[med-svn] [Git][med-team/phast][master] Get package building

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / phast


Commits:
a667d0df by Nilesh Patra at 2024-03-25T19:55:11+00:00
Get package building

- - - - -


2 changed files:

- debian/control
- debian/patches/clapack.patch


Changes:

=====================================
debian/control
=====================================
@@ -6,6 +6,7 @@ Priority: optional
 Build-Depends: debhelper-compat (= 13),
                liblapack-dev | liblapack.so,
                libblas-dev | libblas.so,
+               liblapacke-dev,
                libtmglib-dev,
                libpcre2-dev,
                help2man


=====================================
debian/patches/clapack.patch
=====================================
@@ -11,7 +11,7 @@ Forwarded: https://github.com/CshlSiepelLab/phast/issues/48
 
 --- a/src/lib/Makefile
 +++ b/src/lib/Makefile
-@@ -12,29 +12,9 @@ endif
+@@ -12,29 +12,9 @@
  
  ifdef CLAPACKPATH		# only do below if using CLAPACK
  
@@ -45,7 +45,7 @@ Forwarded: https://github.com/CshlSiepelLab/phast/issues/48
  
 --- a/src/make-include.mk
 +++ b/src/make-include.mk
-@@ -120,8 +120,6 @@ ifneq ($(TARGETOS), Windows)
+@@ -120,8 +120,6 @@
      # PLAT is empty for windows builds
      PLAT =
    endif
@@ -54,7 +54,7 @@ Forwarded: https://github.com/CshlSiepelLab/phast/issues/48
  endif
  
  # if neither VECLIB nor CLAPACKPATH is defined, then LAPACK will be
-@@ -139,8 +137,7 @@ LIBS = -lphast -framework Accelerate -lc
+@@ -139,8 +137,7 @@
  else
  ifdef CLAPACKPATH
  ifneq ($(TARGETOS), Windows)
@@ -64,7 +64,7 @@ Forwarded: https://github.com/CshlSiepelLab/phast/issues/48
  else
    CFLAGS += -I${CLAPACKPATH}/INCLUDE -I${F2CPATH} -DPCRE_STATIC
    LIBS = -lphast -lm  ${CLAPACKPATH}/liblapack.a ${CLAPACKPATH}/libf2c.a ${CLAPACKPATH}/libblas.a
-@@ -149,7 +146,6 @@ endif
+@@ -149,7 +146,6 @@
  # older than 3.1.1
  #CFLAGS += -I${CLAPACKPATH} -I${F2CPATH}
  #LIBS = -lphast -llapack -ltmg -lblaswr -lc -lF77 -lI77 -lm
@@ -87,3 +87,97 @@ Forwarded: https://github.com/CshlSiepelLab/phast/issues/48
  #endif  /*ifndef SKIP_LAPACK */
  
  #endif  /*ifdef VECLIB */
+--- a/src/lib/base/phast_eigen.c
++++ b/src/lib/base/phast_eigen.c
+@@ -19,7 +19,7 @@
+ #include <math.h>
+ #include <phast/external_libs.h>
+ #include <phast/misc.h>
+-
++#include <lapack.h>
+ 
+ /* Diagonalize a square, real, nonsymmetric matrix.  Computes vector
+    of eigenvalues and matrices of right and left eigenvectors,
+@@ -59,7 +59,7 @@
+   F77_CALL(dgeev)(&jobvl, &jobvr, &n, tmp, &n, wr, wi, vl, &n,
+ 		  vr, &n, work, &lwork, &info);
+ #else
+-  dgeev_(&jobvl, &jobvr, &n, tmp, &n, wr, wi, vl,
++  LAPACK_dgeev(&jobvl, &jobvr, &n, tmp, &n, wr, wi, vl,
+ 	 &n, vr, &n, work, &lwork, &info);
+ #endif
+ 
+@@ -196,7 +196,7 @@
+   F77_CALL(dgeev)(&jobvl, &jobvr, &n, tmp, &n, wr, wi, NULL,
+ 		  &n, NULL, &n, work, &lwork, &info);
+ #else
+-  dgeev_(&jobvl, &jobvr, &n, tmp, &n, wr, wi, NULL,
++  LAPACK_dgeev(&jobvl, &jobvr, &n, tmp, &n, wr, wi, NULL,
+          &n, NULL, &n, work, &lwork, &info);
+ #endif
+ 
+--- a/src/lib/base/phast_markov_matrix.c
++++ b/src/lib/base/phast_markov_matrix.c
+@@ -21,6 +21,7 @@
+ #include <phast/eigen.h>
+ #include <phast/prob_vector.h>
+ #include <phast/external_libs.h>
++#include <lapack.h>
+ 
+ #define SUM_EPSILON 0.0001
+ #define ELEMENT_EPSILON 0.00001
+@@ -285,7 +286,7 @@
+ #ifdef R_LAPACK
+     F77_CALL(dgebal)(&job, &ln, mat, &ln, &ilo, &ihi, scale, &info);
+ #else
+-    dgebal_(&job, &ln, mat, &ln, &ilo, &ihi, scale, &info);
++    LAPACK_dgebal(&job, &ln, mat, &ln, &ilo, &ihi, scale, &info);
+ #endif
+     if (info != 0)
+       die("Error in balancing matrix in lapack routine dgebal info=%i\n", info);
+@@ -400,7 +401,7 @@
+ #ifdef R_LAPACK
+   F77_CALL(dgesv)(&ln, &ln, matU, &ln, ipiv, matV, &ln, &info);
+ #else
+-  dgesv_(&ln, &ln, matU, &ln, ipiv, matV, &ln, &info);
++  LAPACK_dgesv(&ln, &ln, matU, &ln, ipiv, matV, &ln, &info);
+ #endif
+   if (info !=0)
+     die("Error solving U'X=V' in mm_exp_higham");
+@@ -425,7 +426,7 @@
+ #ifdef R_LAPACK
+     F77_CALL(dgebak)(&job, &side, &ln, &ilo, &ihi, scale, &ln, mat, &ln, &info);
+ #else
+-    dgebak_(&job, &side, &ln, &ilo, &ihi, scale, &ln, mat, &ln, &info);
++    LAPACK_dgebak(&job, &side, &ln, &ilo, &ihi, scale, &ln, mat, &ln, &info);
+ #endif
+     mat_from_lapack(P->matrix, mat);
+   }
+--- a/src/lib/base/phast_matrix.c
++++ b/src/lib/base/phast_matrix.c
+@@ -15,6 +15,7 @@
+ #include <phast/external_libs.h>
+ #include <math.h>
+ #include <phast/misc.h>
++#include <lapack.h>
+ 
+ Matrix *mat_new(int nrows, int ncols) {
+   int i;
+@@ -260,7 +261,7 @@
+ #ifdef R_LAPACK
+   F77_CALL(dgetrf)(&n, &n, (LAPACK_DOUBLE*)tmp, &n, ipiv, &info);
+ #else
+-  dgetrf_(&n, &n, (LAPACK_DOUBLE*)tmp, &n, ipiv, &info);
++  LAPACK_dgetrf(&n, &n, (LAPACK_DOUBLE*)tmp, &n, ipiv, &info);
+ #endif
+ 
+   if (info != 0) {
+@@ -270,7 +271,7 @@
+ #ifdef R_LAPACK
+   F77_CALL(dgetri)(&n, (LAPACK_DOUBLE*)tmp, &n, ipiv, work, &lwork, &info);
+ #else
+-  dgetri_(&n, (LAPACK_DOUBLE*)tmp, &n, ipiv, work, &lwork, &info);
++  LAPACK_dgetri(&n, (LAPACK_DOUBLE*)tmp, &n, ipiv, work, &lwork, &info);
+ #endif
+ 
+   if (info != 0) {



View it on GitLab: https://salsa.debian.org/med-team/phast/-/commit/a667d0df9966b4952271eb7e9ca11b356830c990

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View it on GitLab: https://salsa.debian.org/med-team/phast/-/commit/a667d0df9966b4952271eb7e9ca11b356830c990
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