From a644e88ab4f997879e5d9d0dfd9213e125be9973 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Wed, 13 Oct 2021 06:51:43 +1100 Subject: [PATCH 1/4] rPackages.DirichletMultinomial: fix build --- pkgs/development/r-modules/default.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 1669162c5295..c714d9a571f9 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -513,6 +513,7 @@ let Rbowtie = with pkgs; [ zlib.dev ]; gaston = with pkgs; [ zlib.dev ]; csaw = with pkgs; [ zlib.dev curl ]; + DirichletMultinomial = with pkgs; [ gsl ]; }; packagesRequiringX = [ From 0e6a38a1b077fdc842edb437510934869797abc3 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Wed, 13 Oct 2021 06:56:35 +1100 Subject: [PATCH 2/4] rPackages.DiffBind: fix build --- pkgs/development/r-modules/default.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index c714d9a571f9..5053d9517676 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -514,6 +514,7 @@ let gaston = with pkgs; [ zlib.dev ]; csaw = with pkgs; [ zlib.dev curl ]; DirichletMultinomial = with pkgs; [ gsl ]; + DiffBind = with pkgs; [ zlib.dev ]; }; packagesRequiringX = [ From db5b03ba895afc3230c9e6b4c2459b984372bbf9 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Wed, 13 Oct 2021 06:59:10 +1100 Subject: [PATCH 3/4] rPackages.EMCluster: fix build --- pkgs/development/r-modules/default.nix | 4 ---- pkgs/development/r-modules/patches/EMCluster.patch | 6 ------ 2 files changed, 10 deletions(-) delete mode 100644 pkgs/development/r-modules/patches/EMCluster.patch diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 5053d9517676..09d18dcb6b9c 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -884,10 +884,6 @@ let PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack"; }); - EMCluster = old.EMCluster.overrideDerivation (attrs: { - patches = [ ./patches/EMCluster.patch ]; - }); - spMC = old.spMC.overrideDerivation (attrs: { patches = [ ./patches/spMC.patch ]; }); diff --git a/pkgs/development/r-modules/patches/EMCluster.patch b/pkgs/development/r-modules/patches/EMCluster.patch deleted file mode 100644 index afc9de3a95a9..000000000000 --- a/pkgs/development/r-modules/patches/EMCluster.patch +++ /dev/null @@ -1,6 +0,0 @@ -diff -ru -x '*~' EMCluster_orig/src/Makevars EMCluster/src/Makevars ---- EMCluster_orig/src/Makevars 2013-07-05 02:43:25.000000000 +0900 -+++ EMCluster/src/Makevars 2014-10-25 18:10:19.190992120 +0900 -@@ -1 +1 @@ --PKG_LIBS = $(FLIBS) $(BLAS_LIBS) $(LAPACK_LIBS) -+PKG_LIBS = $(FLIBS) $(LAPACK_LIBS) $(BLAS_LIBS) From 4c96ee566de5655f7b9dde5386c41182c90254bd Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Wed, 13 Oct 2021 07:02:08 +1100 Subject: [PATCH 4/4] rPackages.CNEr: fix build --- pkgs/development/r-modules/default.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 09d18dcb6b9c..d1309024613e 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -515,6 +515,7 @@ let csaw = with pkgs; [ zlib.dev curl ]; DirichletMultinomial = with pkgs; [ gsl ]; DiffBind = with pkgs; [ zlib.dev ]; + CNEr = with pkgs; [ zlib ]; }; packagesRequiringX = [