Commit 2e6ea862 authored by Jerome Benoit's avatar Jerome Benoit

Debian patch 1.0+ds-8

parent f63c7103
apophenia (1.0+ds-8) UNRELEASED; urgency=medium
apophenia (1.0+ds-8) unstable; urgency=medium
* Use secure copyright file specification URI.
-- Jelmer Vernooij <jelmer@debian.org> Sat, 20 Oct 2018 12:48:38 +0000
* RC fix release (Closes: #925634), implement workaround that works
(this looks like a gcc9 compiler issue).
* Debianization:
- debian/copyright:
- Copyright year tuples, refresh;
- Format URI, secure;
- debian/control:
- debhelper, bump to 12;
- Standards-Version, bump to 4.4.0 (no change);
- Vcs-*, migration to Salsa;
- debian/rules:
- get-orig-source target, discard;
- debian/patches/*:
- d/p/upstream-{mysql-8.0,fix-implicit-model-ols_log_likelihood}.patch,
introduce;
- d/p/debianization-bug-gcc9-XXX.patch, introduce;
- debian/source/*:
- d/s/lintian-overrides, refresh;
- d/s/options, discard;
- debian/compat, delete.
-- Jerome Benoit <calculus@rezozer.net> Fri, 16 Aug 2019 15:20:10 +0000
apophenia (1.0+ds-7) unstable; urgency=medium
......
......@@ -4,8 +4,8 @@ Priority: optional
Maintainer: Debian Science Maintainers <debian-science-maintainers@lists.alioth.debian.org>
Uploaders: Jerome Benoit <calculus@rezozer.net>
Build-Depends:
debhelper (>= 9),
autotools-dev, autoconf-archive, gnulib, dh-autoreconf, libtool,
debhelper-compat (= 12),
autoconf-archive, gnulib, libtool,
pkg-config, help2man,
zlib1g-dev, default-libmysqlclient-dev, libsqlite3-dev, libgsl-dev,
bc, sqlite3
......@@ -13,10 +13,10 @@ Build-Depends-Indep:
graphviz,
doxygen, texlive-latex-recommended, texlive-fonts-recommended, ghostscript,
rdfind, symlinks
Standards-Version: 3.9.8
Standards-Version: 4.4.0
Homepage: http://apophenia.info/
Vcs-Git: https://anonscm.debian.org/git/debian-science/packages/apophenia.git
Vcs-Browser: https://anonscm.debian.org/cgit/debian-science/packages/apophenia.git
Vcs-Git: https://salsa.debian.org/science-team/apophenia.git
Vcs-Browser: https://salsa.debian.org/science-team/apophenia
Package: libapophenia2
Provides: libapophenia
......
......@@ -37,7 +37,7 @@ Files-Excluded:
apop.h
Files: *
Copyright: 2005-2016 Ben Klemens <fluffmail@f-m.fm>
Copyright: 2005-2019 Ben Klemens <fluffmail@f-m.fm>
License: GPL-2
Files: apop_fexact.c
......@@ -81,7 +81,7 @@ License: GPL-2+
Files: debian/*
Copyright:
2014-2016 Jerome Benoit <calculus@rezozer.net>
2014-2019 Jerome Benoit <calculus@rezozer.net>
License: GPL-2+
License: GPL-2
......
Description: debianization -- workaround around a gcc9 bug
Meant to workaround what looks like a gcc9 compiler bug:
the merit of this patch is that it works, do not ask me why.
Origin: vendor, debian
Forwarded: not-needed
Author: Jerome Benoit <calculus@rezozer.net>
Last-Update: 2019-08-16
--- a/apop_arms.c
+++ b/apop_arms.c
@@ -37,11 +37,15 @@
)
Apop_settings_init(apop_arms,
- if ((in.xl || in.xr) && !in.xinit)
+ if ((in.xl || in.xr) && !in.xinit){
+ char ADHOC[64];
out->xinit = (double []) {in.xl+GSL_DBL_EPSILON, (in.xl+in.xr)/2., in.xr-GSL_DBL_EPSILON};
- else{
+ snprintf(ADHOC,sizeof(ADHOC),"{%g,%g,%g}",out->xinit[0],out->xinit[1],out->xinit[2]);
+ } else{
+ char ADHOC[64];
//Apop_varad_set(xinit, ((double []) {0, 0.5, 1}));
Apop_varad_set(xinit, ((double []) {-1, 0, 1}));
+ snprintf(ADHOC,sizeof(ADHOC),"{%g,%g,%g}",out->xinit[0],out->xinit[1],out->xinit[2]);
}
Apop_varad_set(ninit, 3);
Apop_varad_set(xl, GSL_MIN(out->xinit[0]/10., out->xinit[0]*10)-.1);
upstream-fix-implicit-model-ols_log_likelihood.patch
upstream-mysql-8.0.patch
upstream-bug-793998-tests_distribution_tests-2.patch
upstream-fix-typo.patch
upstream-enhancement-eg_test_updating.patch
......@@ -7,3 +9,4 @@ debianization-help2man.patch
debianization-documentation.patch
debianization-bug-597187_757967_841636-mysql_config.patch
debianization-adhoc.patch
debianization-bug-gcc9-XXX.patch
Description: upstream - fix implicit in ols_log_likelihood
Fix what looks like an implicit in behaviour in function
ols_log_likelihood; thanks to Christian Ehrhardt
<christian.ehrhardt@canonical.com> for figuring out the
issue.
Origin: vendor, Debian
Forwarded: https://github.com/b-k/apophenia/pull/39
Author: Jerome Benoit <calculus@rezozer.net>
Last-Update: 2019-08-16
--- a/model/apop_ols.c
+++ b/model/apop_ols.c
@@ -137,9 +137,12 @@
gsl_vector *errors;
apop_data *pred = apop_data_get_page(p->info, "<Predicted>");
- if (pred && d==p->data) //use already-stored errors for this data set.
- errors = Apop_cv(pred, 2);
- else {
+ if (pred && d==p->data){ //use already-stored errors for this data set.
+ gsl_vector *as_errors = Apop_cv(pred, 2);
+ errors = gsl_vector_calloc(data->size1);
+ for (size_t i=0;i< GSL_MIN(as_errors->size,data->size1); i++)
+ gsl_vector_set(errors, i, gsl_vector_get(as_errors, i));
+ } else {
errors = gsl_vector_alloc(data->size1);
for (size_t i=0;i< data->size1; i++){
gsl_blas_ddot(p->parameters->vector, Apop_rv(d, i), &expected);
@@ -165,7 +168,6 @@
weight = d->weights ? gsl_vector_get(d->weights, i) : 1;
ll += logl(gsl_ran_gaussian_pdf(gsl_vector_get(errors, i), sigma)* weight * x_prob);
}
- if (!pred) gsl_vector_free(errors);
return ll;
}
Description: upstream -- mysql8
Transition to mysql8.
Origin: vendor, canonical
Forwarded: https://github.com/b-k/apophenia/pull/40
Author: Christian Ehrhardt <christian.ehrhardt@canonical.com>
Last-Update: 2019-08-16
--- a/apop_db_mysql.c
+++ b/apop_db_mysql.c
@@ -3,8 +3,6 @@
/* Copyright (c) 2006--2007 by Ben Klemens. Licensed under the GPLv2; see COPYING. */
-#include <my_global.h>
-#include <my_sys.h>
#include <mysql.h>
#include <math.h>
......@@ -19,7 +19,7 @@ default:
@uscan --no-conf --dehs --report || true
%:
dh $@ --with autoreconf --builddirectory=_build --parallel
dh $@ --builddirectory=_build
override_dh_auto_configure:
dh_auto_configure -- --enable-maintainer-mode
......@@ -33,6 +33,3 @@ override_dh_auto_install-indep:
override_dh_compress-indep:
dh_compress -X.pdf -Xexamples
get-orig-source:
uscan --no-conf --download-current-version --compression xz --verbose
debian-watch-may-check-gpg-signature
debian-watch-does-not-check-gpg-signature
compression = xz
compression-level = 9
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