From 829921e643c27178cd565b76ef0e3df44f0e28af Mon Sep 17 00:00:00 2001 From: Maximilian Bosch Date: Thu, 3 Sep 2026 18:21:11 +0200 Subject: [PATCH] dragmap: drop Failing Hydra build: https://hydra.nixos.org/build/344145730 Repo is archived as well. --- .../dr/dragmap/boost-iterator-range.patch | 12 --- pkgs/by-name/dr/dragmap/cstdint.patch | 73 ----------------- pkgs/by-name/dr/dragmap/getHostVersion.patch | 11 --- pkgs/by-name/dr/dragmap/package.nix | 82 ------------------- pkgs/by-name/dr/dragmap/stdio-pclose.patch | 12 --- pkgs/top-level/aliases.nix | 1 + 6 files changed, 1 insertion(+), 190 deletions(-) delete mode 100644 pkgs/by-name/dr/dragmap/boost-iterator-range.patch delete mode 100644 pkgs/by-name/dr/dragmap/cstdint.patch delete mode 100644 pkgs/by-name/dr/dragmap/getHostVersion.patch delete mode 100644 pkgs/by-name/dr/dragmap/package.nix delete mode 100644 pkgs/by-name/dr/dragmap/stdio-pclose.patch diff --git a/pkgs/by-name/dr/dragmap/boost-iterator-range.patch b/pkgs/by-name/dr/dragmap/boost-iterator-range.patch deleted file mode 100644 index bd70eab43f49..000000000000 --- a/pkgs/by-name/dr/dragmap/boost-iterator-range.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/src/lib/map/Mapper.cpp b/src/lib/map/Mapper.cpp -index 6eaa2c5..781988c 100644 ---- a/src/lib/map/Mapper.cpp -+++ b/src/lib/map/Mapper.cpp -@@ -22,6 +22,7 @@ - //#include "common/Crc32Hw.hpp" - #include "common/DragenLogger.hpp" - #include "map/Mapper.hpp" -+#include - - namespace dragenos { - namespace map { diff --git a/pkgs/by-name/dr/dragmap/cstdint.patch b/pkgs/by-name/dr/dragmap/cstdint.patch deleted file mode 100644 index 6004510d2999..000000000000 --- a/pkgs/by-name/dr/dragmap/cstdint.patch +++ /dev/null @@ -1,73 +0,0 @@ -diff --git a/src/include/map/SeedPosition.hpp b/src/include/map/SeedPosition.hpp -index 30a7d47..c05af16 100644 ---- a/src/include/map/SeedPosition.hpp -+++ b/src/include/map/SeedPosition.hpp -@@ -16,6 +16,7 @@ - #define MAP_SEED_POSITION_HPP - - #include -+#include - - #include "sequences/Seed.hpp" - -diff --git a/src/include/sequences/Read.hpp b/src/include/sequences/Read.hpp -index 460c1cb..c7ff619 100644 ---- a/src/include/sequences/Read.hpp -+++ b/src/include/sequences/Read.hpp -@@ -16,6 +16,7 @@ - #define SEQUENCES_READ_HPP - - #include -+#include - #include - #include - -diff --git a/src/include/sequences/Seed.hpp b/src/include/sequences/Seed.hpp -index a242153..dd4d23b 100644 ---- a/src/include/sequences/Seed.hpp -+++ b/src/include/sequences/Seed.hpp -@@ -16,6 +16,7 @@ - #define SEQUENCES_SEED_HPP - - #include -+#include - #include - - #include "sequences/Read.hpp" -diff --git a/src/lib/sequences/tests/unit/CrcHasherMocks.hpp b/src/lib/sequences/tests/unit/CrcHasherMocks.hpp -index 1866be7..5d9b7d7 100644 ---- a/src/lib/sequences/tests/unit/CrcHasherMocks.hpp -+++ b/src/lib/sequences/tests/unit/CrcHasherMocks.hpp -@@ -2,6 +2,7 @@ - - #include - #include -+#include - #include - #include - -diff --git a/stubs/dragen/src/host/dragen_api/read_group_list.hpp b/stubs/dragen/src/host/dragen_api/read_group_list.hpp -index eefb9ae..623a77f 100644 ---- a/stubs/dragen/src/host/dragen_api/read_group_list.hpp -+++ b/stubs/dragen/src/host/dragen_api/read_group_list.hpp -@@ -14,6 +14,7 @@ - #define __READ_GROUP_LIST_HPP__ - - #include "dragen_exception.hpp" -+#include - class ReadGroupList { - public: - const std::string &getReadGroupName(const uint16_t idx) const { - -diff --git a/stubs/dragen/src/host/metrics/public/run_stats.hpp b/stubs/dragen/src/host/metrics/public/run_stats.hpp -index 998fe4e..9561b0b 100644 ---- a/stubs/dragen/src/host/metrics/public/run_stats.hpp -+++ b/stubs/dragen/src/host/metrics/public/run_stats.hpp -@@ -10,6 +10,7 @@ - #include - #include - #include -+#include - // - // RP: HA! HA! HA! That's what you get when you write code logging to cout all - // over the place! diff --git a/pkgs/by-name/dr/dragmap/getHostVersion.patch b/pkgs/by-name/dr/dragmap/getHostVersion.patch deleted file mode 100644 index ba769c9b09a3..000000000000 --- a/pkgs/by-name/dr/dragmap/getHostVersion.patch +++ /dev/null @@ -1,11 +0,0 @@ -diff --git a/thirdparty/dragen/src/common/hash_generation/gen_hash_table.c b/thirdparty/dragen/src/common/hash_generation/gen_hash_table.c -index cdca3df..5a55699 100644 ---- a/thirdparty/dragen/src/common/hash_generation/gen_hash_table.c -+++ b/thirdparty/dragen/src/common/hash_generation/gen_hash_table.c -@@ -249,7 +249,7 @@ void setDefaultHashParams(hashTableConfig_t* defConfig, const char* destDir, Has - free(dir); - } - -- defConfig->hostVersion = (char*)getHostVersion(0); -+ defConfig->hostVersion = (char*)getHostVersion(); - } diff --git a/pkgs/by-name/dr/dragmap/package.nix b/pkgs/by-name/dr/dragmap/package.nix deleted file mode 100644 index 8f554102db65..000000000000 --- a/pkgs/by-name/dr/dragmap/package.nix +++ /dev/null @@ -1,82 +0,0 @@ -{ - lib, - stdenv, - fetchFromGitHub, - boost, - gtest, - zlib, -}: - -stdenv.mkDerivation (finalAttrs: { - pname = "dragmap"; - version = "1.3.0"; - - src = fetchFromGitHub { - owner = "Illumina"; - repo = "DRAGMAP"; - tag = finalAttrs.version; - fetchSubmodules = true; - hash = "sha256-f1jsOErriS1I/iUS4CzJ3+Dz8SMUve/ccb3KaE+L7U8="; - }; - - nativeBuildInputs = [ boost ]; - buildInputs = [ - gtest - zlib - ]; - - # Latest boost do not need system as a linking flag - postPatch = '' - sed -i 's/system filesystem/filesystem/' config.mk - ''; - - patches = [ - # getHostVersion use an empty parameter list. This is now an error for GC - ./getHostVersion.patch - - # pclose is called on a NULL value. This is no longer allowed since - # https://github.com/bminor/glibc/commit/64b1a44183a3094672ed304532bedb9acc707554 - ./stdio-pclose.patch - - # Add missing include cstdint. Upstream does not accept PR. Issue opened at - # https://github.com/Illumina/DRAGMAP/issues/63 - ./cstdint.patch - - # Missing import in Mapper.cpp - # Issue opened upstream https://github.com/Illumina/DRAGMAP/pull/66 - ./boost-iterator-range.patch - ]; - - env = { - GTEST_INCLUDEDIR = "${gtest.dev}/include"; - CPPFLAGS = "-I ${boost.dev}/include"; - LDFLAGS = "-L ${boost.out}/lib"; - }; - - installPhase = '' - runHook preInstall - - mkdir -p $out/bin - cp build/release/dragen-os $out/bin/ - - runHook postInstall - ''; - - # Tests are launched by default from makefile - doCheck = false; - - meta = { - description = "Open Source version of Dragen mapper for genomics"; - mainProgram = "dragen-os"; - longDescription = '' - DRAGMAP is an open-source software implementation of the DRAGEN mapper, - which the Illumina team created to produce the same results as their - proprietary DRAGEN hardware. - ''; - homepage = "https://github.com/Illumina/DRAGMAP"; - changelog = "https://github.com/Illumina/DRAGMAP/releases/tag/${finalAttrs.version}"; - license = lib.licenses.gpl3; - platforms = [ "x86_64-linux" ]; - maintainers = with lib.maintainers; [ apraga ]; - }; -}) diff --git a/pkgs/by-name/dr/dragmap/stdio-pclose.patch b/pkgs/by-name/dr/dragmap/stdio-pclose.patch deleted file mode 100644 index 74e8d57e9fa5..000000000000 --- a/pkgs/by-name/dr/dragmap/stdio-pclose.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/stubs/dragen/src/host/infra/linux/infra_linux_utils.cpp b/stubs/dragen/src/host/infra/linux/infra_linux_utils.cpp -index cd02cd4..c26e9cf 100644 ---- a/stubs/dragen/src/host/infra/linux/infra_linux_utils.cpp -+++ b/stubs/dragen/src/host/infra/linux/infra_linux_utils.cpp -@@ -57,7 +57,6 @@ int GetDmiValue(const std::string& label, std::string& value) - FILE* dmiOutput = popen("sudo /usr/sbin/dmidecode -t 2", "r"); - if (dmiOutput == NULL) { - perror("dmidecode popen"); -- pclose(dmiOutput); - return -1; - } - diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix index 79b886d1de47..f6d9491bcce4 100644 --- a/pkgs/top-level/aliases.nix +++ b/pkgs/top-level/aliases.nix @@ -722,6 +722,7 @@ mapAliases { dotnetfx40 = throw "'dotnetfx40' has been removed because it was unmaintained in Nixpkgs"; # Added 2026-01-27 dotty = throw "'dotty' has been renamed to/replaced by 'scala_3'"; # Converted to throw 2025-10-27 dovecot_fts_xapian = throw "'dovecot_fts_xapian' has been removed because it was unmaintained in Nixpkgs. Consider using dovecot-fts-flatcurve instead"; # Added 2025-08-16 + dragmap = throw "'dragmap' doesn't build with latest glibc anymore and upstream repo is archived"; # Added 2026-09-03 drone-runner-exec = throw "'drone-runner-exec' has been removed as it was deprecated and archived upstream."; # Added 2026-07-20 dsd = throw "dsd has been removed, as it was broken and lack of upstream maintenance"; # Added 2025-08-25 dtv-scan-tables_linuxtv = throw "'dtv-scan-tables_linuxtv' has been renamed to/replaced by 'dtv-scan-tables'"; # Converted to throw 2025-10-27