From 483b356575e4b583b1e7e146ac1e6375d9c7c0d3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?L=C3=A1szl=C3=B3=20Kupcsik?= Date: Thu, 24 Apr 2025 21:12:58 +0200 Subject: [PATCH 1/3] rPackages.scDDboost: fix build Revert unneeded backported fix. It must build on EBSeq fix, because EBSeq is a dependency as well. --- pkgs/development/r-modules/default.nix | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 3a23a6b79c7f..0874de40781b 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -1777,17 +1777,6 @@ let ]; }); - scDDboost = old.scDDboost.overrideAttrs (attrs: { - postPatch = '' - # https://code.bioconductor.org/browse/scDDboost/commit/f704a727c906075a2e271e9e2db93cf31e3822f5 - substituteInPlace "DESCRIPTION" \ - --replace-fail "c++11" "c++14" - # https://code.bioconductor.org/browse/scDDboost/commit/74d46e266957b38fe77185fa3ce683f891706538 - substituteInPlace "src/Makevars" \ - --replace-fail "#CXX_STD = CXX11" "CXX_STD = CXX14" - ''; - }); - sf = old.sf.overrideAttrs (attrs: { configureFlags = [ "--with-proj-lib=${pkgs.lib.getLib pkgs.proj}/lib" From efcd75030648116bcb84a2ca90f4b6a6e5e5baf8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?L=C3=A1szl=C3=B3=20Kupcsik?= Date: Thu, 24 Apr 2025 21:19:39 +0200 Subject: [PATCH 2/3] rPackages.bandle: fix build revert unneeded backport fix --- pkgs/development/r-modules/default.nix | 8 -------- 1 file changed, 8 deletions(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 0874de40781b..d8773979e01f 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -1900,14 +1900,6 @@ let postPatch = "patchShebangs configure"; }); - bandle = old.bandle.overrideAttrs (attrs: { - postPatch = '' - # https://code.bioconductor.org/browse/bandle/commit/e8f7aaa29c1ba772cee5d51e09b1f500bfee44b8 - substituteInPlace "src/Makevars" \ - --replace-fail "CXX_STD = CXX11" "CXX_STD = CXX14" - ''; - }); - graper = old.graper.overrideAttrs (attrs: { postPatch = '' substituteInPlace "src/Makevars" \ From 81079a9ebc0497f7f5b50253fe077623a95b9947 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?L=C3=A1szl=C3=B3=20Kupcsik?= Date: Thu, 24 Apr 2025 21:48:47 +0200 Subject: [PATCH 3/3] rPackages.methylKit: fix build revert unneeded backport fix --- pkgs/development/r-modules/default.nix | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index d8773979e01f..b8a51f48c204 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -2509,16 +2509,6 @@ let RGL_USE_NULL = "true"; }); - methylKit = old.methylKit.overrideAttrs (attrs: { - # resolve missing function from data.table - patches = [ - (pkgs.fetchpatch { - url = "https://github.com/al2na/methylKit/commit/5c30347630bc064d7aefc918923f723671f35253.patch"; - sha256 = "sha256-hwtybBmSYwVInMIEZ7i7zudJWjiRJmrD0/tU7v78pPc="; - }) - ]; - }); - Rrdrand = old.Rrdrand.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; }; symengine = old.symengine.overrideAttrs (_: {