[med-svn] [Git][med-team/emmax][master] 5 commits: * Build-Depends libopenblas-dev | libblas-dev | libblas.so instead of
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Nov 28 17:40:44 GMT 2023
Andreas Tille pushed to branch master at Debian Med / emmax
Commits:
212bae04 by Andreas Tille at 2023-07-10T21:45:47+02:00
* Build-Depends libopenblas-dev | libblas-dev | libblas.so instead of
libatlas-base-dev which is wrong on one hand and will be possibly removed
soon on the other hand
* Do not Build-Depend from shared lib packages
- - - - -
1a8d0733 by Andreas Tille at 2023-07-10T21:46:16+02:00
routine-update: Standards-Version: 4.6.2
- - - - -
aca1dd57 by Andreas Tille at 2023-11-28T17:00:31+01:00
Try to use LAPACKE instead of clapack
- - - - -
da5d3727 by Andreas Tille at 2023-11-28T17:31:13+01:00
Suppress warnings to clean up build log, first attempt to port to lapacke
- - - - -
ab4a6f2c by Andreas Tille at 2023-11-28T18:40:13+01:00
More syntax fixes
- - - - -
7 changed files:
- debian/changelog
- debian/control
- − debian/patches/atlas.patch
- + debian/patches/lapacke.patch
- debian/patches/paths.patch
- debian/patches/series
- + debian/patches/syntax.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+emmax (0~beta.20100307-4) UNRELEASED; urgency=medium
+
+ * Build-Depends libopenblas-dev | libblas-dev | libblas.so instead of
+ libatlas-base-dev which is wrong on one hand and will be possibly removed
+ soon on the other hand
+ * Build-Depends: s/liblapack-dev/liblapacke-dev/
+ Closes: #1056671
+ * Do not Build-Depend from shared lib packages
+ * Standards-Version: 4.6.2 (routine-update)
+ * Suppress warnings to clean up build log
+
+ -- Andreas Tille <tille at debian.org> Mon, 10 Jul 2023 21:43:42 +0200
+
emmax (0~beta.20100307-3) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -5,13 +5,10 @@ Uploaders: SteffenSteffen Moeller <moeller at debian.org>,
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
- libatlas-base-dev,
- liblapack-dev,
- zlib1g-dev,
- libblas3,
- liblapack3,
- libatlas3-base
-Standards-Version: 4.6.1
+ libopenblas-dev | libblas-dev | libblas.so,
+ liblapacke-dev,
+ zlib1g-dev
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/emmax
Vcs-Git: https://salsa.debian.org/med-team/emmax.git
Homepage: http://genome.sph.umich.edu/wiki/EMMAX
=====================================
debian/patches/atlas.patch deleted
=====================================
@@ -1,15 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 11 Feb 2018 12:00:11 +0100
-Description: Adapt to new libatlas-base-dev layout
-
---- a/emmax.c
-+++ b/emmax.c
-@@ -7,7 +7,7 @@
- #include <float.h>
- #include <time.h>
- #include <cblas.h>
--#include <atlas/clapack.h>
-+#include <clapack.h>
- #include <zlib.h>
- //#include "lapack_wrapper.h"
-
=====================================
debian/patches/lapacke.patch
=====================================
@@ -0,0 +1,23 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 28 Nov 2023 17:29:11 +0100
+Bug-Debian: https://bugs.debian.org/1056671
+Description:
+
+--- a/emmax.c
++++ b/emmax.c
+@@ -1747,13 +1747,13 @@ int matrix_invert(int n, double *X, doub
+ }
+
+ /* Turn Y into its LU form, store pivot matrix */
+- info = clapack_dgetrf (CblasColMajor, n, n, Y, n, ipiv);
++ info = LAPACK_dgetrf (CblasColMajor, n, n, Y, n, ipiv);
+
+ /* Don't bother continuing when illegal argument (info<0) or singularity (info>0) occurs */
+ if (info!=0) return info;
+
+ /* Feed this to the lapack inversion routine. */
+- info = clapack_dgetri (CblasColMajor, n, Y, n, ipiv);
++ info = LAPACK_dgetri (CblasColMajor, n, Y, n, ipiv);
+
+ /* Cleanup and exit */
+ free(ipiv);
=====================================
debian/patches/paths.patch
=====================================
@@ -11,7 +11,7 @@ Index: emmax-0~beta.20100307/emmax.c
#include <time.h>
#include <cblas.h>
-#include <clapack.h>
-+#include <atlas/clapack.h>
++#include <lapack.h>
#include <zlib.h>
//#include "lapack_wrapper.h"
=====================================
debian/patches/series
=====================================
@@ -4,6 +4,7 @@ aborts.patch
install.patch
clean.patch
logfile.patch
-atlas.patch
hardening.patch
fix-autopkgtest.patch
+lapacke.patch
+syntax.patch
=====================================
debian/patches/syntax.patch
=====================================
@@ -0,0 +1,72 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 28 Nov 2023 17:29:11 +0100
+Description: Suppress warnings to clean up build log
+
+--- a/emmax.c
++++ b/emmax.c
+@@ -101,7 +101,7 @@ double tcdf(double t, double nu);
+ int main(int argc, char** argv) {
+ int i, j, k, l, n, nf, q0, ngrids, ndigits, istart, iend, nelems, nmiss, *wids;
+ char *kinf, *phenof, *tpedf, *covf, *outf, *inf, *delims, *lbuf;
+- int mphenoflag, write_eig_flag, gz_flag, tped_nheadercols, tfam_nheadercols, zero_miss_flag, isnpid, gen_kin_method, dosage_flag, gls_flag, c;
++ int mphenoflag, write_eig_flag, gz_flag, tped_nheadercols, tfam_nheadercols, zero_miss_flag, isnpid, gen_kin_method, /*dosage_flag,*/ gls_flag, c;
+ double *phenos, *covs, *kins, *snps;
+ double sum, llim, ulim, stat, p;
+ clock_t cstart, cend, sum0, sum1, sum2, clapstart, clapend;
+@@ -120,7 +120,7 @@ int main(int argc, char** argv) {
+ tfam_nheadercols = DEFAULT_TFAM_NUM_HEADER_COLS;
+ zero_miss_flag = 1;
+ isnpid = DEFAULT_TPED_SNPID_INDEX;
+- dosage_flag = 0;
++ /*dosage_flag = 0;*/
+ gls_flag = 1;
+
+ // Read optional parameters
+@@ -188,7 +188,8 @@ int main(int argc, char** argv) {
+ zero_miss_flag = 0;
+ break;
+ case 'O' :
+- dosage_flag = 1;
++ /* dosage_flag = 1; */
++ /* This flag is not used */
+ break;
+ case 'N' :
+ gls_flag = 0;
+@@ -515,12 +516,12 @@ int main(int argc, char** argv) {
+ eLvecs = (double*)malloc(sizeof(double)*nf*nf);
+
+ remlh = open_file_with_suffix(inf,"reml",0,0);
+- fscanf(remlh.fp,"%lf",&REML);
+- fscanf(remlh.fp,"%lf",&REML0);
+- fscanf(remlh.fp,"%lf",&optdelta);
+- fscanf(remlh.fp,"%lf",&optvg);
+- fscanf(remlh.fp,"%lf",&optve);
+- fscanf(remlh.fp,"%lf",&hg);
++ if ( fscanf(remlh.fp,"%lf",&REML) != 1 ) { emmax_error("Parser error"); }
++ if ( fscanf(remlh.fp,"%lf",&REML0) != 1 ) { emmax_error("Parser error"); }
++ if ( fscanf(remlh.fp,"%lf",&optdelta) != 1 ) { emmax_error("Parser error"); }
++ if ( fscanf(remlh.fp,"%lf",&optvg) != 1 ) { emmax_error("Parser error"); }
++ if ( fscanf(remlh.fp,"%lf",&optve) != 1 ) { emmax_error("Parser error"); }
++ if ( fscanf(remlh.fp,"%lf",&hg) != 1 ) { emmax_error("Parser error"); }
+ fclose(remlh.fp);
+
+ eLvalsh = open_file_with_suffix(inf,"eLvals",0,0);
+--- a/emmax-kin.c
++++ b/emmax-kin.c
+@@ -59,7 +59,7 @@ void print_help(void) {
+
+ int main(int argc, char** argv) {
+ int i, j, k, n, ac0, ac1, nmiss, nelems, nex, *nexes;
+- int verbose, ndigits, tped_nheadercols, tfam_nheadercols, flag_autosomal, rand_fill_flag, ibs_flag, gz_flag, hetero_division_flag;
++ int verbose, ndigits, tped_nheadercols, tfam_nheadercols, flag_autosomal, rand_fill_flag, ibs_flag, hetero_division_flag;
+ unsigned char *snprow;
+ char buf[SZBUF];
+ int c;
+@@ -82,7 +82,6 @@ int main(int argc, char** argv) {
+ rand_fill_flag = 0;
+ hetero_division_flag = 0;
+ ibs_flag = 0;
+- gz_flag = 0;
+
+ verbose = 0;
+ ndigits = DEFAULT_NDIGITS;
View it on GitLab: https://salsa.debian.org/med-team/emmax/-/compare/f5a35e648f219ac5ed5a2a28ea1542d2b3f4925c...ab4a6f2cc69f30bf1bd273ced219912fb3b07119
--
View it on GitLab: https://salsa.debian.org/med-team/emmax/-/compare/f5a35e648f219ac5ed5a2a28ea1542d2b3f4925c...ab4a6f2cc69f30bf1bd273ced219912fb3b07119
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