[med-svn] [libseqlib] 01/01: Workaround for using test files from htslib - may be the needed files should be moved from htslib-test to libhts-dev package
Andreas Tille
tille at debian.org
Fri Feb 3 14:23:37 UTC 2017
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tille pushed a commit to branch master
in repository libseqlib.
commit c850b8c533fdc0c9d10948378cc14ab1536ec50d
Author: Andreas Tille <tille at debian.org>
Date: Fri Feb 3 15:22:17 2017 +0100
Workaround for using test files from htslib - may be the needed files should be moved from htslib-test to libhts-dev package
---
debian/changelog | 25 ++++++++++++-------------
debian/control | 3 ++-
debian/patches/fml_include_path.patch | 2 +-
debian/rules | 22 +++++++---------------
4 files changed, 22 insertions(+), 30 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 09f6d16..89ddcf9 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,18 +2,17 @@ libseqlib (1.1.1-1) UNRELEASED; urgency=medium
* Initial release (Closes: #???)
TODO:
- g++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/build/libseqlib-1.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqlib_a-SeqPlot.o `test -f 'SeqPlot.cpp' || echo './'`SeqPlot.cpp
- In file included from ../SeqLib/UnalignedSequence.h:5:0,
- from ../SeqLib/BamRecord.h:23,
- from ../SeqLib/BFC.h:8,
- from BFC.cpp:33:
- /usr/include/bwa/bwa.h:33:3: error: conflicting declaration ‘typedef struct bseq1_t bseq1_t’
- } bseq1_t;
- ^~~~~~~
- In file included from ../SeqLib/BFC.h:5:0,
- from BFC.cpp:33:
- /usr/include/fml.h:11:3: note: previous declaration as ‘typedef struct bseq1_t bseq1_t’
- } bseq1_t;
- ^~~~~~~
+g++ -DHAVE_CONFIG_H -I. -I.. -I../ -I/usr/include/fml -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/build/libseqlib-1.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqlib_a-RefGenome.o `test -f 'RefGenome.cpp' || echo './'`RefGenome.cpp
+g++ -DHAVE_CONFIG_H -I. -I.. -I../ -I/usr/include/fml -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/build/libseqlib-1.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqlib_a-BamWriter.o `test -f 'BamWriter.cpp' || echo './'`BamWriter.cpp
+In file included from ../SeqLib/BamWalker.h:15:0,
+ from BamWriter.cpp:1:
+../htslib/cram/cram.h:45:32: fatal error: cram/cram_samtools.h: No such file or directory
+ #include "cram/cram_samtools.h"
+ ^
+compilation terminated.
+Makefile:518: recipe for target 'libseqlib_a-BamWriter.o' failed
+make[4]: *** [libseqlib_a-BamWriter.o] Error 1
+make[4]: *** Waiting for unfinished jobs....
+
-- Andreas Tille <tille at debian.org> Fri, 27 Jan 2017 13:18:48 +0100
diff --git a/debian/control b/debian/control
index faf74f7..1791c2c 100644
--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,8 @@ Build-Depends: debhelper (>= 10),
libcurl4-openssl-dev | libcurl4-dev,
zlib1g-dev,
libfml-dev (>= 0.1-3),
- libbwa-dev (>= 0.7.15-3)
+ libbwa-dev (>= 0.7.15-3),
+ htslib-test
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libseqlib.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/libseqlib.git
diff --git a/debian/patches/fml_include_path.patch b/debian/patches/fml_include_path.patch
index a4d3e65..fe0a500 100644
--- a/debian/patches/fml_include_path.patch
+++ b/debian/patches/fml_include_path.patch
@@ -27,7 +27,7 @@ Description: Make sure header files will be found in /usr/include/fml
noinst_LIBRARIES = libseqlib.a
-libseqlib_a_CPPFLAGS = -I../ -I../htslib -Wno-sign-compare
-+libseqlib_a_CPPFLAGS = -I../ -I/usr/include/fml -Wno-sign-compare
++libseqlib_a_CPPFLAGS = -I../ -I../htslib -I/usr/include/fml -Wno-sign-compare
libseqlib_a_SOURCES = FastqReader.cpp BFC.cpp ReadFilter.cpp SeqPlot.cpp jsoncpp.cpp ssw_cpp.cpp ssw.c \
GenomicRegion.cpp RefGenome.cpp BamWriter.cpp BamReader.cpp \
diff --git a/debian/rules b/debian/rules
index 1ef14d9..e884011 100755
--- a/debian/rules
+++ b/debian/rules
@@ -3,24 +3,16 @@
# DH_VERBOSE := 1
export LC_ALL=C.UTF-8
-# some helpful variables - uncomment them if needed
-# shamelessly stolen from http://jmtd.net/log/awk/
-#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
-#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
-#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
-#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
-#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
-#GIT_TAG := $(subst ~,_,$(VERSION))
-
-# alternatively to manually set those variables, you can
-# include /usr/share/dpkg/default.mk
-# and use what is set there.
-
# for hardening you might like to uncomment this:
# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
%:
dh $@
-#get-orig-source:
-# . debian/get-orig-source
+override_dh_auto_build:
+ # FIXME
+ # upstream is using code from htslib-test which is made
+ # available via this hackish link. The proper solution
+ # would surely be to move cram/cram.h to libhts-dev
+ ln -s /usr/share/htslib-test/cram/ htslib
+ dh_auto_build
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libseqlib.git
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