[apophenia] 03/03: Imported Debian patch 1.0+ds-1
Jerome Benoit
calculus-guest at moszumanska.debian.org
Wed Dec 2 05:18:08 UTC 2015
This is an automated email from the git hooks/post-receive script.
calculus-guest pushed a commit to branch master
in repository apophenia.
commit 2a0dc24390919d4a10f1c2c16de632a29f4597c6
Author: Jerome Benoit <calculus at rezozer.net>
Date: Tue Dec 1 20:38:17 2015 +0100
Imported Debian patch 1.0+ds-1
---
debian/changelog | 11 +++++
debian/control | 4 +-
debian/patches/debianization-adhoc.patch | 2 +-
...ianization-bug-597187_757967-mysql_config.patch | 2 +-
debian/patches/debianization.patch | 6 +--
debian/patches/series | 6 +--
.../upstream-bug-793998-eg_t_test_by_rows.patch | 19 --------
.../upstream-bug-793998-eg_test_updating.patch | 52 ----------------------
...tream-bug-793998-tests_distribution_tests.patch | 33 --------------
.../upstream-enhancement-eg_test_updating.patch | 19 ++++++++
debian/patches/upstream-fix-typo.patch | 19 ++++++++
.../patches/upstream-typo-eg_t_test_by_rows.patch | 26 -----------
12 files changed, 58 insertions(+), 141 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index f002d8b..64b545f 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,14 @@
+apophenia (1.0+ds-1) unstable; urgency=medium
+
+ * New upstream release, all upstream patches were integrated.
+ * Debianization:
+ - debian/control:
+ - Build-Depends field, refresh (gsl2 migration);
+ - Vcs-Browser field, correct;
+ - debian/patches/*, refresh.
+
+ -- Jerome Benoit <calculus at rezozer.net> Wed, 02 Dec 2015 04:46:01 +0000
+
apophenia (0.999e+ds-4) unstable; urgency=medium
* RC bug fix release:
diff --git a/debian/control b/debian/control
index 9b570d9..f32b608 100644
--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,7 @@ Build-Depends:
debhelper (>= 9),
autotools-dev, autoconf-archive, gnulib, dh-autoreconf, libtool,
pkg-config, help2man,
- zlib1g-dev, libmysqlclient-dev, libsqlite3-dev, libgsl0-dev,
+ zlib1g-dev, libmysqlclient-dev, libsqlite3-dev, libgsl-dev,
bc, sqlite3
Build-Depends-Indep:
graphviz,
@@ -16,7 +16,7 @@ Build-Depends-Indep:
Standards-Version: 3.9.6
Homepage: http://apophenia.info/
Vcs-Git: git://anonscm.debian.org/debian-science/packages/apophenia.git
-Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-science/packages/apophenia.git
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-science/packages/apophenia.git
Package: libapophenia2
Provides: libapophenia
diff --git a/debian/patches/debianization-adhoc.patch b/debian/patches/debianization-adhoc.patch
index ed071f8..556791f 100644
--- a/debian/patches/debianization-adhoc.patch
+++ b/debian/patches/debianization-adhoc.patch
@@ -9,7 +9,7 @@ Last-Update: 2015-07-08
--- a/docs/documentation.h
+++ b/docs/documentation.h
-@@ -2618,8 +2618,8 @@
+@@ -2637,8 +2637,8 @@
relate. It is taken from this
<a href="http://modelingwithdata.org/pdfs/cheatsheet.pdf">cheat sheet</a> on general C and SQL use (2 page PDF).
diff --git a/debian/patches/debianization-bug-597187_757967-mysql_config.patch b/debian/patches/debianization-bug-597187_757967-mysql_config.patch
index 93ef68a..efb10a7 100644
--- a/debian/patches/debianization-bug-597187_757967-mysql_config.patch
+++ b/debian/patches/debianization-bug-597187_757967-mysql_config.patch
@@ -8,7 +8,7 @@ Last-Update: 2015-07-10
+++ b/configure.ac
@@ -87,6 +87,9 @@
## Debian package version
- DEB_PKG_VERSION=$(dpkg-parsechangelog | sed -n -e '/^Version:/s/Version: //p')
+ DEB_PKG_VERSION=$(dpkg-parsechangelog -S Version)
AC_SUBST(DEB_PKG_VERSION)
+## work around for bugs #597187 and #757967
+MYSQL_CFLAGS=$(echo "${MYSQL_CFLAGS}" | sed -e 's/-DNDEBUG//g;s/-g//g;s/-fabi-version=2//g;s/-fno-omit-frame-pointer//g;s/-fno-strict-aliasing//g;s/[ ]*$//g' | tr -s ' ')
diff --git a/debian/patches/debianization.patch b/debian/patches/debianization.patch
index f1082eb..17e0d51 100644
--- a/debian/patches/debianization.patch
+++ b/debian/patches/debianization.patch
@@ -3,7 +3,7 @@ Description: debianization
to address Debian specific stuff in general.
Origin: debian
Author: Jerome Benoit <calculus at rezozer.net>
-Last-Update: 2015-07-09
+Last-Update: 2015-12-01
--- a/docs/Makefile.am
+++ b/docs/Makefile.am
@@ -60,7 +60,7 @@ Last-Update: 2015-07-09
@@ -4,13 +4,13 @@
AC_PREREQ(2.60)
- AC_INIT([apophenia], [0.999e], [fluffmail at f-m.fm])
+ AC_INIT([apophenia], [1.0], [fluffmail at f-m.fm])
-AM_SILENT_RULES([yes])
+AM_SILENT_RULES([no])
AC_CONFIG_SRCDIR([apop_arms.c])
@@ -79,7 +79,7 @@ Last-Update: 2015-07-09
+# Debian stuff
+## Debian package version
-+DEB_PKG_VERSION=$(dpkg-parsechangelog | sed -n -e '/^Version:/s/Version: //p')
++DEB_PKG_VERSION=$(dpkg-parsechangelog -S Version)
+AC_SUBST(DEB_PKG_VERSION)
+
AC_CONFIG_FILES([
diff --git a/debian/patches/series b/debian/patches/series
index 68592b3..1553d51 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,7 +1,5 @@
-upstream-typo-eg_t_test_by_rows.patch
-upstream-bug-793998-eg_t_test_by_rows.patch
-upstream-bug-793998-eg_test_updating.patch
-upstream-bug-793998-tests_distribution_tests.patch
+upstream-fix-typo.patch
+upstream-enhancement-eg_test_updating.patch
debianization.patch
debianization-help2man.patch
debianization-documentation.patch
diff --git a/debian/patches/upstream-bug-793998-eg_t_test_by_rows.patch b/debian/patches/upstream-bug-793998-eg_t_test_by_rows.patch
deleted file mode 100644
index 7d18274..0000000
--- a/debian/patches/upstream-bug-793998-eg_t_test_by_rows.patch
+++ /dev/null
@@ -1,19 +0,0 @@
-Description: upstream -- RC bug fix 793998 -- eg/t_test_by_rows.c
- Fix a careless mistake that had introduced a type mismatch: size_t vs int.
- The patch was designed with 'gcc (Debian 5.2.1-22) 5.2.1 20151010' on
- a s390x Debian porter (sid).
-Origin: debian
-Author: Jerome Benoit <calculus at rezozer.net>
-Last-Update: 2015-10-16
-
---- a/eg/t_test_by_rows.c
-+++ b/eg/t_test_by_rows.c
-@@ -4,7 +4,7 @@
-
- void offset_rng(double *v){*v = gsl_rng_uniform(apop_rng_get_thread()) + row_offset;}
- double find_tstat(gsl_vector *in){ return apop_mean(in)/sqrt(apop_var(in));}
--double conf(double in, void *df){ return gsl_cdf_tdist_P(in, *(int *)df);}
-+double conf(double in, void *df){ return gsl_cdf_tdist_P(in, *(size_t *)df);}
-
- //apop_vector_mean is a macro, so we can't point a pointer to it.
- double mu(gsl_vector *in){ return apop_vector_mean(in);}
diff --git a/debian/patches/upstream-bug-793998-eg_test_updating.patch b/debian/patches/upstream-bug-793998-eg_test_updating.patch
deleted file mode 100644
index 3387e08..0000000
--- a/debian/patches/upstream-bug-793998-eg_test_updating.patch
+++ /dev/null
@@ -1,52 +0,0 @@
-Description: upstream -- RC bug fix 793998 -- eg/test_updating
- Fix a type conversion bug that failed the eg/test_updating test on some
- architectures (e.g., arm64 and ppc64el). The initial fix has been harden
- as it raised new issues on the 32bit i386 architecture.
- The patch was designed with 'gcc (Debian 5.2.1-15) 5.2.1 20150808' on
- i386, arm64, and ppc64el Debian porters (sid).
- The raised issue is likely due to some unexpected (broken ?) optimization
- at compile time: the use of the function modf appeared to break the
- faulty optimization.
-Origin: debian
-Author: Jerome Benoit <calculus at rezozer.net>
-Last-Update: 2015-08-30
-
---- a/apop_mcmc.c
-+++ b/apop_mcmc.c
-@@ -196,13 +196,14 @@
- }
-
-
--void main_mcmc_loop(apop_data *d, apop_model *m, apop_data *out, gsl_vector *draw,
-+void main_mcmc_loop(apop_data *d, apop_model *m, apop_data *out, gsl_vector *draw,
- apop_mcmc_settings *s, gsl_rng *rng, int *constraint_fails){
-+ double integerpart_periods_burnin = GSL_NAN; modf((double)(s->periods)*s->burnin,&integerpart_periods_burnin);
- s->accept_count = 0;
-+ int out_row = -lround(integerpart_periods_burnin);
- int block = 0;
-- for (s->proposal_count=1; s->proposal_count< s->periods+1; s->proposal_count++){
-- one_step(d, draw, m, s, rng, constraint_fails, out, block
-- , s->proposal_count-1 - s->periods*s->burnin);
-+ for (s->proposal_count=1; s->proposal_count< s->periods+1; s->proposal_count++, out_row++){
-+ one_step(d, draw, m, s, rng, constraint_fails, out, block, out_row);
- block = (block+1) % s->block_count;
- s->proposals[block].adapt_fn(s->proposals+block, s);
- //if (constraint_fails>10000) break;
-@@ -300,11 +301,14 @@
- apop_prep(d, m); //typically a no-op
- s->last_ll = GSL_NEGINF;
- gsl_vector * drawv = apop_data_pack(m->parameters);
-- Apop_stopif(s->burnin > 1, s->burnin/=(s->periods + 0.0),
-+ const double double_periods = (double)(s->periods);
-+ Apop_stopif(s->burnin > 1, s->burnin/=double_periods,
- 1, "Burn-in should be a fraction of the number of periods, "
- "not a whole number of periods. Rescaling to burnin=%g."
-- , s->burnin/(s->periods+0.0));
-- apop_data *out = apop_data_alloc(s->periods*(1-s->burnin), drawv->size);
-+ , s->burnin/double_periods);
-+ double integerpart_periods_cburnin = GSL_NAN; modf(double_periods*(1.0-s->burnin),&integerpart_periods_cburnin);
-+ const size_t data_size1 = llround(integerpart_periods_cburnin);
-+ apop_data *out = apop_data_alloc(data_size1, drawv->size);
-
- if (!s->proposals){
- set_block_count_and_block_starts(m->parameters, s, drawv->size);
diff --git a/debian/patches/upstream-bug-793998-tests_distribution_tests.patch b/debian/patches/upstream-bug-793998-tests_distribution_tests.patch
deleted file mode 100644
index 625fe94..0000000
--- a/debian/patches/upstream-bug-793998-tests_distribution_tests.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-Description: upstream -- RC bug fix 793998 -- tests/distribution_tests
- Fix a machine precision issue by relying on a more numerical approach,
- given that the employed numerical library is GSL.
- It appears that on i386 architecture (at least) the last digits are chopped:
- 1-(*out) = 0x1p-63 verifies the test !(*out >= 1) inside the beta_rng function,
- but inside the calling function (1-(*out)) is 0x0p+0 , that is *out is 1 .
- (Note that GSL_DBL_EPSILON has the value 0x1p-52 .) The patch was designed with
- 'gcc (Debian 5.2.1-15) 5.2.1 20150808' on a i386 Debian porter (sid).
- A more architecture oriented approach might exist, but anyway the numerical
- approach is satisfactory given that advanced numerical computations are done
- via GSL which relies on GSL_DBL_EPSILON.
-Origin: debian
-Author: Jerome Benoit <calculus at rezozer.net>
-Last-Update: 2015-08-30
-
---- a/model/apop_beta.c
-+++ b/model/apop_beta.c
-@@ -88,11 +88,13 @@
- }
-
- static int beta_rng(double *out, gsl_rng *r, apop_model* eps){
-+ double ans = GSL_NAN;
- Nullcheck_mp(eps, 1)
- Get_ab(eps)
- do {
-- *out = gsl_ran_beta(r, ab.alpha, ab.beta);
-- } while (*out <= 0 || *out >= 1);
-+ ans = gsl_ran_beta(r, ab.alpha, ab.beta);
-+ } while (!((0.0 < ans) && (GSL_DBL_EPSILON <= 1.0 - ans)));
-+ *out = ans;
- return 0;
- }
-
diff --git a/debian/patches/upstream-enhancement-eg_test_updating.patch b/debian/patches/upstream-enhancement-eg_test_updating.patch
new file mode 100644
index 0000000..ac2738c
--- /dev/null
+++ b/debian/patches/upstream-enhancement-eg_test_updating.patch
@@ -0,0 +1,19 @@
+Description: upstream -- enhancement -- test_updating
+ Render Apop_stopif message emitted by eg/test_updating.c more precise.
+Origin: debian
+Forwarded: https://github.com/b-k/apophenia/pull/28
+Author:
+ Jerome Benoit <calculus at rezozer.net>
+Last-Update: 2015-12-02
+
+--- a/eg/test_updating.c
++++ b/eg/test_updating.c
+@@ -4,7 +4,7 @@
+ void distances(gsl_vector *v1, gsl_vector *v2, double tol){
+ double error = apop_vector_distance(v1, v2, .metric='m');
+ double updated_size = apop_vector_sum(v1);
+- Apop_stopif(error/updated_size > tol, exit(1), 0, "The error is %g, which is too big.", error/updated_size);
++ Apop_stopif(error/updated_size > tol, exit(1), 0, "The error is %g, which is too big (> %g).", error/updated_size, tol);
+ }
+
+ int main(){
diff --git a/debian/patches/upstream-fix-typo.patch b/debian/patches/upstream-fix-typo.patch
new file mode 100644
index 0000000..cdf1e11
--- /dev/null
+++ b/debian/patches/upstream-fix-typo.patch
@@ -0,0 +1,19 @@
+Description: upstream -- typo -- model/apop_loess.c
+ Fix a misstyped GSL macro: DBL_EPSILON instead of GSL_DBL_EPSILON .
+Origin: debian
+Forwarded: https://github.com/b-k/apophenia/pull/28
+Author:
+ Jerome Benoit <calculus at rezozer.net>
+Last-Update: 2015-12-02
+
+--- a/model/apop_loess.c
++++ b/model/apop_loess.c
+@@ -1216,7 +1216,7 @@
+
+ ++execnt;
+ if (execnt == 1)
+- machep = DBL_EPSILON;
++ machep = GSL_DBL_EPSILON;
+ /* sort by distance */
+ for (i3 = 1; i3 <= *n; ++i3)
+ dist[i3] = 0.;
diff --git a/debian/patches/upstream-typo-eg_t_test_by_rows.patch b/debian/patches/upstream-typo-eg_t_test_by_rows.patch
deleted file mode 100644
index 3541cf0..0000000
--- a/debian/patches/upstream-typo-eg_t_test_by_rows.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-Description: upstream -- typo -- eg/t_test_by_rows
- Fix a faulty left parenthesis that had hidden a serious numerical bug.
- The so raised bug has been submitted alongside to the upstream maintainer:
- the numerical fix was provided by him.
-Origin: debian/upstream
-Author:
- Jerome Benoit <calculus at rezozer.net>
- Ben Klemens <fluffmail at f-m.fm>
-Last-Update: 2015-10-16
-Comment:
- The typo and the raised numerical issue were isolated by Jerome Benoit on
- behalf of the Debian Science Team; the numerical fix was provided by Ben
- Klemens as upstream maintainer.
-
---- a/eg/t_test_by_rows.c
-+++ b/eg/t_test_by_rows.c
-@@ -32,7 +32,7 @@
- assert(apop_data_get(means, i, -1) * apop_data_get(tstats, i, -1) >=0);
-
- //inverse of P-value should be the t statistic.
-- assert(fabs(gsl_cdf_tdist_Pinv(apop_data_get(confidences, i, -1),100)
-- - apop_data_get(tstats, i, -1) < 1e-3));
-+ assert(fabs(gsl_cdf_tdist_Pinv(apop_data_get(confidences, i, -1), 99)
-+ - apop_data_get(tstats, i, -1)) < 1e-5);
- }
- }
--
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