** Patch added: "debdiff_bedtools_kinetic_from_2.30.0+dfsg-2_to_2.30.0+dfsg-2ubuntu1.patch" https://bugs.launchpad.net/ubuntu/focal/+source/bedtools/+bug/1961427/+attachment/5597488/+files/debdiff_bedtools_kinetic_from_2.30.0+dfsg-2_to_2.30.0+dfsg-2ubuntu1.patch
-- You received this bug notification because you are a member of Ubuntu Touch seeded packages, which is subscribed to zlib in Ubuntu. https://bugs.launchpad.net/bugs/1961427 Title: zlib: compressBound() returns an incorrect result on z15 Status in Ubuntu on IBM z Systems: Incomplete Status in bedtools package in Ubuntu: New Status in htslib package in Ubuntu: New Status in zlib package in Ubuntu: Incomplete Status in bedtools source package in Focal: Invalid Status in htslib source package in Focal: New Status in zlib source package in Focal: New Status in bedtools source package in Impish: New Status in htslib source package in Impish: Invalid Status in zlib source package in Impish: New Status in bedtools source package in Jammy: New Status in htslib source package in Jammy: Invalid Status in zlib source package in Jammy: Incomplete Bug description: SRU Justification: ================== [Impact] * zlib: compressBound() returns an incorrect result on IBM z15 hardware. * Passing the result of compressBound() to compress() results in an error code. * This is because compressBound() is not adjusted for DFLTCC. [Fix] * Adjust compressBound() for DFLTCC like it's already done for deflateBound(). * Since zlib project does not accept patches at the moment, the fix has been integrated into the DFLTCC pull request: https://github.com/madler/zlib/pull/410 The commitid is b25781e735363e04f6c56e21431c47e4afc50b17. * The fix extracted out of the above is: https://launchpadlibrarian.net/589857296/debdiff_zlib_1.2.11.dfsg-2ubuntu7_to_zlib_1.2.11.dfsg-2ubuntu8_jammy.diff * On top of this actual zlib fix, there is another patch needed: 'Remove compressBound assertions. (PR #1258)' for htslib. * But there is a standalone 'htslib' package version, as well as a htslib version included in (some) 'bedtools' packages. Both need to be patched (see '[Other]' for more details). [Test Plan] * An IBM z15 system (LPAR, z/VM guest or KVM virtual machine) with Ubuntu Server 21.10 (or 22.04). * A test can be done based on the following C test program: #include <assert.h> #include <stdlib.h> #include <zlib.h> int main() { Bytef in_buf[128], out_buf[1024]; for (size_t i = 0; i < sizeof(in_buf); i++) in_buf[i] = rand(); uLongf dest_len = compressBound(sizeof(in_buf)); assert(dest_len <= sizeof(out_buf)); int ret = compress(out_buf, &dest_len, in_buf, sizeof(in_buf)); assert(ret == Z_OK); } * The test needs to be done by IBM, due to the requirements for the special z15 hardware. * A successful test was just completed, based on the version in jammy- proposed, which is at the same code level that the impish version this SRU is targeted for. [Where problems could occur] * If the adjustment of compressBound() for DFLTCC is done erroneously the issue can still be present or in worst case even affect Z systems other than z15 only. * The compression can become errorneous with the new changes, e.g. in compressBound. * Mistakes in dfltcc_free_window OF and especially DEFLATE_BOUND_COMPLEN, (incl. the bit definitions), may cause various and unforseen defects. * Any build time issues that might have been introduced by this patch can be identified by a test build; this was done and is available here: https://launchpad.net/~fheimes/+archive/ubuntu/lp1961427 [Other Info] * Ubuntu jammy, impish and focal are affected by the zlib issue. * The 'htslib' version '1.13+ds' (as it is part of I, J and K), already includes the patch, hence only htslib '1.10.2' in focal needs to be patched. * The bedtools version '2.30.0+dfsg' (as it is part of I, J and K), requires the patch, but version '2.27.1+dfsg' bedtools in focal does not incl. an embedded htslib, hence does not need to be (actually can't be) patched. * Patched version of the affected htslib and bedtools packages are build and also available at this PPA: https://launchpad.net/~fheimes/+archive/ubuntu/lp1961427 __________ Description: zlib: compressBound() returns an incorrect result on z15 Symptom: Passing the result of compressBound() to compress() results in an error code. Problem: compressBound() is not adjusted for DFLTCC. Solution: Adjust compressBound() for DFLTCC like it's already done for deflateBound(). Since zlib project does not accept patches at the moment, the fix has been integrated into the DFLTCC pull request: https://github.com/madler/zlib/pull/410 The commitid is b25781e735363e04f6c56e21431c47e4afc50b17. Reproduction: z15 only: #include <assert.h> #include <stdlib.h> #include <zlib.h> int main() { Bytef in_buf[128], out_buf[1024]; for (size_t i = 0; i < sizeof(in_buf); i++) in_buf[i] = rand(); uLongf dest_len = compressBound(sizeof(in_buf)); assert(dest_len <= sizeof(out_buf)); int ret = compress(out_buf, &dest_len, in_buf, sizeof(in_buf)); assert(ret == Z_OK); } To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1961427/+subscriptions -- Mailing list: https://launchpad.net/~touch-packages Post to : touch-packages@lists.launchpad.net Unsubscribe : https://launchpad.net/~touch-packages More help : https://help.launchpad.net/ListHelp
