[med-svn] [Git][med-team/hmmer][master] 9 commits: restrict archs to those mandated by upstream
Michael R. Crusoe
gitlab at salsa.debian.org
Tue Sep 24 21:53:36 BST 2019
Michael R. Crusoe pushed to branch master at Debian Med / hmmer
Commits:
0618003d by Michael R. Crusoe at 2019-09-24T16:15:58Z
restrict archs to those mandated by upstream
- - - - -
38fb2f8a by Michael R. Crusoe at 2019-09-24T16:16:29Z
debhelper-compat 12
- - - - -
f1a863b6 by Michael R. Crusoe at 2019-09-24T18:35:09Z
enable a verbose build log
- - - - -
131be862 by Michael R. Crusoe at 2019-09-24T18:35:27Z
improve hardening
- - - - -
62d7f44f by Michael R. Crusoe at 2019-09-24T18:35:40Z
spelling
- - - - -
e1a22d82 by Michael R. Crusoe at 2019-09-24T18:35:42Z
refinements to the libdivsufsort patch
- - - - -
b46a0271 by Michael R. Crusoe at 2019-09-24T18:35:42Z
jobserver-test
- - - - -
e29dcb84 by Michael R. Crusoe at 2019-09-24T18:36:01Z
autopkgtests: verbose
- - - - -
b4b79633 by Michael R. Crusoe at 2019-09-24T18:36:02Z
install hmmc2 for the autopkgtest
- - - - -
11 changed files:
- debian/changelog
- − debian/compat
- debian/control
- debian/hmmer.install
- + debian/patches/hardening
- debian/patches/series
- + debian/patches/spelling
- debian/patches/use_debian_packaged_libdivsufsort.patch
- + debian/patches/verbose-easel
- debian/rules
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+hmmer (3.2.1+dfsg-3) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * HMMER3 has long required SSE or Altivec/VMX instruction support and the
+ 3.2.1 release enforces this, so we will follow upstreams lead:
+ debian/control: Architecture: any-amd64 any-i386 powerpc ppc64 x32
+ * debhelper-compat 12
+ * Enable a verbose build log
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Tue, 24 Sep 2019 18:13:19 +0200
+
hmmer (3.2.1+dfsg-2) unstable; urgency=medium
[ Jelmer Vernooij ]
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
libdivsufsort-dev
Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/hmmer
@@ -11,7 +11,7 @@ Vcs-Git: https://salsa.debian.org/med-team/hmmer.git
Homepage: http://hmmer.org/
Package: hmmer
-Architecture: any
+Architecture: any-amd64 any-i386 powerpc ppc64 x32
Depends: ${shlibs:Depends},
${misc:Depends}
Suggests: hmmer-doc (>= ${source:Version})
=====================================
debian/hmmer.install
=====================================
@@ -1,2 +1,3 @@
usr/bin
usr/share/man
+src/hmmc2 /usr/bin/
=====================================
debian/patches/hardening
=====================================
@@ -0,0 +1,44 @@
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Descriptions: Don't stomp on Debian's CFLAGS
+--- hmmer.orig/configure.ac
++++ hmmer/configure.ac
+@@ -78,12 +78,6 @@
+ AC_INIT(HMMER, 3.2.1, sean at eddylab.org, hmmer)
+ AC_MSG_NOTICE([Configuring HMMER3 for your system.])
+
+-# remember if the user is overriding CFLAGS
+-esl_cflags_env_set=no
+-if test x"$CFLAGS" != x; then
+- esl_cflags_env_set=yes
+-fi
+-
+ ################################################################
+ # 3. Info on the package
+ ################################################################
+@@ -236,21 +230,15 @@
+ # --enable-gcov, --enable-gprof, and --enable-debugging are mutually exclusive.
+ #
+ if test "$enable_gcov" = "yes"; then
+- if test "$esl_cflags_env_set" = "yes"; then
+- AC_MSG_ERROR([--enable-gcov overrides CFLAGS, so don't set CFLAGS])
+- fi
+- CFLAGS="-g -Wall -fprofile-arcs -ftest-coverage"
++ CFLAGS="${CLFAGS} -g -Wall -fprofile-arcs -ftest-coverage"
+ elif test "$enable_gprof" = "yes"; then
+- if test "$esl_cflags_env_set" = "yes"; then
+- AC_MSG_ERROR([--enable-gprof overrides CFLAGS, so don't set CFLAGS])
+- fi
+- CFLAGS="-O -g -pg"
++ CFLAGS="${CFLAGS} -O -g -pg"
+ elif test "$enable_debugging" != "no"; then
+ if test "$GCC" = "yes"; then
+- CFLAGS="-g -Wall"
++ CFLAGS="${CFLAGS} -g -Wall"
+ fi
+-elif test "$esl_cflags_env_set" != "yes"; then
+- CFLAGS="-O3"
++else
++ CFLAGS="${CFLAGS} -O3"
+ fi
+
+
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,5 @@
fix_manpage_extension.patch
use_debian_packaged_libdivsufsort.patch
+verbose-easel
+hardening
+spelling
=====================================
debian/patches/spelling
=====================================
@@ -0,0 +1,24 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: Debian Lintian inspired typo fixes
+--- hmmer.orig/src/hmmdmstr.c
++++ hmmer/src/hmmdmstr.c
+@@ -1252,7 +1252,7 @@
+
+ /* skip leading white spaces */
+ while (*ptr == ' ' || *ptr == '\t') ++ptr;
+- if (!*ptr) { client_msg(fd, eslEINVAL, "Load command missing ip addres\n"); return; }
++ if (!*ptr) { client_msg(fd, eslEINVAL, "Load command missing ip address\n"); return; }
+
+ while (ptr && *ptr) {
+ if (ip_addr != NULL) { client_msg(fd, eslEINVAL, "Multiple ip addresses on command line %s\n", s); return; }
+--- hmmer.orig/src/nhmmer.c
++++ hmmer/src/nhmmer.c
+@@ -358,7 +358,7 @@
+
+ #if defined (eslENABLE_SSE)
+ if (esl_opt_IsUsed(go, "--seed_max_depth") && fprintf(ofp, "# FM Seed length: %d\n", esl_opt_GetInteger(go, "--seed_max_depth")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
+- if (esl_opt_IsUsed(go, "--seed_sc_thresh") && fprintf(ofp, "# FM score threshhold (bits): %g\n", esl_opt_GetReal(go, "--seed_sc_thresh")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
++ if (esl_opt_IsUsed(go, "--seed_sc_thresh") && fprintf(ofp, "# FM score threshold (bits): %g\n", esl_opt_GetReal(go, "--seed_sc_thresh")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
+ if (esl_opt_IsUsed(go, "--seed_sc_density") && fprintf(ofp, "# FM score density (bits/pos): %g\n", esl_opt_GetReal(go, "--seed_sc_density")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
+ if (esl_opt_IsUsed(go, "--seed_drop_max_len") && fprintf(ofp, "# FM max neg-growth length: %d\n", esl_opt_GetInteger(go, "--seed_drop_max_len")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
+ if (esl_opt_IsUsed(go, "--seed_drop_lim") && fprintf(ofp, "# FM max run drop: %g\n", esl_opt_GetReal(go, "--seed_drop_lim")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
=====================================
debian/patches/use_debian_packaged_libdivsufsort.patch
=====================================
@@ -2,9 +2,9 @@ Author: Andreas Tille <tille at debian.org>
Last-Update: Sun, 26 Jun 2016 00:53:18 +0200
Description: Use Debian packaged libdivsufsort
---- a/configure.ac
-+++ b/configure.ac
-@@ -114,7 +114,6 @@ HMMER_VERSION=$PACKAGE_VERSION
+--- hmmer.orig/configure.ac
++++ hmmer/configure.ac
+@@ -114,7 +114,6 @@
HMMER_URL="http://hmmer.org/"
HMMER_ESLDIR="easel"
@@ -12,7 +12,7 @@ Description: Use Debian packaged libdivsufsort
EASEL_DATE="June 2018"
EASEL_COPYRIGHT="Copyright (C) 2018 Howard Hughes Medical Institute."
-@@ -129,7 +128,6 @@ AC_SUBST(HMMER_VERSION)
+@@ -129,7 +128,6 @@
AC_SUBST(HMMER_URL)
AC_SUBST(HMMER_ESLDIR)
@@ -20,7 +20,7 @@ Description: Use Debian packaged libdivsufsort
AC_SUBST(EASEL_DATE)
AC_SUBST(EASEL_COPYRIGHT)
-@@ -584,7 +582,6 @@ AC_CONFIG_FILES([ \
+@@ -584,7 +582,6 @@
documentation/Makefile \
documentation/man/Makefile \
documentation/userguide/Makefile \
@@ -28,7 +28,7 @@ Description: Use Debian packaged libdivsufsort
])
# Easel Makefiles.
-@@ -656,7 +653,6 @@ AC_CONFIG_FILES([ \
+@@ -656,7 +653,6 @@
AC_CONFIG_HEADERS([easel/decoy_config.h]) # Put this first to keep gnu 'autoheader' from overwriting a real config file.
AC_CONFIG_HEADERS([src/p7_config.h])
AC_CONFIG_HEADERS([easel/esl_config.h])
@@ -36,9 +36,9 @@ Description: Use Debian packaged libdivsufsort
# the following incantation establishes a symlink of
# src/impl_{whatever} to src/impl in the *build* directory.
---- a/Makefile.in
-+++ b/Makefile.in
-@@ -26,8 +26,6 @@ SHELL = /bin/sh
+--- hmmer.orig/Makefile.in
++++ hmmer/Makefile.in
+@@ -26,8 +26,6 @@
# location of easel
ESLDIR = @HMMER_ESLDIR@
@@ -47,7 +47,7 @@ Description: Use Debian packaged libdivsufsort
# Package information
-@@ -88,7 +86,6 @@ endif
+@@ -88,7 +86,6 @@
#
all:
${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} all
@@ -55,7 +55,7 @@ Description: Use Debian packaged libdivsufsort
${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} all
${QUIET_SUBDIR0}profmark ${QUIET_SUBDIR1} all
-@@ -96,7 +93,6 @@ all:
+@@ -96,7 +93,6 @@
#
dev:
${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} dev
@@ -63,7 +63,7 @@ Description: Use Debian packaged libdivsufsort
${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} dev
${QUIET_SUBDIR0}profmark ${QUIET_SUBDIR1} dev
-@@ -110,7 +106,6 @@ tests:
+@@ -110,7 +106,6 @@
#
check:
${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} tests
@@ -71,7 +71,7 @@ Description: Use Debian packaged libdivsufsort
${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} tests
${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} check
${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} check
-@@ -148,7 +143,6 @@ clean:
+@@ -148,7 +143,6 @@
${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} clean
${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} clean
${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} clean
@@ -79,7 +79,7 @@ Description: Use Debian packaged libdivsufsort
${QUIET}-rm -f *.o *~ Makefile.bak core TAGS gmon.out
ifndef V
@echo ' ' CLEAN hmmer
-@@ -162,7 +156,6 @@ distclean:
+@@ -162,7 +156,6 @@
${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} distclean
${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} distclean
${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} distclean
@@ -87,3 +87,18 @@ Description: Use Debian packaged libdivsufsort
${QUIET}-rm config.log config.status
${QUIET}-rm -rf autom4te.cache
${QUIET}-rm -f *.o *~ Makefile.bak core TAGS gmon.out
+--- hmmer.orig/src/Makefile.in
++++ hmmer/src/Makefile.in
+@@ -36,11 +36,9 @@
+
+ IMPLDIR = impl_ at IMPL_CHOICE@
+ ESLDIR = @HMMER_ESLDIR@
+-SADIR = @HMMER_SADIR@
+
+-MYLIBDIRS = -L../${ESLDIR} -L./${IMPLDIR} -L../${SADIR} -L.
++MYLIBDIRS = -L../${ESLDIR} -L./${IMPLDIR} -L.
+ MYINCDIRS = -I../${ESLDIR} \
+- -I../${SADIR} \
+ -I${top_srcdir}/easel \
+ -I. \
+ -I${srcdir}
=====================================
debian/patches/verbose-easel
=====================================
@@ -0,0 +1,181 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: Allow the easel Makefile to be verbosely run from the hmmer Makefile
+--- hmmer.orig/Makefile.in
++++ hmmer/Makefile.in
+@@ -67,16 +67,16 @@
+
+ # beautification magic stolen from git
+ #
+-QUIET_SUBDIR0 = +${MAKE} -C #space separator after -c
++QUIET_SUBDIR0 = $(MAKE) -C #space separator after -c
+ QUIET_SUBDIR1 =
+ ifndef V
+ QUIET = @
+ QUIET_CC = @echo ' ' CC $@;
+ QUIET_GEN = @echo ' ' GEN $@;
+ QUIET_AR = @echo ' ' AR $@;
+- QUIET_SUBDIR0 = + at subdir=
++ QUIET_SUBDIR0 = @subdir=
+ QUIET_SUBDIR1 = ; echo ' ' SUBDIR $$subdir; \
+- ${MAKE} -s -C $$subdir
++ $(MAKE) -s -C $$subdir
+ endif
+
+ .PHONY: all dev check pdf install uninstall clean distclean TAGS
+@@ -85,35 +85,35 @@
+ # (Excludes test programs.)
+ #
+ all:
+- ${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} all
+- ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} all
+- ${QUIET_SUBDIR0}profmark ${QUIET_SUBDIR1} all
++ +${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} all
++ +${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} all
++ +${QUIET_SUBDIR0}profmark ${QUIET_SUBDIR1} all
+
+ # dev: compile all executables, including drivers.
+ #
+ dev:
+- ${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} dev
+- ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} dev
+- ${QUIET_SUBDIR0}profmark ${QUIET_SUBDIR1} dev
++ +${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} dev
++ +${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} dev
++ +${QUIET_SUBDIR0}profmark ${QUIET_SUBDIR1} dev
+
+ # tests: compile all test drivers for 'make check'
+ #
+ tests:
+- ${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} tests
+- ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} tests
++ +${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} tests
++ +${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} tests
+
+ # check: Run test suites.
+ #
+ check:
+- ${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} tests
+- ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} tests
+- ${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} check
+- ${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} check
++ +${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} tests
++ +${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} tests
++ +${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} check
++ +${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} check
+
+ # pdf: compile the User Guides.
+ #
+ pdf:
+- ${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} pdf
++ +${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} pdf
+
+ # install: binaries in ${bindir}/, man pages in ${man1dir}/
+ # Creates these directories if they don't exist.
+@@ -126,8 +126,8 @@
+ install:
+ ${INSTALL} -d ${DESTDIR}${bindir}
+ ${INSTALL} -d ${DESTDIR}${man1dir}
+- ${MAKE} -C src install
+- ${MAKE} -C documentation install
++ +$(MAKE) -C src install
++ +$(MAKE) -C documentation install
+
+ # uninstall: reverses the steps of "make install".
+ #
+@@ -138,11 +138,11 @@
+ # "make clean" removes almost everything except configuration files.
+ #
+ clean:
+- ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} clean
+- ${QUIET_SUBDIR0}profmark ${QUIET_SUBDIR1} clean
+- ${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} clean
+- ${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} clean
+- ${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} clean
++ +${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} clean
++ +${QUIET_SUBDIR0}profmark ${QUIET_SUBDIR1} clean
++ +${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} clean
++ +${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} clean
++ +${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} clean
+ ${QUIET}-rm -f *.o *~ Makefile.bak core TAGS gmon.out
+ ifndef V
+ @echo ' ' CLEAN hmmer
+--- hmmer.orig/easel/Makefile.in
++++ hmmer/easel/Makefile.in
+@@ -80,7 +80,7 @@
+
+ # beautification magic, stolen from git
+ #
+-QUIET_SUBDIR0 = +${MAKE} -C #space separator after -c
++QUIET_SUBDIR0 = $(MAKE) -C #space separator after -c
+ QUIET_SUBDIR1 =
+ ifndef V
+ QUIET = @
+@@ -89,7 +89,7 @@
+ QUIET_AR = @echo ' ' AR $@;
+ QUIET_SUBDIR0 = + at subdir=
+ QUIET_SUBDIR1 = ; echo ' ' SUBDIR $$subdir; \
+- ${MAKE} -s -C $$subdir
++ $(MAKE) -s -C $$subdir
+ endif
+
+
+@@ -495,24 +495,24 @@
+ .FORCE:
+
+ all: libeasel.a .FORCE
+- ${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} all
++ +${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} all
+
+ dev: libeasel.a ${ALL_UTESTS} ${BENCHMARKS} ${EXPERIMENTS} ${EXAMPLES} .FORCE
+- ${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} dev
++ +${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} dev
+
+ tests: ${ALL_UTESTS}
+- ${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} tests
++ +${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} tests
+
+ check: ${ALL_UTESTS} .FORCE
+- ${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} check
+- ${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} check
++ +${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} check
++ +${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} check
+
+ # `make dcheck`: run developer testsuite, save output in testsuite/dcheck.report
+ dcheck:
+ ${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} dcheck
+
+ pdf:
+- ${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} pdf
++ +${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} pdf
+
+ libeasel.a: ${ALL_OBJS}
+ ${QUIET_AR}${AR} -r libeasel.a $(ALL_OBJS) > /dev/null 2>&1
+@@ -599,7 +599,7 @@
+ install:
+ ${INSTALL} -d ${DESTDIR}${bindir}
+ ${INSTALL} -d ${DESTDIR}${man1dir}
+- ${MAKE} -C miniapps install
++ +$(MAKE) -C miniapps install
+
+ uninstall:
+ ${MAKE} -C miniapps uninstall
+--- hmmer.orig/src/Makefile.in
++++ hmmer/src/Makefile.in
+@@ -217,7 +217,7 @@
+ p7_spensemble_example
+
+ # beautification magic stolen from git
+-QUIET_SUBDIR0 = +${MAKE} -C #space separator after -c
++QUIET_SUBDIR0 = $(MAKE) -C #space separator after -c
+ QUIET_SUBDIR1 =
+ ifndef V
+ QUIET_CC = @echo ' ' CC $@;
+@@ -225,7 +225,7 @@
+ QUIET_AR = @echo ' ' AR $@;
+ QUIET_SUBDIR0 = + at subdir=
+ QUIET_SUBDIR1 = ; echo ' ' SUBDIR $$subdir; \
+- ${MAKE} -s -C $$subdir
++ $(MAKE) -s -C $$subdir
+ endif
+
+ .PHONY: all dev tests check install uninstall distclean clean TAGS
=====================================
debian/rules
=====================================
@@ -8,8 +8,8 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
include /usr/share/dpkg/default.mk
ifeq (,$(filter nolto,$(DEB_BUILD_OPTIONS)))
-export LDFLAGS=-flto
-export CFLAGS=-flto
+export DEB_LDFLAGS_MAINT_APPEND+=-flto
+export DEB_CFLAGS_MAINT_APPEND+=-flto
endif
sampledir:=$(CURDIR)/debian/$(DEB_SOURCE)-examples/usr/share/doc/$(DEB_SOURCE)/examples
@@ -33,13 +33,16 @@ override_dh_autoreconf:
AUTOHEADER=true dh_autoreconf
override_dh_auto_configure:
- dh_auto_configure -- $(DEB_CONFIGURE_EXTRA_FLAGS)
+ CPPFLAGS="$(shell dpkg-buildflags --get CPPFLAGS)" dh_auto_configure -- $(DEB_CONFIGURE_EXTRA_FLAGS)
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- make check
+ export V=VERBOSE ; make check -j$(shell nproc)
endif
+override_dh_auto_build:
+ export V=VERBOSE ; dh_auto_build
+
override_dh_auto_clean:
dh_auto_clean
rm -f testsuite/esltmp*
=====================================
debian/tests/run-unit-test
=====================================
@@ -16,12 +16,12 @@ find . -name "*.gz" -exec gunzip \{\} \;
chmod -R +x .
echo easel testsuite
-$AUTOPKGTEST_TMP/easel/devkit/sqc 2 ./easel/testsuite/testsuite.sqc ./easel ./easel/ \
+$AUTOPKGTEST_TMP/easel/devkit/sqc -v 2 ./easel/testsuite/testsuite.sqc ./easel ./easel/ \
| tee $AUTOPKGTEST_TMP/easel.log
echo hmmer testsuite
find /usr/bin -name "*hmm*" -exec ln -s \{\} src \;
-./testsuite/../easel/devkit/sqc 2 ./testsuite/testsuite.sqc . ./testsuite/.. \
+./testsuite/../easel/devkit/sqc -v 2 ./testsuite/testsuite.sqc . ./testsuite/.. \
| tee $AUTOPKGTEST_TMP/hmmer.log
echo $top_builddir
View it on GitLab: https://salsa.debian.org/med-team/hmmer/compare/1b4b22b2c783cea03e81564ab63a2a0d75a55dd5...b4b796332b20c3f66c2db136d9c4c738d45852a4
--
View it on GitLab: https://salsa.debian.org/med-team/hmmer/compare/1b4b22b2c783cea03e81564ab63a2a0d75a55dd5...b4b796332b20c3f66c2db136d9c4c738d45852a4
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