUBLE; Dtypelens[0] = jobs;
+- MPI_Address(&(DMVector[0]), &(Dtypeaddr[0]));
++ MPI_Get_address(&(DMVector[0]), &(Dtypeaddr[0]));
+ Dtypes[1] = MPI_DOUBLE; Dtypelens[1] = numcats;
+- MPI_Address(&(Rates[0]), &(Dtypeaddr[1]));
++ MPI_Get_address(&(Rates[0]), &(Dtypeaddr[1]));
+ Dtypes[2] = MPI_DOUBLE; Dtypelens[2] = 1;
+- MPI_Address(&(fracinv), &(Dtypeaddr[2]));
++ MPI_Get_address(&(fracinv), &(Dtypeaddr[2]));
+ Dtypes[3] = MPI_DOUBLE; Dtypelens[3] = tpmradix;
+- MPI_Address(&(Eval[0]), &(Dtypeaddr[3]));
++ MPI_Get_address(&(Eval[0]), &(Dtypeaddr[3]));
+ Dtypes[4] = MPI_DOUBLE; Dtypelens[4] = tpmradix * tpmradix;
+- MPI_Address(&(Evec[0][0]), &(Dtypeaddr[4]));
++ MPI_Get_address(&(Evec[0][0]), &(Dtypeaddr[4]));
+ Dtypes[5] = MPI_DOUBLE; Dtypelens[5] = tpmradix * tpmradix;
+- MPI_Address(&(Ievc[0][0]), &(Dtypeaddr[5]));
++ MPI_Get_address(&(Ievc[0][0]), &(Dtypeaddr[5]));
+
+- MPI_Type_struct(6, Dtypelens, Dtypeaddr, Dtypes, _Data);
++ MPI_Type_create_struct(6, Dtypelens, Dtypeaddr, Dtypes, _Data);
+ MPI_Type_commit(_Data);
+
+ if (PP_IamMaster) {
+@@ -719,10 +719,10 @@
+ #endif
+ doubles[0] = frconst;
+
+- MPI_Address(ints, Dtypeaddr);
+- MPI_Address(doubles, (Dtypeaddr+1));
++ MPI_Get_address(ints, Dtypeaddr);
++ MPI_Get_address(doubles, (Dtypeaddr+1));
+
+- MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, _Sizes);
++ MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, _Sizes);
+ MPI_Type_commit(_Sizes);
+
+ for (dest=1; dest%d: [%d/%d] #=%d \"%s\"\n",
+@@ -1764,9 +1764,9 @@
+ }
+ Dtypes[((int)blocksize + pstnum)]= MPI_INT;
+ Dtypelens[((int)blocksize + pstnum)] = pstnum;
+- MPI_Address(&(pstnumarr[0]), &(Dtypeaddr[((int)blocksize + pstnum)]));
++ MPI_Get_address(&(pstnumarr[0]), &(Dtypeaddr[((int)blocksize + pstnum)]));
+
+- MPI_Type_struct(((int)blocksize + pstnum + 1), Dtypelens, Dtypeaddr,
Dtypes, _Biparts);
++ MPI_Type_create_struct(((int)blocksize + pstnum + 1), Dtypelens, Dtypeaddr,
Dtypes, _Biparts);
+ MPI_Type_commit(_Biparts);
+
+ error = MPI_Ssend(MPI_BOTTOM, 1, PP_Biparts, PP_MyMaster, PP_PUZZLEBLOCK,
PP_Comm);
+@@ -1843,20 +1843,20 @@
+ (*bip)[n]= new_cmatrix(*taxa - 3, *taxa);
+ Dtypes[n]= MPI_CHAR;
+ Dtypelens[n] = (*taxa - 3) * *taxa;
+-MPI_Address(&((*bip)[n][0][0]), &(Dtypeaddr[n]));
++MPI_Get_address(&((*bip)[n][0][0]), &(Dtypeaddr[n]));
+ }
+ for (n=0; n
