[med-svn] [Git][med-team/hmmer][master] 11 commits: New upstream version 3.3+dfsg
Michael R. Crusoe
gitlab at salsa.debian.org
Wed Dec 4 12:41:04 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / hmmer
Commits:
eceb62f2 by Steffen Moeller at 2019-11-22T19:04:10Z
New upstream version 3.3+dfsg
- - - - -
1dbd7425 by Michael R. Crusoe at 2019-12-04T09:21:57Z
fix FTBFS: restore config.guess and config.sub
- - - - -
8c2d6d57 by Michael R. Crusoe at 2019-12-04T09:27:52Z
New upstream version 3.3+dfsg2
- - - - -
40c52b67 by Michael R. Crusoe at 2019-12-04T09:28:12Z
Update upstream source from tag 'upstream/3.3+dfsg2'
Update to upstream version '3.3+dfsg2'
with Debian dir 98b0cc79e087254b79d4066975ee776bf4222c96
- - - - -
865ad796 by Michael R. Crusoe at 2019-12-04T09:28:52Z
readded config.{sub,guess} to the orig tarball
- - - - -
c3b3a02c by Michael R. Crusoe at 2019-12-04T09:32:30Z
python3 build-dep so that the checks run
- - - - -
a3d2b8cb by Michael R. Crusoe at 2019-12-04T09:51:57Z
enable parallel sub builds
- - - - -
f74f02fc by Michael R. Crusoe at 2019-12-04T10:16:38Z
autopkgtest: copy and dereference symlinks
- - - - -
f823a0a2 by Michael R. Crusoe at 2019-12-04T10:33:14Z
better hardening
- - - - -
dbf9e8e9 by Michael R. Crusoe at 2019-12-04T10:52:42Z
fix a typo
- - - - -
4b937bfe by Michael R. Crusoe at 2019-12-04T10:52:47Z
release to unstable
- - - - -
11 changed files:
- − configure
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/hardening
- debian/patches/series
- + debian/patches/spelling
- + debian/patches/sub_make_parallel
- debian/rules
- + debian/source/options
- debian/tests/run-unit-test
Changes:
=====================================
configure deleted
=====================================
The diff for this file was not included because it is too large.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+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 at 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 at 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 at genetics.wustl.edu>
=====================================
debian/patches/hardening
=====================================
@@ -1,10 +1,8 @@
Author: Michael R. Crusoe <michael.crusoe at 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 at 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
=====================================
@@ -0,0 +1,13 @@
+From: Michael R. Crusoe <michael.crusoe at 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
=====================================
@@ -0,0 +1,50 @@
+From: Michael R. Crusoe <michael.crusoe at 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 $? > /dev/null 2>&1
=====================================
debian/rules
=====================================
@@ -49,7 +49,7 @@ override_dh_auto_clean:
rm -f testsuite/esltmp*
rm -f easel/testsuite/esltmp*
rm -f tutorial/MADE1.hmm.h3?
- rm -f config.log config.status configure config.guess config.sub
+ rm -f config.log config.status configure
find . -name Makefile -delete
override_dh_compress:
=====================================
debian/source/options
=====================================
@@ -0,0 +1,2 @@
+# Do not generate diff for changes in config.(sub|guess)
+extend-diff-ignore = "(^|/)config.(sub|guess)$"
=====================================
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 .
View it on GitLab: https://salsa.debian.org/med-team/hmmer/compare/aefa773b74e003568c7d21f78e772868a67cc0ee...4b937bfea8c045510ddfa7c625d9bc058edd5b8e
--
View it on GitLab: https://salsa.debian.org/med-team/hmmer/compare/aefa773b74e003568c7d21f78e772868a67cc0ee...4b937bfea8c045510ddfa7c625d9bc058edd5b8e
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