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Rebuild Comet and MaRaCluster with zlib 1.3.2 and expat 2.8.5; remove X!Tandem - #115
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timosachsenberg wants to merge 11 commits into
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timosachsenberg wants to merge 11 commits into
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The upstream binaries of Comet 2025.01 rev. 1 and MaRaCluster 1.04.1 carry copies of zlib and expat with known vulnerabilities: Comet's MSToolkit bundles zlib 1.2.11 and expat 2.2.9, and MaRaCluster links ProteoWizard's zlib 1.2.3. recipes/ rebuilds the same engine versions with zlib 1.3.2 and expat 2.8.5, and .github/workflows/rebuild-engines.yml runs the builds on the runners of the upstream release builds: - versions.env pins the sources: the zlib and expat archives by SHA-256, Comet, MaRaCluster and ProteoWizard by commit. - Comet: the patch points its Makefiles and Visual Studio projects at the new zlib and expat, which prepare.sh puts into MSToolkit/src in place of the old ones. The builds are those of Comet's release workflows. - MaRaCluster: the patch makes its builder scripts build the ProteoWizard tree that prepare.sh provides, with --zlib-src pointing to zlib 1.3.2, so that ProteoWizard, Boost and MaRaCluster use it. ProteoWizard is pinned to the commit that the rel-1-04-1 release build used. - check-bundled-libs.sh checks the zlib and expat versions in the binaries, and compare/ requires the same results as from the binaries they replace on OpenMS's test data, with uncompressed, zlib-compressed and gzipped spectra. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Rw4h2NgPw5vPhVynmADGPx
…ners - The MSFileReader DLLs, whose type library MSToolkit #imports, need the Visual C++ 2010 runtime. The windows-2019 image of Comet's release builds had it, windows-2022 has not, so regsvr32 could not load XRawfile2_x64.dll. Install it, and register only XRawfile2_x64.dll, the one DLL with DllRegisterServer. - In the Linux containers the checkout belongs to another user, and git refused to fetch the baseline binaries into it. Mark it safe. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Rw4h2NgPw5vPhVynmADGPx
The sparse checkout left out all of pwiz_tools/Shared, which the tarballs have but for a few folders and libraries, and the Windows build of ProteoWizard stopped after 48 seconds. Leave out exactly what the tarballs leave out (Jamroot.jam's .pwiz-src-exclusions): this keeps pwiz_tools/Shared and doc, and drops from libraries/ the archives the tarballs do not have, such as expat 2.0.1. Show ProteoWizard's build log when a MaRaCluster build fails; the builders write it to a file. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Rw4h2NgPw5vPhVynmADGPx
No OpenMS tool runs X!Tandem since XTandemAdapter was removed in OpenMS 3.4.0. #111 meant to remove its binaries, but it was merged after #112 had renamed the 64bit folders to x86_64, so the copies in Linux/x86_64, MacOS/x86_64 and Windows/x86_64 stayed, and the Windows installer and the x86_64 DEB kept shipping tandem.exe. They also carry outdated expat: the Linux binary expat 2.0.1, and the Windows binary, linked in December 2015, an expat older than 2.2.0 (released in June 2016). Both are affected by Critical CVEs such as CVE-2016-0718 (fixed in 2.2.0) and CVE-2022-25235 (fixed in 2.4.5). The macOS binary uses the system's libexpat. VERSION and Licenses.txt no longer list X!Tandem. OpenMS/OpenMS#10344 keeps it out of the installers for THIRDPARTY revisions that still have it. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Rw4h2NgPw5vPhVynmADGPx
Git Bash did not find msbuild on the path that setup-msbuild sets up
("msbuild: command not found"). Comet's own release workflow runs it
from the default Windows shell.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Rw4h2NgPw5vPhVynmADGPx
- check-bundled-libs.sh failed the Windows Comet build on three "expat_2" strings in MSToolkitLite.lib, next to one "expat_2.8.5": fragments in the objects of MSVC's link-time code generation, whose only expat is 2.8.5. A bundled expat or zlib shows its full version, as the old binaries do, so only full versions count now. - A download of the expat archive failed with HTTP 500 for seven seconds on one runner; retry five times, ten seconds apart, on any error. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Rw4h2NgPw5vPhVynmADGPx
- The macOS build stopped in ProteoWizard's build of zlib 1.3.2: clang rejects gzlib.c, gzread.c and gzwrite.c calling lseek, read, write and close undeclared. ProteoWizard compiles zlib's sources without running zlib's configure, which leaves zconf.h without <unistd.h>; zlib 1.2.3's gzio.c did not need it. GCC only warns. prepare.sh now runs zlib's configure on Linux and macOS, as zlib's own build does. - One run of the rebuilt Windows binary crashed (access violation) in the batch step on the uncompressed spectra; an earlier build of the same sources passed the same comparison, and 500 runs of each Linux binary did not crash. MaRaCluster reads its input files in parallel threads. compare/maracluster.sh can now repeat the batch step of the old and new binary, and of the new one in one thread, and the workflow does so 100 times, keeps minidumps of maracluster.exe on Windows, and uploads the logs, dumps and binary when the job fails. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Rw4h2NgPw5vPhVynmADGPx
…ests - The Windows crash of the last run is MaRaCluster's, not the rebuild's. On a windows-2022 runner, the batch step alone on the two test files crashed with an access violation in 42 of 100 runs of the 1.04.1 release binary, in 35 of 100 runs of the rebuilt one, and in none of 100 runs of the rebuilt one with OMP_NUM_THREADS=1. batch converts the input files in one OpenMP thread per file; MaRaClusterAdapter has run the index step in one thread first since OpenMS/OpenMS#10259, for this crash, and batch then reuses the converted files. compare/maracluster.sh now runs index (one thread), batch and consensus as the adapter does, and repeats index and batch 25 times per binary. The crash dumps did not come about (Windows Error Reporting does not handle these processes), so that step is gone. - Build on pull requests and on pushes to master only: a push to a branch with a pull request ran the workflow twice. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Rw4h2NgPw5vPhVynmADGPx
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Inline comments:
Review comments at @recipes/compare/comet.sh:
- Around line 67-76: Update the comparison loop in the `comet.sh`
output-checking block to verify that `out/old/$name-$variant` and
`out/new/$name-$variant` contain the same set of `r.*.norm` files, including
when either set is empty. Mark `status` as failed when the sets differ, while
preserving the existing per-file content comparisons.
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⛔ Files ignored due to path filters (2)
Linux/x86_64/XTandem/tandem.exeis excluded by!**/*.exeWindows/x86_64/XTandem/tandem.exeis excluded by!**/*.exe
📒 Files selected for processing (19)
.gitattributes.github/workflows/rebuild-engines.ymlLicenses.txtLinux/x86_64/XTandem/LICENSEMacOS/x86_64/XTandem/LICENSEMacOS/x86_64/XTandem/tandemVERSIONWindows/x86_64/XTandem/LICENSErecipes/README.mdrecipes/check-bundled-libs.shrecipes/comet/prepare.shrecipes/comet/zlib-1.3.2-expat-2.8.5.patchrecipes/compare/comet.shrecipes/compare/maracluster.shrecipes/compare/mzml-zlib.pyrecipes/fetch-sources.shrecipes/maracluster/prepare.shrecipes/maracluster/pwiz-zlib-1.3.2.patchrecipes/versions.env
💤 Files with no reviewable changes (5)
- Linux/x86_64/XTandem/LICENSE
- Windows/x86_64/XTandem/LICENSE
- MacOS/x86_64/XTandem/LICENSE
- VERSION
- Licenses.txt
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CodeRabbit's pre-merge check counted 5 of the 13 functions as documented (a comment on the line above; the others had it after the brace, or had none). The comment above init_repo described checkout; each has its own now. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Rw4h2NgPw5vPhVynmADGPx
An output file that only the new binary wrote was never compared; one it left out failed only through cmp. Compare the two sets of files as well (CodeRabbit on #115), and skip the normalization of a run that wrote no output instead of stopping at the unmatched glob. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Rw4h2NgPw5vPhVynmADGPx
…t 2.8.5 The upstream binaries of Comet 2025.01 rev. 1 and MaRaCluster 1.04.1 carry copies of zlib and expat with known vulnerabilities: Comet the zlib 1.2.11 and expat 2.2.9 of its MSToolkit, MaRaCluster the zlib 1.2.3 of ProteoWizard. These are the same versions (Comet v2025.01.1 at 4181df6, MaRaCluster rel-1-04-1 at c122929, with the ProteoWizard revision of its release build), built by recipes/ with zlib 1.3.2 and expat 2.8.5 in run https://github.com/OpenMS/THIRDPARTY/actions/runs/36621931217 (8634ce4, the engines artifact): - every binary carries only zlib 1.3.2, and Comet only expat 2.8.5 (check-bundled-libs.sh; on Windows through the static libraries); - on OpenMS's test data, with uncompressed, zlib-compressed and gzipped spectra, the results are those of the binaries they replace: Comet's txt, pepXML, mzIdentML, pin and SQT output of four searches, and MaRaCluster's clusters and consensus spectra, run as MaRaClusterAdapter runs it; - file types, linking, the glibc symbol versions (MaRaCluster: up to 2.34), the macOS minimum versions (Comet 14.0 on arm64 and 13.0 on x86_64, MaRaCluster 11.0) and the Windows imports are those of the binaries they replace. Each Comet and MaRaCluster folder gets a README.md with the provenance, the Comet folders expat's license (LICENSE-expat.txt), and VERSION says that these are rebuilds. The README.md files that the Comet folders had were stale (Comet's own README, and notes of a build on Ubuntu 20.04). SHA-256: 33e925d17e618467ce7198b4aaccabae3e2909db6e9599698fed859a5ff9038d Linux/aarch64/Comet/comet.exe 067dcf7aea937a243337e0a2b191310589c57a5fffa1297e81233abb7f2c4354 Linux/x86_64/Comet/comet.exe b346e96aa453fc8faee05536efb4287a09487d0e8b2f715a9222422ed6fed479 Linux/x86_64/MaRaCluster/maracluster 10ec5b03b0282dfe66602c33ee4df823da3c4f9be739521c0dd26a6c8b8c3558 MacOS/arm64/Comet/comet.exe 9feeb81bff243d4466a8689b4a2ff71beef88b7010d839c0f9ea359ffe92e1f8 MacOS/arm64/MaRaCluster/maracluster 8557b59c1d964874fb3cb43c7a0fdb03598b98836485ec4022fdf194edfcf242 MacOS/x86_64/Comet/comet.exe 6870f2207caec05d6eebef123cd8e1871b71f870963c1e231338c1ecb63246cf Windows/x86_64/Comet/comet.exe 68cdd048cdf9f6b809386c13e0014cf7b95bf6d851b5494104bc150ddf619a82 Windows/x86_64/MaRaCluster/maracluster.exe Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Rw4h2NgPw5vPhVynmADGPx
🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
Full details: Docstring CoverageExplanation Docstring coverage is 38.46% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 13 functions across 8 files. (5 skipped: 5 unsupported.)
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timosachsenberg
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The OpenMS 3.6.0 release-readiness check F6 ("no known-vulnerable bundled library") found old zlib and expat statically linked in engines of this repository (abe0956):
Changes
recipes/rebuilds the same engine versions with zlib 1.3.2 and expat 2.8.5, as their upstream release builds do (same runners, compilers and builder scripts), from pinned sources: Comet v2025.01.1 (4181df6) with MSToolkit's zlib and expat swapped, and MaRaCluster rel-1-04-1 (c122929) with the ProteoWizard revision of its release build (9ba7317), built with--zlib-srcpointing to zlib 1.3.2 and zlib'sconfigurerun first..github/workflows/rebuild-engines.ymlruns the builds and checks on pull requests and pushes to master that changerecipes/.recipes/README.mddescribes all of it.Verification (in the workflow, per platform)
check-bundled-libs.sh: the binaries carry only zlib 1.3.2 and, for Comet, expat 2.8.5 (on Windows, where MSVC drops the version strings, through the static libraries that are linked). The upstream binaries fail the same check.compare/: on OpenMS's test data, with uncompressed, zlib-compressed and gzipped spectra, the results are identical to those of the binaries they replace: Comet's txt, pepXML, mzIdentML, pin and SQT output of four searches (68 comparisons), and MaRaCluster's clusters and consensus spectra, run as MaRaClusterAdapter runs it.Notes
batchstep, which converts its input files in parallel OpenMP threads, crashes on Windows with an access violation: on a windows-2022 runner in 42 of 100 runs of the 1.04.1 release binary, 35 of 100 of the rebuilt one, and 0 of 100 in one thread (Linux and macOS: none). This is not from the rebuild; MaRaClusterAdapter has run theindexstep in one thread first since Debian package: drop padded RUNPATH entries, bridge dev files and stale Depends; MaRaCluster 1.04.1 OpenMS#10259, and the comparison does the same.Summary by CodeRabbit
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