Bug#1093752: coot: fix ftbfs on riscv64 and mips64el

[Bo YU]

Hi,

On Wed, Jan 22, 2025 at 09:59:11AM +0200, Andrius Merkys wrote:
>Hi,
>
>On 2025-01-22 09:51, Bo YU wrote:
>>coot has FTBFS issues on riscv64 and mips64el due to atomic issue:
>>
>>```
>>...
>>/usr/bin/ld: mini-rsr.o: in function `bool
>>boost::lockfree::queue<std::function<void
>>(int)>*>::pop<std::function<void
>>(int)>*>(std::function<void (int)>*&)':
>>/usr/include/boost/lockfree/queue.hpp:448:(.text._ZN5boost8lockfree5queueIPSt8functionIFviEEJEE3popIS5_EEbRT_[_ZN5boost8lockfree5queueIPSt8functionIFviEEJEE3popIS5_EEbRT_]+0xfa): undefined reference to `__atomic_compare_exchange_16'
>>collect2: error: ld returned 1 exit status
>>...
>>```
>>
>>Seehttps://buildd.debian.org/status/fetch.php?pkg=coot&arch=mips64el&ver=1.1.09%2Bdfsg-3&stamp=1736993525&raw=0
>>andhttps://buildd.debian.org/status/fetch.php?pkg=coot&arch=riscv64&ver=1.1.09%2Bdfsg-3&stamp=1737361754&raw=0
>>
>>The workaround is to link libatomic explicitly and I have tested it on
>>riscv64 but no test on mips64el.
>
>Thanks a lot for giving this a look. Am I right that I should just add 
>-latomic to LDFLAGS? Can I do this for all the architectures, or just 
>is this riscv64 and mips64el specific?

Oops, sorry I forget the patch in the previous email. Please find it at
attachment.

Thanks!
>
>Best,
>Andrius

-- 
Regards,
--
   Bo YU

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diff -Nru coot-1.1.09+dfsg/debian/changelog coot-1.1.09+dfsg/debian/changelog
--- coot-1.1.09+dfsg/debian/changelog	2025-01-14 14:15:52.000000000 +0000
+++ coot-1.1.09+dfsg/debian/changelog	2025-01-21 01:14:15.000000000 +0000
@@ -1,3 +1,11 @@
+coot (1.1.09+dfsg-3.1) UNRELEASED; urgency=medium
+
+  * Non-maintainer upload.
+  * Fix FTBFS issues with libatomic on riscv64 and mips64el. 
+    (Closes: #-1)
+
+ -- Bo YU <tsu.yubo at gmail.com>  Tue, 21 Jan 2025 01:14:15 +0000
+
 coot (1.1.09+dfsg-3) unstable; urgency=medium
 
   * Backport upstream's commit fixing Python 3.13 compatibility.
diff -Nru coot-1.1.09+dfsg/debian/rules coot-1.1.09+dfsg/debian/rules
--- coot-1.1.09+dfsg/debian/rules	2025-01-14 14:13:40.000000000 +0000
+++ coot-1.1.09+dfsg/debian/rules	2025-01-21 01:14:15.000000000 +0000
@@ -14,6 +14,11 @@
 	CONFIGURATION_OPTIONS += --with-sound
 endif
 
+# Link with libatomic on riscv64 and mips64el
+ifneq (,$(filter $(DEB_HOST_ARCH),riscv64 mips64el))
+	export DEB_LDFLAGS_MAINT_APPEND += -Wl,--no-as-needed -latomic -Wl,--as-needed
+endif
+
 override_dh_auto_configure:
 	dh_auto_configure -- $(CONFIGURATION_OPTIONS)
 	dh_auto_configure --buildsystem cmake
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