Debian Patches
Status for libsonlib/1.1+git20220915.5cbc158+dfsg1-3
| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| fix_build_errors.patch | Fix build errors and make the library build cleanly: - C/impl/sonLibTreap.c: stTreap_remove read rmnode after freeing it (use-after-free); save the parent pointer before free(). - C/impl/stSafeC.c: nbytes was set but not used (with -Werror=unused-but-set-variable this fails the build). - include.mk: drop --pedantic from the release flags; sonLibList.c uses sort_r which needs object<->function pointer casts that ISO C forbids under -pedantic. |
Andreas Tille <tille@debian.org> | no | |||
| use_debian_packaged_quicktree.patch | To avoid a code copy of quicktree here inside the quicktree package a static lib is built and used to link here | Andreas Tille <tille@debian.org> | no | 2020-06-16 | ||
| 2to3.patch | Port to Python3 | Andreas Tille <tille@debian.org> | no | 2020-06-16 | ||
| fix_test.patch | Somehow the test suite was non-functional. Fix some PATHs here | Andreas Tille <tille@debian.org> | no | 2020-06-16 | ||
| rpath.patch | No rpath | Andreas Tille <tille@debian.org> | no | 2020-06-16 | ||
| fix_warnings.patch | Fix comparison between pointer and zero character constant ([-Werror=pointer-compare]) in C/impl/bioioC.c: the code compared the pointer *string against the character constant '\0', which is always true; it must compare the pointed-to character **string. |
Andreas Tille <tille@debian.org> | no | |||
| python313_compat.patch | unittest.makeSuite() was removed in Python 3.13; use unittest.defaultTestLoader.loadTestsFromTestCase() instead so the test suite runs on current Python. |
Andreas Tille <tille@debian.org> | no | |||
| fix_quicktree_clone_child_ids.patch | Clear uninitialized child_ids before freeing cloned quicktree trees quicktree >= 2.5's clone_Tnode() (used by get_root_Tnode()) does not initialize the child_ids member of the cloned nodes. free_Tnode() frees child_ids whenever it is non-NULL, so freeing the tree returned by get_root_Tnode() with free_Tree() frees uninitialized pointers and corrupts the heap (seen as a segfault / heap corruption in the sonLibTests neighbour-joining tests). Clear child_ids on the cloned tree before freeing it. |
Andreas Tille <tille@debian.org> | no | 2026-10-21 | ||
| add_shared_library.patch | Build a shared library libsonlib.so.1.1.0 in addition to the static one Upstream sonLib only builds the static archive sonLib.a. Add a parallel target that compiles the same sources with -fPIC and links them into libsonlib.so.1.1.0 (soname libsonlib.so.1). The shared library is linked against the shared libquicktree so that the TreeREP symbols (neighbour_joining_buildtree and friends) are resolved at run time and consumers do not have to add -lquicktree themselves. The static archive still leaves these symbols unresolved, so static consumers keep linking -lquicktree. |
Andreas Tille <tille@debian.org> | no | 2026-11-06 | ||
| use_debian_packaged_cutest.patch | Build against the Debian packaged CuTest instead of the copy in externalTools, which is not part of the repacked upstream tarball. Add /usr/include/cutest to the include path (sonLib's internal headers include CuTest.h) and link the test programs with -lcutest from libcutest-dev. |
Andreas Tille <tille@debian.org> | no | 2026-11-02 | ||
| fix_char_getc_eof.patch | Fix infinite loop in file line-reading on unsigned-char architectures getc(3) returns an int (0..255 or EOF, which is -1). The line-reading helpers in sonLibFile.c and bioioC.c cast the result to char before checking it against EOF. That cast is implementation-defined: on architectures where plain char is unsigned (arm64, armhf, ppc64, ppc64el, powerpc, s390x, ...) EOF (-1) becomes 255, so the `ch == EOF` termination check never fires and the reader loops forever on the last (newline-less or empty) line of a file. . This makes the sonLibTests suite hang indefinitely on those architectures at test_stFile_getLineFromFile / benLine, causing the build to be killed by the buildd timeout. Reading into an int64_t directly without the char truncation fixes EOF detection everywhere and is behaviour-identical on signed-char architectures. |
Andreas Tille <tille@debian.org> | no | 2026-11-09 | ||
| fix_stString_print_varargs.patch | Fix undefined behaviour in stString_print test test_stString_print passes the integer literal 5 for an argument that the format string consumes with the PRIi64 (int64_t) conversion. On ABIs where varargs are passed on the stack (i386) or in a mixed register/stack layout (hppa) this reads the wrong words and the test fails with a garbage value (e.g. "foo 10903929910156347803952691740557 6524209428700210687939411819354183979772946877523748264649767777482424 97536.0" instead of "foo 5 7.0"). On amd64/arm64 the register-based varargs happen to mask the bug. Cast the argument to int64_t so the call is well-defined on every ABI. |
Andreas Tille <tille@debian.org> | no | 2026-11-09 |
All known versions for source package 'libsonlib'
- 1.1+git20220915.5cbc158+dfsg1-3 (sid, forky)