Your message dated Fri, 26 Jul 2019 21:14:04 +0000
with message-id <[email protected]>
and subject line Bug#933024: fixed in crac 2.5.2+dfsg-2
has caused the Debian Bug report #933024,
regarding crac FTCBFS: uses the build architecture pkg-config
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
933024: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=933024
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: crac
Version: 2.5.2+dfsg-1
Tags: patch upstream
User: [email protected]
Usertags: ftcbfs
crac fails to cross build from source, because it uses the build
architecture pkg-config in its Makefile.am files. Doing so is an
anti-pattern. You should never call pkg-config from a Makefile.am.
Instead such checks should be performed at configure time. The attached
patch implements that and makes crac cross buildable. Please consider
applying it.
Helmut
--- crac-2.5.2+dfsg.orig/configure.ac
+++ crac-2.5.2+dfsg/configure.ac
@@ -282,6 +282,7 @@
[with_libProgressBar_prefix=""])
dnl Check if we need included ProgressBar library.
+PKG_CHECK_MODULES([PROGRESSBAR],[libProgressBar])
PB_OK=0
AS_IF([test "x$with_included_ProgressBar" == "xcheck"],
[AS_IF([test "x$with_libProgressBar_prefix" != "x"],
@@ -315,6 +316,7 @@
AC_CHECK_LIB([hts], [hts_hopen], ,
[AC_MSG_ERROR([htslib not found, see http://www.htslib.org/])])
+PKG_CHECK_MODULES([GKARRAYS],[libGkArrays])
GK_OK=1
AS_IF([test "x$with_included_GkArrays" != "xyes"],
[AC_CHECK_LIB([GkArrays],
--- crac-2.5.2+dfsg.orig/src/Makefile.am
+++ crac-2.5.2+dfsg/src/Makefile.am
@@ -149,11 +149,11 @@
endif
if INCLUDED_GKARRAYS
- AM_LDFLAGS += `pkg-config --libs libGkArrays`
- AM_CPPFLAGS += `pkg-config --cflags libGkArrays`
+ AM_LDFLAGS += $(GKARRAYS_LIBS)
+ AM_CPPFLAGS += $(GKARRAYS_CFLAGS)
if INCLUDED_PROGRESSBAR
- AM_LDFLAGS += `pkg-config --libs libProgressBar`
- AM_CPPFLAGS += `pkg-config --cflags libProgressBar`
+ AM_LDFLAGS += $(PROGRESSBAR_LIBS)
+ AM_CPPFLAGS += $(PROGRESSBAR_CFLAGS)
endif
endif
--- crac-2.5.2+dfsg.orig/src/libReadsInfo/Makefile.am
+++ crac-2.5.2+dfsg/src/libReadsInfo/Makefile.am
@@ -124,7 +124,7 @@
libReadsInfo_a_CPPFLAGS = -I@abs_top_srcdir@ -I@abs_top_srcdir@/src -I@abs_top_srcdir@/src/libSSA
if INCLUDED_GKARRAYS
- libReadsInfo_a_CPPFLAGS += `pkg-config --cflags libGkArrays`
+ libReadsInfo_a_CPPFLAGS += $(GKARRAYS_CFLAGS)
endif
--- crac-2.5.2+dfsg.orig/src/libSSA/Makefile.am
+++ crac-2.5.2+dfsg/src/libSSA/Makefile.am
@@ -101,7 +101,7 @@
bin_PROGRAMS = crac-index
crac_index_SOURCES = cracIndex.cpp cracIndex.h
-AM_CPPFLAGS = -I@abs_top_srcdir@ -I@abs_srcdir@/karkkainen_bwt `pkg-config --cflags libGkArrays`
+AM_CPPFLAGS = -I@abs_top_srcdir@ -I@abs_srcdir@/karkkainen_bwt $(GKARRAYS_CFLAGS)
AM_LDFLAGS = -lm -lpthread -lSSA -L@abs_builddir@/
LDADD = libSSA.a
--- End Message ---
--- Begin Message ---
Source: crac
Source-Version: 2.5.2+dfsg-2
We believe that the bug you reported is fixed in the latest version of
crac, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated crac package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Fri, 26 Jul 2019 22:40:52 +0200
Source: crac
Binary: crac
Architecture: source
Version: 2.5.2+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
crac - integrated RNA-Seq read analysis
Closes: 933024
Changes:
crac (2.5.2+dfsg-2) unstable; urgency=medium
.
[ Helmut Grohne ]
* Do not use pkg-config in Makefile.am to enable cross building
Closes: #933024
.
[ Andreas Tille ]
* debhelper-compat 12
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