[med-svn] [Git][med-team/infernal][master] 3 commits: Enable a verbose build log
Michael R. Crusoe
gitlab at salsa.debian.org
Sat Nov 30 12:32:55 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / infernal
Commits:
c763413a by Michael R. Crusoe at 2019-11-30T11:45:27Z
Enable a verbose build log
- - - - -
f80d3b0e by Michael R. Crusoe at 2019-11-30T11:47:10Z
infernal-doc: mark Multi-Arch: foreign
- - - - -
aca65ff9 by Michael R. Crusoe at 2019-11-30T12:31:00Z
CPPFLAGS for easel
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/hardening
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -6,6 +6,9 @@ infernal (1.1.3-2) UNRELEASED; urgency=medium
* Remove trailing whitespace in debian/changelog
* Trim trailing whitespace.
* Set upstream metadata fields: Bug-Submit.
+ * Enable a verbose build log
+ * infernal-doc: mark Multi-Arch: foreign (thanks Multiarch hinter!)
+ * debian/patches/hardening: added CPPFLAGS to easel, rmark, and hmmer/profmark
-- Michael R. Crusoe <michael.crusoe at gmail.com> Sat, 30 Nov 2019 11:00:30 +0100
=====================================
debian/control
=====================================
@@ -31,6 +31,7 @@ Description: inference of RNA secondary structural alignments
Package: infernal-doc
Architecture: all
Section: doc
+Multi-Arch: foreign
Depends: ${shlibs:Depends},
${misc:Depends}
Description: inference of RNA secondary structural alignments – documentation
=====================================
debian/patches/hardening
=====================================
@@ -0,0 +1,118 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: insert CPPFLAGS in easel
+--- infernal.orig/easel/Makefile.in
++++ infernal/easel/Makefile.in
+@@ -549,7 +549,7 @@
+ @${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} ${CPPFLAGS} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${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} $${DFILE} -leasel -lm ${LIBS}" ;\
++ then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${CPPFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${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} $${DFILE} -leasel -lm ${LIBS}
++ ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${CPPFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${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}
+
+
+
+--- infernal.orig/easel/miniapps/Makefile.in
++++ infernal/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} ${LDFLAGS} ${CPPFLAGS} -L.. -I. -I.. -I${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} ${LDFLAGS} ${CPPFLAGS} -L.. -I. -I.. -I${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} ${CPPFLAGS} -I. -I.. -I${srcdir} -I${srcdir}/.. ${CFLAGS} ${PTHREAD_CFLAGS} ${SIMD_CFLAGS} ${DEFS} -c $<
+
+ install: ${PROGS}
+ ${INSTALL} -m 0755 easel ${DESTDIR}${bindir}/
+--- infernal.orig/hmmer/profmark/Makefile.in
++++ infernal/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} ${CPPFLAGS} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L../${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} ${CPPFLAGS} ${ESLINC} ${SRCINC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} -o $@ -c $<
+
+ clean:
+ -rm -f *.o *~ ${PROGS}
+--- infernal.orig/rmark/Makefile.in
++++ infernal/rmark/Makefile.in
+@@ -43,12 +43,12 @@
+ dev: ${PROGS}
+
+ ${PROGS}: % : %.o ../${HMMERDIR}/src/libhmmer.a ../${ESLDIR}/libeasel.a
+- ${QUIET_GEN}${CC} ${CFLAGS} ${DEFS} ${LDFLAGS} -L../${HMMERDIR}/src -L../${ESLDIR} -L${SRCDIR} -o $@ $@.o ${LIBS}
++ ${QUIET_GEN}${CC} ${CPPFLAGS} ${CFLAGS} ${DEFS} ${LDFLAGS} -L../${HMMERDIR}/src -L../${ESLDIR} -L${SRCDIR} -o $@ $@.o ${LIBS}
+
+ ${PROGOBJS}: ../${HMMERDIR}/src/hmmer.h ../${HMMERDIR}/src/p7_config.h ../src/infernal.h ../src/config.h
+
+ .c.o:
+- ${QUIET_CC}${CC} ${ESLINC} ${SRCINC} ${CFLAGS} ${DEFS} -o $@ -c $<
++ ${QUIET_CC}${CC} ${CPPFLAGS} ${ESLINC} ${SRCINC} ${CFLAGS} ${DEFS} -o $@ -c $<
+
+ distclean: clean
+ -rm -f Makefile
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
#format_security.patch
#autoreconf.patch
spelling.patch
+hardening
=====================================
debian/rules
=====================================
@@ -20,8 +20,11 @@ override_dh_auto_clean:
override_dh_compress :
dh_compress -X.pdf
+override_dh_auto_build:
+ dh_auto_build -- V=1
+
override_dh_auto_install:
- $(MAKE) install prefix=$(CURDIR)/debian/tmp
+ $(MAKE) install -j$(shell nproc) AM_UPDATE_INFO_DIR=no V=1 prefix=$(CURDIR)/debian/tmp
override_dh_install:
dh_install
View it on GitLab: https://salsa.debian.org/med-team/infernal/compare/21c20708447abd0b24921c624af953f4983e555a...aca65ff937b1cd5d961ba8f56e787444525ad5b4
--
View it on GitLab: https://salsa.debian.org/med-team/infernal/compare/21c20708447abd0b24921c624af953f4983e555a...aca65ff937b1cd5d961ba8f56e787444525ad5b4
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