debian/changelog

+hmmer (3.3+dfsg2-1) unstable; urgency=medium
+
+  * Team upload.
+  * Restore config.guess and config.sub so that dh_update_autotools_config can
+    update them. This fixes the FTBFS.
+  * Added python3 build-dep so that the checks run (and the build doesn't
+    fail)
+  * debian/patches/spelling: fix a typo
+  * debian/patches/hardenng: finished CPPFLAGS propogation
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 04 Dec 2019 11:26:08 +0100
+
 hmmer (3.3+dfsg-1) unstable; urgency=medium
 
   * Team upload.

debian/control

@@ -4,7 +4,8 @@ Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 12),
-               libdivsufsort-dev
+               libdivsufsort-dev,
+               python3
 Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/hmmer
 Vcs-Git: https://salsa.debian.org/med-team/hmmer.git

debian/copyright

@@ -5,8 +5,6 @@ Source: http://hmmer.org/download.html
 Files-Excluded: */libdivsufsort
                 */.gitignore
                 configure
-                config.guess
-                config.sub
 
 Files: *
 Copyright: 1992-2010 Sean R. Eddy <eddy@genetics.wustl.edu>

debian/patches/hardening

 Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 Descriptions: Don't stomp on Debian's CFLAGS
-Index: hmmer/configure.ac
-===================================================================
 --- hmmer.orig/configure.ac
 +++ hmmer/configure.ac
-@@ -78,12 +78,6 @@ m4_include([easel/m4/esl_pic_flags.m4])
+@@ -78,12 +78,6 @@
  AC_INIT(HMMER, 3.3, sean@eddylab.org, hmmer)
  AC_MSG_NOTICE([Configuring HMMER3 for your system.])
  
@@ -17,7 +15,7 @@ Index: hmmer/configure.ac
  ################################################################
  # 3. Info on the package
  ################################################################
-@@ -234,21 +228,15 @@ AC_PROG_LN_S
+@@ -234,21 +228,15 @@
  #  --enable-gcov, --enable-gprof, and --enable-debugging are mutually exclusive.
  #
  if test "$enable_gcov" = "yes"; then
@@ -44,3 +42,120 @@ Index: hmmer/configure.ac
  fi
  
  
+--- hmmer.orig/easel/Makefile.in
++++ hmmer/easel/Makefile.in
+@@ -549,7 +549,7 @@
+ 	@${RANLIB} libeasel.a
+ 
+ ${ALL_OBJS}: %.o : %.c ${HDRS} esl_config.h
+-	${QUIET_CC}${CC} -I. -I${srcdir} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} -c $<
++	${QUIET_CC}${CC} -I. -I${srcdir} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${CPPFLAGS} ${DEFS} -c $<
+ 
+ 
+ # Driver compilation:
+@@ -573,10 +573,10 @@
+ 	   else DFILE=${srcdir}/esl_$${BASENAME}.c ;\
+         fi;\
+ 	if test ${V} ;\
+-	   then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${UTEST_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
++	   then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
+ 	   else echo '    ' GEN $@ ;\
+ 	fi ;\
+-	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
++	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
+ 
+ ${ALL_BENCHMARKS}: libeasel.a
+ 	@BASENAME=`echo $@ | sed -e 's/_benchmark//'| sed -e 's/^esl_//'` ;\
+@@ -587,10 +587,10 @@
+ 	   else DFILE=${srcdir}/esl_$${BASENAME}.c ;\
+         fi;\
+ 	if test ${V} ;\
+-	   then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
++	   then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
+ 	   else echo '    ' GEN $@ ;\
+ 	fi ;\
+-	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
++	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
+ 
+ ${ALL_EXPERIMENTS}: libeasel.a
+ 	@BASENAME=`echo $@ | sed -e 's/_experiment//'| sed -e 's/^esl_//'` ;\
+@@ -601,10 +601,10 @@
+ 	   else DFILE=${srcdir}/esl_$${BASENAME}.c ;\
+         fi;\
+ 	if test ${V} ;\
+-	   then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
++	   then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
+ 	   else echo '    ' GEN $@ ;\
+ 	fi ;\
+-	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
++	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
+ 
+ ${ALL_EXAMPLES}: libeasel.a
+ 	@BASENAME=`echo $@ | sed -e 's/_example[0-9]*//'| sed -e 's/^esl_//'` ;\
+@@ -614,10 +614,10 @@
+            else DFILE=${srcdir}/esl_$${BASENAME}.c ;\
+         fi ;\
+ 	if test ${V}; \
+-	   then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
++	   then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
+ 	   else echo '    ' GEN $@ ;\
+ 	fi ;\
+-	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
++	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
+ 
+ 
+ 
+--- hmmer.orig/easel/miniapps/Makefile.in
++++ hmmer/easel/miniapps/Makefile.in
+@@ -94,13 +94,13 @@
+ check:  ${PROGS} easel
+ 
+ easel:  % : %.c ../libeasel.a ${SUBCMDOBJS}
+-	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${SUBCMDOBJS} ${LIBS}
++	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${SUBCMDOBJS} ${LIBS}
+ 
+ ${PROGS}: % : %.c ../libeasel.a 
+-	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${LIBS}
++	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${LIBS}
+ 
+ ${SUBCMDOBJS}: %.o : %.c ../libeasel.a
+-	${QUIET_CC}${CC} -I. -I.. -I${srcdir} -I${srcdir}/.. ${CFLAGS} ${PTHREAD_CFLAGS} ${SIMD_CFLAGS} ${DEFS} -c $<
++	${QUIET_CC}${CC} -I. -I.. -I${srcdir} -I${srcdir}/.. ${CFLAGS} ${PTHREAD_CFLAGS} ${SIMD_CFLAGS} ${CPPFLAGS} ${DEFS} -c $<
+ 
+ install: ${PROGS} 
+ 	${INSTALL} -m 0755 easel ${DESTDIR}${bindir}/
+--- hmmer.orig/profmark/Makefile.in
++++ hmmer/profmark/Makefile.in
+@@ -43,12 +43,12 @@
+ dev:    ${PROGS}
+ 
+ ${PROGS}: % : %.o ../${ESLDIR}/libeasel.a ../src/libhmmer.a 
+-	${QUIET_GEN}${CC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L../${ESLDIR} -L../src -o $@ $@.o ${LIBS}
++	${QUIET_GEN}${CC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -L../${ESLDIR} -L../src -o $@ $@.o ${LIBS}
+ 
+ ${PROGOBJS}: ../src/hmmer.h ../src/p7_config.h
+ 
+ .c.o: 
+-	${QUIET_CC}${CC} ${ESLINC} ${SRCINC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} -o $@ -c $<		
++	${QUIET_CC}${CC} ${ESLINC} ${SRCINC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${CPPFLAGS} ${DEFS} -o $@ -c $<		
+ 
+ clean:
+ 	-rm -f *.o *~ ${PROGS} 
+--- hmmer.orig/src/Makefile.in
++++ hmmer/src/Makefile.in
+@@ -270,13 +270,13 @@
+ ${AUXPROGOBJS}: ${HDRS} p7_config.h
+ 
+ ${PROGS} ${AUXPROGS}: % : %.o  libhmmer.a ../${ESLDIR}/libeasel.a 
+-	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${MPILIBS} ${LIBS}
++	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${MPILIBS} ${LIBS}
+ 
+ .c.o:
+ 	${QUIET_CC}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${CPPFLAGS} ${MYINCDIRS} -o $@ -c $<
+ 
+ ${ITESTS}: % : %.o libhmmer.a ${HDRS} p7_config.h
+-	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${MPILIBS} ${LIBS}
++	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${MPILIBS} ${LIBS}
+ 
+ ${UTESTS}: libhmmer.a  ${HDRS} p7_config.h
+ 	@BASENAME=`echo $@ | sed -e 's/_utest//' | sed -e 's/^p7_//'` ;\

debian/patches/series

@@ -3,3 +3,5 @@ use_debian_packaged_libdivsufsort.patch
 verbose-easel
 hardening
 skip_threads_check
+sub_make_parallel
+spelling

debian/patches/spelling

+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: fix a typo
+--- 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/sub_make_parallel

+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: Enable parallel sub-builds
+--- hmmer.orig/easel/Makefile.in
++++ hmmer/easel/Makefile.in
+@@ -523,18 +523,18 @@
+ .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
+ 
+ tests:  ${ALL_UTESTS} 
+-	${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} tests
++	+${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} tests
+ 
+ check:  ${ALL_UTESTS} .FORCE
+ 	@command -v python3 >/dev/null 2>&1 || { echo >&2 "python3 is required for 'make check', but is not in your PATH. Aborting."; exit 1; }
+-	${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:
+--- hmmer.orig/src/Makefile.in
++++ hmmer/src/Makefile.in
+@@ -246,16 +246,16 @@
+ all:   ${PROGS} ${AUXPROGS} .FORCE
+ 
+ dev:   ${PROGS} ${AUXPROGS} ${UTESTS} ${ITESTS} ${STATS} ${BENCHMARKS} ${EXAMPLES} .FORCE
+-	${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} dev
++	+${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} dev
+ 
+ tests: ${PROGS} ${AUXPROGS} ${UTESTS} ${ITESTS} .FORCE
+-	${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} tests
++	+${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} tests
+ 
+ check: ${PROGS} ${AUXPROGS} ${UTESTS} ${ITESTS} .FORCE
+-	${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} check
++	+${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} check
+ 
+ libhmmer.a: libhmmer-src.stamp .FORCE
+-	${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} libhmmer-impl.stamp
++	+${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} libhmmer-impl.stamp
+ 
+ libhmmer-src.stamp: ${OBJS}
+ 	${QUIET_AR}${AR} -r libhmmer.a $? > /dev/null 2>&1 

debian/rules

@@ -49,7 +49,7 @@ override_dh_auto_clean:
 	rm -f testsuite/esltmp*
 	rm -f easel/testsuite/esltmp*
 	rm -f tutorial/MADE1.hmm.h3?
-	rm -f config.log config.status configure config.guess config.sub
+	rm -f config.log config.status configure
 	find . -name Makefile -delete
 
 override_dh_compress:

debian/source/options

+# Do not generate diff for changes in config.(sub|guess)
+extend-diff-ignore = "(^|/)config.(sub|guess)$"

debian/tests/run-unit-test

@@ -7,11 +7,11 @@ if [ "$AUTOPKGTEST_TMP" = "" ] ; then
   AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
 fi
 
-cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
+cp -H -r --dereference --preserve=all /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
 
 cd $AUTOPKGTEST_TMP
 
-find . -name "*.gz" -exec gunzip \{\} \;
+find . -name "*.gz" -exec gunzip --force \{\} \;
 
 chmod -R +x .