Re: libsonlib test failing (help needed)
Hi Shayan,
On Fri, Jul 03, 2020 at 01:03:25PM +0100, Shayan Doust wrote:
> ...
> Running test case testStPhylogeny_getSplits
> Running test case testStPhylogeny_nni
> Running test case testJoinCosts_random
> Running test case testStPhylogeny_reconcileAtMostBinary_degree2Nodes
> Running test case testSimpleNeighborJoin
> Segmentation fault
I tried running sonLibTests under gdb
$ LC_ALL=C gdb sonLibTests
run
...
Running test case testJoinCosts_random
Running test case testStPhylogeny_reconcileAtMostBinary_degree2Nodes
Running test case testSimpleNeighborJoin
--Type <RET> for more, q to quit, c to continue without paging--
Thread 1 "sonLibTests" received signal SIGSEGV, Segmentation fault.
__GI___libc_free (mem=0x9074) at malloc.c:3102
3102 malloc.c: No such file or directory.
No idea how to continue here.
I also tried the following patch:
index bd92da0..a3d3c78 100755
--- a/debian/rules
+++ b/debian/rules
@@ -12,11 +12,11 @@ override_dh_auto_build:
# Somehow Makefile does not deal with this ...
#mkdir -p bin
#cp -a src/sonLib/test/sonLib_daemonize.py .
- dh_auto_build
+ CGL_DEBUG=ultra dh_auto_build
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- dh_auto_test || true
+ CGL_DEBUG=ultra dh_auto_test || true
endif
override_dh_install:
which needed debian/patches/fix_warnings.patch but I have no idea how to
fix this build error:
...
gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Werror --pedantic -g -O1 -fno-inline -fno-omit-frame-pointer -fsanitize=address -I/usr/include -DHAVE_TOKYO_CABINET=1 -Iusr/include/quicktree -g -O2 -fdebug-prefix-map=/build/libsonlib-1.1+git20200429.1040ab0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I inc -I ../lib/ -I/usr/include/quicktree/ -c impl/*.c
impl/sonLibList.c: In function ‘st_list_sortP’:
impl/sonLibList.c:258:13: error: ISO C forbids conversion of object pointer to function pointer type [-Werror=pedantic]
258 | return ((int (*)(const void *, const void *))fn)(*((char **)a), *((char **)b));
| ^
impl/sonLibList.c: In function ‘stList_sort’:
impl/sonLibList.c:262:76: error: ISO C forbids conversion of function pointer to object pointer type [-Werror=pedantic]
262 | sort_r(list->list, stList_length(list), sizeof(void *), st_list_sortP, (void *)cmpFn);
| ^
impl/sonLibList.c: In function ‘st_list_sort2P’:
impl/sonLibList.c:267:56: error: ISO C forbids conversion of object pointer to function pointer type [-Werror=pedantic]
267 | int (*cmpFn)(const void *, const void *, void *) = (int (*)(const void *, const void *, void *))(((void **)extra)[0]);
| ^
impl/sonLibList.c: In function ‘stList_sort2’:
impl/sonLibList.c:273:24: error: ISO C forbids conversion of function pointer to object pointer type [-Werror=pedantic]
273 | void *extra[2] = { (void *)cmpFn, (void *)extraArg };
| ^
cc1: all warnings being treated as errors
make[3]: *** [Makefile:54: ../lib/sonLib.a] Error 1
I think we should try the maximim debug options and try gdb again.
> Any help is much appreciated!
Seems more help is needed here.
Kind regards
Andreas.
> [1]: https://salsa.debian.org/med-team/libsonlib
--
http://fam-tille.de
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