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debian/changelog
View file @ b4b79633
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@gmail.com> Tue, 24 Sep 2019 18:13:19 +0200
hmmer (3.2.1+dfsg-2) unstable; urgency=medium
[ Jelmer Vernooij ]
......
debian/control
View file @ b4b79633
......@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
Uploaders: Andreas Tille <tille@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 (>= ${source:Version})
......
debian/hmmer.install
View file @ b4b79633
usr/bin
usr/share/man
src/hmmc2 /usr/bin/
debian/patches/hardening 0 → 100644
View file @ b4b79633
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Descriptions: Don't stomp on Debian's CFLAGS
--- hmmer.orig/configure.ac
+++ hmmer/configure.ac
@@ -78,12 +78,6 @@
AC_INIT(HMMER, 3.2.1, sean@eddylab.org, hmmer)
AC_MSG_NOTICE([Configuring HMMER3 for your system.])
-# remember if the user is overriding CFLAGS
-esl_cflags_env_set=no
-if test x"$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
View file @ b4b79633
fix_manpage_extension.patch
use_debian_packaged_libdivsufsort.patch
verbose-easel
hardening
spelling
debian/patches/spelling 0 → 100644
View file @ b4b79633
From: Michael R. Crusoe <michael.crusoe@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
View file @ b4b79633
......@@ -2,9 +2,9 @@ Author: Andreas Tille <tille@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
${QUIET}-rm -f *.o *~ Makefile.bak core TAGS gmon.out
--- hmmer.orig/src/Makefile.in
+++ hmmer/src/Makefile.in
@@ -36,11 +36,9 @@
IMPLDIR = impl_@IMPL_CHOICE@
ESLDIR = @HMMER_ESLDIR@
-SADIR = @HMMER_SADIR@
-MYLIBDIRS = -L../${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 → 100644
View file @ b4b79633
From: Michael R. Crusoe <michael.crusoe@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 = +@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 = +@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 = +@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
View file @ b4b79633
......@@ -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
View file @ b4b79633
......@@ -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
......