diff -Nru emmax-0~beta.20100307/debian/changelog emmax-0~beta.20100307/debian/changelog --- emmax-0~beta.20100307/debian/changelog 2019-03-20 17:28:20.000000000 +0000 +++ emmax-0~beta.20100307/debian/changelog 2022-07-20 08:49:39.000000000 +0000 @@ -1,3 +1,21 @@ +emmax (0~beta.20100307-2) unstable; urgency=medium + + [ Steffen Möller ] + * Team upload. + * Update metadata with ref to conda + + [ Mohammed Bilal ] + * routine-update: Packaging update + * routine-update: Standards-Version: 4.6.1 + * routine-update: debhelper-compat 13 + * routine-update: Remove trailing whitespace in debian/copyright + * routine-update: Add salsa-ci file + * routine-update: Rules-Requires-Root: no + * Add autopkgtests + * Update hardening patch + + -- Mohammed Bilal Wed, 20 Jul 2022 14:19:39 +0530 + emmax (0~beta.20100307-1) unstable; urgency=low * Initial release (Closes: #925158) diff -Nru emmax-0~beta.20100307/debian/compat emmax-0~beta.20100307/debian/compat --- emmax-0~beta.20100307/debian/compat 2019-03-20 17:28:20.000000000 +0000 +++ emmax-0~beta.20100307/debian/compat 1970-01-01 00:00:00.000000000 +0000 @@ -1 +0,0 @@ -12 diff -Nru emmax-0~beta.20100307/debian/control emmax-0~beta.20100307/debian/control --- emmax-0~beta.20100307/debian/control 2019-03-20 17:28:20.000000000 +0000 +++ emmax-0~beta.20100307/debian/control 2022-07-20 08:47:48.000000000 +0000 @@ -4,17 +4,18 @@ Andreas Tille Section: science Priority: optional -Build-Depends: debhelper (>= 12~), +Build-Depends: debhelper-compat (= 13), libatlas-base-dev, liblapack-dev, zlib1g-dev, libblas3, liblapack3, libatlas3-base -Standards-Version: 4.3.0 +Standards-Version: 4.6.1 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 +Rules-Requires-Root: no Package: emmax Architecture: any diff -Nru emmax-0~beta.20100307/debian/copyright emmax-0~beta.20100307/debian/copyright --- emmax-0~beta.20100307/debian/copyright 2019-03-20 17:28:20.000000000 +0000 +++ emmax-0~beta.20100307/debian/copyright 2022-07-20 08:47:48.000000000 +0000 @@ -1,6 +1,6 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: emmax -Upstream-Contact: Hyun Min Kang +Upstream-Contact: Hyun Min Kang Source: http://genetics.cs.ucla.edu/emmax/ Files: * diff -Nru emmax-0~beta.20100307/debian/patches/hardening.patch emmax-0~beta.20100307/debian/patches/hardening.patch --- emmax-0~beta.20100307/debian/patches/hardening.patch 2019-03-20 17:28:20.000000000 +0000 +++ emmax-0~beta.20100307/debian/patches/hardening.patch 2022-07-20 08:47:48.000000000 +0000 @@ -4,12 +4,12 @@ --- a/makefile +++ b/makefile -@@ -5,9 +5,9 @@ PREFIX=/usr +@@ -5,9 +5,9 @@ INCFLAGS = LIBFLAGS = -Wall -COMPFLAGS = ${INCFLAGS} -O2 -Wall -g -+COMPFLAGS = ${INCFLAGS} -O2 -Wall -g $(CFLAGS) ++COMPFLAGS = ${INCFLAGS} -O2 -Wall -g $(CFLAGS) $(CPPFLAGS) CC = gcc -CLIBS = -L/usr/lib/atlas-base -L/usr/lib/lapack/ -llapack_atlas -llapack -lcblas -lblas -latlas -lcblas -lm -lz +CLIBS = -L/usr/lib/atlas-base -L/usr/lib/lapack/ -llapack_atlas -llapack -lcblas -lblas -latlas -lcblas -lm -lz $(LDFLAGS) diff -Nru emmax-0~beta.20100307/debian/salsa-ci.yml emmax-0~beta.20100307/debian/salsa-ci.yml --- emmax-0~beta.20100307/debian/salsa-ci.yml 1970-01-01 00:00:00.000000000 +0000 +++ emmax-0~beta.20100307/debian/salsa-ci.yml 2022-07-20 08:47:48.000000000 +0000 @@ -0,0 +1,4 @@ +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml diff -Nru emmax-0~beta.20100307/debian/tests/control emmax-0~beta.20100307/debian/tests/control --- emmax-0~beta.20100307/debian/tests/control 1970-01-01 00:00:00.000000000 +0000 +++ emmax-0~beta.20100307/debian/tests/control 2022-07-20 08:47:48.000000000 +0000 @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @, plink +Restrictions: allow-stderr diff -Nru emmax-0~beta.20100307/debian/tests/run-unit-test emmax-0~beta.20100307/debian/tests/run-unit-test --- emmax-0~beta.20100307/debian/tests/run-unit-test 1970-01-01 00:00:00.000000000 +0000 +++ emmax-0~beta.20100307/debian/tests/run-unit-test 2022-07-20 08:49:37.000000000 +0000 @@ -0,0 +1,38 @@ +#!/bin/bash +set -e + +pkg=plink + +export LC_ALL=C.UTF-8 +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" + +echo "247395d4cfd4bef03befd9672a2afe0a test.emmax.ps" >> checksums + +p-link --noweb --file test --recode12 --output-missing-genotype 0 --transpose --out test + +awk '{print $1,$2,$6}' test.ped > test.emmax_phenotypes +sed -i 's/-9$/NA/' test.emmax_phenotypes +sed -i 's/0$/NA/' test.emmax_phenotypes + +echo -e "\e[93m\e[1mRunning Tests\e[0m" + +echo -e "\e[93m\e[1mTest 1\e[0m" + +emmax-kin -v -d 10 test + +echo -e "\e[93m\e[1mTest 2\e[0m" + +emmax -v -d 10 -t test -p test.emmax_phenotypes -k test.BN.kinf -o test.emmax + +md5sum --check checksums +echo -e "\e[92m\e[1mPASS\e[0m" + +# Clean up +rm -f test.* diff -Nru emmax-0~beta.20100307/debian/upstream/metadata emmax-0~beta.20100307/debian/upstream/metadata --- emmax-0~beta.20100307/debian/upstream/metadata 2019-03-20 17:28:20.000000000 +0000 +++ emmax-0~beta.20100307/debian/upstream/metadata 2022-07-20 08:47:48.000000000 +0000 @@ -20,3 +20,5 @@ Entry: EMMAX - Name: SciCrunch Entry: NA + - Name: conda:bioconda + Entry: NA