Your message dated Mon, 31 Mar 2014 22:33:32 +0000
with message-id <[email protected]>
and subject line Bug#742843: fixed in altree 1.3.1-2
has caused the Debian Bug report #742843,
regarding altree: FTBFS with clang instead of gcc
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.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
742843: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=742843
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: altree
Severity: minor
Usertags: clang-ftbfs
User: [email protected]
Tag: patch
Hello,
Using the rebuild infrastructure, your package fails to build with clang
(instead of gcc).
Thanks,
Arthur
diff -Naur altree.orig/altree-1.3.1/debian/changelog altree/altree-1.3.1/debian/changelog
--- altree.orig/altree-1.3.1/debian/changelog 2013-12-13 16:38:21.000000000 -0600
+++ altree/altree-1.3.1/debian/changelog 2014-03-27 19:16:36.626359549 -0500
@@ -1,3 +1,13 @@
+altree (1.3.1-2) unstable; urgency=low
+
+ * Fix FTBFS with clang:
+ - Fixed 'Function definition is not allowed here' error
+ - In CUtils/c_sources/rhyper.c I removed the compute function
+ and I moved the code into the else if clause
+ - Variable i from compute is now x and n is now i
+
+ -- Arthur Marble <[email protected]> Thu, 27 Mar 2014 19:16:36 -0500
+
altree (1.3.1-1) unstable; urgency=low
* New upstream release
diff -Naur altree.orig/altree-1.3.1/debian/patches/clang-ftbfs.diff altree/altree-1.3.1/debian/patches/clang-ftbfs.diff
--- altree.orig/altree-1.3.1/debian/patches/clang-ftbfs.diff 1969-12-31 18:00:00.000000000 -0600
+++ altree/altree-1.3.1/debian/patches/clang-ftbfs.diff 2014-03-27 19:18:52.698361918 -0500
@@ -0,0 +1,67 @@
+--- a/CUtils/c_sources/rhyper.c
++++ b/CUtils/c_sources/rhyper.c
+@@ -52,6 +52,10 @@
+ * If (i > 7), use Stirling's approximation, otherwise use table lookup.
+ */
+
++double compute(int n) {
++};
++
++
+ static double afc(int i)
+ {
+ static int computed=10;
+@@ -70,27 +74,6 @@ static double afc(int i)
+ 12.8018274800814696,/*ln(9!)*/
+ 15.1044125730755153,/*ln(10!)*/
+ };
+- double compute(int n) {
+- static long double cur=3628800;
+- static int i=11;
+- static volatile int mutex=0;
+-
+- while (__sync_lock_test_and_set(&mutex, 1)) {
+- /* Internal loop with only read to avoid cache line ping-pong
+- on multi-processors */
+- while(mutex) {
+- /* spinlock */
+- }
+- }
+-
+- for(; i<=n; i++) {
+- cur*=i;
+- al[i+1]=logl(cur);
+- }
+- computed=n;
+- __sync_lock_release(&mutex);
+- return al[i];
+- };
+
+ double di, value;
+
+@@ -100,7 +83,24 @@ static double afc(int i)
+ } else if (i <= computed) {
+ value = al[i + 1];
+ } else if (i <= 1754) {
+- value = compute(i);
++ static long double cur=3628800;
++ static int x=11;
++ static volatile int mutex=0;
++
++ while (__sync_lock_test_and_set(&mutex, 1)) {
++ /* Internal loop with only read to avoid cache line ping-pong
++ on multi-processors */
++ while(mutex) {
++ /* spinlock */
++ }
++ }
++
++ for(; x<=i; x++) {
++ cur*=i;
++ al[i+1]=logl(cur);
++ }
++ computed=i;
++ __sync_lock_release(&mutex);
+ } else {
+ di = i;
+ value = (di + 0.5) * log(di) - di + 0.08333333333333 / di
diff -Naur altree.orig/altree-1.3.1/debian/patches/series altree/altree-1.3.1/debian/patches/series
--- altree.orig/altree-1.3.1/debian/patches/series 1969-12-31 18:00:00.000000000 -0600
+++ altree/altree-1.3.1/debian/patches/series 2014-03-27 18:50:00.978331761 -0500
@@ -0,0 +1 @@
+clang-ftbfs.diff
--- End Message ---
--- Begin Message ---
Source: altree
Source-Version: 1.3.1-2
We believe that the bug you reported is fixed in the latest version of
altree, 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.
Vincent Danjean <[email protected]> (supplier of updated altree 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: Sun, 30 Mar 2014 23:43:51 +0200
Source: altree
Binary: altree altree-examples
Architecture: all amd64 source
Version: 1.3.1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Vincent Danjean <[email protected]>
Closes: 742843
Description:
altree-examples - example files for ALTree
altree - program to perform phylogeny-based association and localization a
Changes:
altree (1.3.1-2) unstable; urgency=medium
.
* Fix "FTBFS with clang instead of gcc"
clang does not support nested functions so removing them.
Instead of inlining the nested function as proposed in the submitted
patch (thanks Arthur <[email protected]>), use a external function
with an explicit context (Closes: #742843)
* bump standard-version (no change needed)
Checksums-Sha1:
83d70111d299e8f2d9570aebed1198af660eda9b 2262 altree_1.3.1-2.dsc
7204eb154bb23f3c1189142815df736029c1511b 5600 altree_1.3.1-2.debian.tar.xz
e1c0717f963f619a8b9712c812788284ce515cb8 340882 altree_1.3.1-2_amd64.deb
473fbf1998526af0f3a07316e8f9bf959629b05d 330990 altree-examples_1.3.1-2_all.deb
Checksums-Sha256:
12a866127fc0a4d4ad98c83092d2e5191af7c0599a3c750dd56c5f713338e7da 2262
altree_1.3.1-2.dsc
437d44b1d08a8af5ed5beaf06ecd395c945effd87c7ce48100a9827df46754b3 5600
altree_1.3.1-2.debian.tar.xz
03d1036ca4a009338c20b6daae4a46b5052f45d0ace3f6cba6771b6fdba3065a 340882
altree_1.3.1-2_amd64.deb
a1af538a21a8d6c642d8445b28fc319e5ef49dedcdbfee1d3478efec18445e77 330990
altree-examples_1.3.1-2_all.deb
Files:
9d9022dd4874e8b886450c3fdb45cbdb 2262 science optional altree_1.3.1-2.dsc
78f5b584383cfbdac6253c4f551cb188 5600 science optional
altree_1.3.1-2.debian.tar.xz
9d07f2c04005e0623b31948fc2e2ced8 340882 science optional
altree_1.3.1-2_amd64.deb
b4afa09097e0d2ea4baad77e4f09c187 330990 science optional
altree-examples_1.3.1-2_all.deb
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1
iQIVAwUBUznqPZZH3mN+x7dRAQiLJg//cdtIzFB0116N+mRkqyDCWKSWV4oaAj3Q
TW+glsD+Iacvxr9esPPYi1uOj5bTHvp7cmIEYbKpOq5HSgpu8Gv4GaF2pkebNBu+
TkfwjJ+DLXyD9ZLPqb1k846y9CZcIZzkNyAE2vg7Yzp4mFnYffz9WjlWp+AJxnf+
yEDZurJzr7XPdR5RIhxs/sp+cRjwAquvvgLIsc4GTDKSsX5Caogqp4wU7a54uvOG
zR6zrseg3iC6Io+hbt9ANKUDbQA87Gihnv859QL3kN3HbQTFroMdc0xPmNSbnlQd
xHVxm53aeT9w6+M5DzmzwORZy+aq5aZYzV7z/UuBV/KJXoT2bRQ7FKwJ3JffJFaf
sm5qGVqJ1p8MUK7DIMUGSnWz1mrDpZlZ7SZGwD4e5OjwIlAfb3ULkXyoie1PVNYG
nRrKPk3QSScsSfcZESfZaVTOqrZhIN0djhMPlqz/RYGOyYxwIJk3eQ5dutyuyoiK
baMwKDmaTCg8/y6BW9n10OxbJyU+QPnL92+1SPQLWvsRtXYqMrD3G1MMtLU4RPw4
OvIQcMmV5SHQoJmABpAaiRUlWTLtO/tMegJ8kVU7UOOTXq2us2I2I/EyvfzXrKVW
zNH7YwM9iKK2qxbsUV5H+vK2y/0REh0AxikbIH40UFP/2DCo2WBip05l1lpfKpDX
mQ4TWG2Ao10=
=Nvp4
-----END PGP SIGNATURE-----
--- End Message ---
