From c417b44d8339ad20451e72f4e8daa12369c9572f Mon Sep 17 00:00:00 2001 From: Thomas Churchman Date: Mon, 11 Oct 2021 09:23:42 +0200 Subject: [PATCH 01/21] rPackages: introduce packagesRequiringHome override Some R packages require access to a home directory to pass install tests. Extend r-modules to allow creating a temporary home directory for packages with such requirements. --- pkgs/development/r-modules/default.nix | 52 ++++++++++++++++++++++---- 1 file changed, 44 insertions(+), 8 deletions(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 5a5b9fc1348..65082832ce3 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -158,6 +158,38 @@ let in builtins.listToAttrs nameValuePairs; + # Overrides package definition requiring a home directory to install or to + # run tests. + # For example, + # + # overrideRequireHome [ + # "foo" + # ] old + # + # results in + # + # { + # foo = old.foo.overrideAttrs (oldAttrs: { + # preInstall = '' + # ${oldAttrs.preInstall or ""} + # export HOME=$(mktemp -d) + # ''; + # }); + # } + overrideRequireHome = packageNames: old: + let + nameValuePairs = map (name: { + inherit name; + value = (builtins.getAttr name old).overrideAttrs (oldAttrs: { + preInstall = '' + ${oldAttrs.preInstall or ""} + export HOME=$(mktemp -d) + ''; + }); + }) packageNames; + in + builtins.listToAttrs nameValuePairs; + # Overrides package definition to skip check. # For example, # @@ -211,13 +243,14 @@ let defaultOverrides = old: new: let old0 = old; in let - old1 = old0 // (overrideRequireX packagesRequireingX old0); - old2 = old1 // (overrideSkipCheck packagesToSkipCheck old1); - old3 = old2 // (overrideRDepends packagesWithRDepends old2); - old4 = old3 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old3); - old5 = old4 // (overrideBuildInputs packagesWithBuildInputs old4); - old6 = old5 // (overrideBroken brokenPackages old5); - old = old6; + old1 = old0 // (overrideRequireX packagesRequiringX old0); + old2 = old1 // (overrideRequireHome packagesRequiringHome old1); + old3 = old2 // (overrideSkipCheck packagesToSkipCheck old2); + old4 = old3 // (overrideRDepends packagesWithRDepends old3); + old5 = old4 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old4); + old6 = old5 // (overrideBuildInputs packagesWithBuildInputs old5); + old7 = old6 // (overrideBroken brokenPackages old6); + old = old7; in old // (otherOverrides old new); # Recursive override pattern. @@ -480,7 +513,7 @@ let csaw = with pkgs; [ zlib.dev curl ]; }; - packagesRequireingX = [ + packagesRequiringX = [ "accrual" "ade4TkGUI" "analogue" @@ -670,6 +703,9 @@ let "x12GUI" ]; + packagesRequiringHome = [ + ]; + packagesToSkipCheck = [ "Rmpi" # tries to run MPI processes "pbdMPI" # tries to run MPI processes From 5e49d8461a30486a15d34b9beea3375a88b14e33 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Thu, 7 Oct 2021 22:18:25 +1100 Subject: [PATCH 02/21] rPackages.rgl: mark as broken --- 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 65082832ce3..4be100fb650 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -714,6 +714,7 @@ let # Packages which cannot be installed due to lack of dependencies or other reasons. brokenPackages = [ + "rgl" ]; otherOverrides = old: new: { From 22e4ee209e9ac75552dd1b1003a60317928f920b Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Thu, 7 Oct 2021 22:20:08 +1100 Subject: [PATCH 03/21] rPackages: unpin all GSL 1 dependencies All packages now successfully build against current GSL. --- pkgs/development/r-modules/default.nix | 36 +++++++++++++------------- 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 4be100fb650..9fdbb99f3fc 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -276,14 +276,14 @@ let adimpro = [ pkgs.imagemagick ]; animation = [ pkgs.which ]; audio = [ pkgs.portaudio ]; - BayesSAE = [ pkgs.gsl_1 ]; - BayesVarSel = [ pkgs.gsl_1 ]; + BayesSAE = [ pkgs.gsl ]; + BayesVarSel = [ pkgs.gsl ]; BayesXsrc = with pkgs; [ readline.dev ncurses ]; bigGP = [ pkgs.mpi ]; bio3d = [ pkgs.zlib ]; BiocCheck = [ pkgs.which ]; Biostrings = [ pkgs.zlib ]; - bnpmr = [ pkgs.gsl_1 ]; + bnpmr = [ pkgs.gsl ]; cairoDevice = [ pkgs.gtk2.dev ]; Cairo = with pkgs; [ libtiff libjpeg cairo.dev x11 fontconfig.lib ]; Cardinal = [ pkgs.which ]; @@ -292,7 +292,7 @@ let curl = [ pkgs.curl.dev ]; data_table = [ pkgs.zlib.dev ] ++ lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp; devEMF = with pkgs; [ xorg.libXft.dev x11 ]; - diversitree = with pkgs; [ gsl_1 fftw ]; + diversitree = with pkgs; [ gsl fftw ]; exactextractr = [ pkgs.geos ]; EMCluster = [ pkgs.lapack ]; fftw = [ pkgs.fftw.dev ]; @@ -300,28 +300,28 @@ let Formula = [ pkgs.gmp ]; gdtools = with pkgs; [ cairo.dev fontconfig.lib freetype.dev ]; git2r = with pkgs; [ zlib.dev openssl.dev libssh2.dev libgit2 pkg-config ]; - GLAD = [ pkgs.gsl_1 ]; + GLAD = [ pkgs.gsl ]; glpkAPI = with pkgs; [ gmp glpk ]; gmp = [ pkgs.gmp.dev ]; - graphscan = [ pkgs.gsl_1 ]; - gsl = [ pkgs.gsl_1 ]; + graphscan = [ pkgs.gsl ]; + gsl = [ pkgs.gsl ]; gert = [ pkgs.libgit2 ]; haven = with pkgs; [ libiconv zlib.dev ]; h5vc = [ pkgs.zlib.dev ]; - HiCseg = [ pkgs.gsl_1 ]; + HiCseg = [ pkgs.gsl ]; imager = [ pkgs.x11 ]; - iBMQ = [ pkgs.gsl_1 ]; + iBMQ = [ pkgs.gsl ]; igraph = with pkgs; [ gmp libxml2.dev ]; JavaGD = [ pkgs.jdk ]; jpeg = [ pkgs.libjpeg.dev ]; jqr = [ pkgs.jq.dev ]; - KFKSDS = [ pkgs.gsl_1 ]; + KFKSDS = [ pkgs.gsl ]; kza = [ pkgs.fftw.dev ]; lpsymphony = with pkgs; [ pkg-config gfortran gettext ]; lwgeom = with pkgs; [ proj geos gdal ]; magick = [ pkgs.imagemagick.dev ]; ModelMetrics = lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp; - mvabund = [ pkgs.gsl_1 ]; + mvabund = [ pkgs.gsl ]; mwaved = [ pkgs.fftw.dev ]; ncdf4 = [ pkgs.netcdf ]; nloptr = with pkgs; [ nlopt pkg-config ]; @@ -344,8 +344,8 @@ let readxl = [ pkgs.libiconv ]; rcdd = [ pkgs.gmp.dev ]; RcppCNPy = [ pkgs.zlib.dev ]; - RcppGSL = [ pkgs.gsl_1 ]; - RcppZiggurat = [ pkgs.gsl_1 ]; + RcppGSL = [ pkgs.gsl ]; + RcppZiggurat = [ pkgs.gsl ]; reprex = [ pkgs.which ]; rgdal = with pkgs; [ proj.dev gdal ]; rgeos = [ pkgs.geos ]; @@ -357,7 +357,7 @@ let Rhtslib = with pkgs; [ zlib.dev automake autoconf bzip2.dev xz.dev curl.dev ]; rjags = [ pkgs.jags ]; rJava = with pkgs; [ zlib bzip2.dev icu xz.dev pcre.dev jdk libzip ]; - Rlibeemd = [ pkgs.gsl_1 ]; + Rlibeemd = [ pkgs.gsl ]; rmatio = [ pkgs.zlib.dev ]; Rmpfr = with pkgs; [ gmp mpfr.dev ]; Rmpi = [ pkgs.mpi ]; @@ -385,12 +385,12 @@ let sf = with pkgs; [ gdal proj geos ]; terra = with pkgs; [ gdal proj geos ]; showtext = with pkgs; [ zlib libpng icu freetype.dev ]; - simplexreg = [ pkgs.gsl_1 ]; + simplexreg = [ pkgs.gsl ]; spate = [ pkgs.fftw.dev ]; ssanv = [ pkgs.proj ]; - stsm = [ pkgs.gsl_1 ]; + stsm = [ pkgs.gsl ]; stringi = [ pkgs.icu.dev ]; - survSNP = [ pkgs.gsl_1 ]; + survSNP = [ pkgs.gsl ]; svglite = [ pkgs.libpng.dev ]; sysfonts = with pkgs; [ zlib libpng freetype.dev ]; systemfonts = with pkgs; [ fontconfig.dev freetype.dev ]; @@ -398,7 +398,7 @@ let tesseract = with pkgs; [ tesseract leptonica ]; tiff = [ pkgs.libtiff.dev ]; tkrplot = with pkgs; [ xorg.libX11 tk.dev ]; - topicmodels = [ pkgs.gsl_1 ]; + topicmodels = [ pkgs.gsl ]; udunits2 = with pkgs; [ udunits expat ]; units = [ pkgs.udunits ]; V8 = [ pkgs.v8 ]; From 2ab8998641a6c8d3358fd4a0592e8c1a98719ba8 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Fri, 8 Oct 2021 14:07:23 +1100 Subject: [PATCH 04/21] rPackages.MatchIt: backport build patch --- pkgs/development/r-modules/default.nix | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 9fdbb99f3fc..fb4e0a66fd4 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -1035,6 +1035,12 @@ let ''; }); + MatchIt = old.MatchIt.overrideDerivation (attrs: { + patches = [ (pkgs.fetchpatch { + url = "https://github.com/kosukeimai/MatchIt/commit/8c15a1afa16b74eb04a45e7e46f8aca64ed89bcb.patch"; + sha256 = "sha256-3UI60n49xuX6LniHpTLOUSsHCEAQ7f1FMBVH0jNlW60="; + }) ]; + }); }; in self From 7f9e8c1d424c2032168f2014c77a0bc6e30025db Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Mon, 11 Oct 2021 15:51:10 +1100 Subject: [PATCH 05/21] rPackages.NetLogoR: mark as broken --- 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 fb4e0a66fd4..2e5c5b354d3 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -715,6 +715,7 @@ let # Packages which cannot be installed due to lack of dependencies or other reasons. brokenPackages = [ "rgl" + "NetLogoR" ]; otherOverrides = old: new: { From e6bf94c61546111bb60aa56a549ea4a4d05eca22 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Mon, 11 Oct 2021 22:11:22 +1100 Subject: [PATCH 06/21] rPackages.OmnipathR: 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 2e5c5b354d3..851fe1a1366 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -704,6 +704,7 @@ let ]; packagesRequiringHome = [ + "OmnipathR" ]; packagesToSkipCheck = [ From a50b96d990f7a6ad5a39260d772518243b40f8c9 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Mon, 11 Oct 2021 22:21:25 +1100 Subject: [PATCH 07/21] rPackages.ggiraph: 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 851fe1a1366..898338ec6f3 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -299,6 +299,7 @@ let fftwtools = with pkgs; [ fftw.dev pkg-config ]; Formula = [ pkgs.gmp ]; gdtools = with pkgs; [ cairo.dev fontconfig.lib freetype.dev ]; + ggiraph = with pkgs; [ pkgs.libpng.dev ]; git2r = with pkgs; [ zlib.dev openssl.dev libssh2.dev libgit2 pkg-config ]; GLAD = [ pkgs.gsl ]; glpkAPI = with pkgs; [ gmp glpk ]; From 07bf8a26b75e8e4fe6510b3a1899fccd52ab5d06 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Mon, 11 Oct 2021 22:26:11 +1100 Subject: [PATCH 08/21] rPackages.x13binary: mark broken --- 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 898338ec6f3..97aa29a6ee8 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -718,6 +718,7 @@ let brokenPackages = [ "rgl" "NetLogoR" + "x13binary" ]; otherOverrides = old: new: { From 95c7c9555aace3f87b279209b60cfecfda1854ec Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Tue, 12 Oct 2021 07:27:40 +1100 Subject: [PATCH 09/21] rPackages.mzR: 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 97aa29a6ee8..500cdf5a0d8 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -324,6 +324,7 @@ let ModelMetrics = lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp; mvabund = [ pkgs.gsl ]; mwaved = [ pkgs.fftw.dev ]; + mzR = [ pkgs.zlib ]; ncdf4 = [ pkgs.netcdf ]; nloptr = with pkgs; [ nlopt pkg-config ]; n1qn1 = [ pkgs.gfortran ]; From 6dbe8156765a3c1b0e32842a5d30191b575ba8f7 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Tue, 12 Oct 2021 07:42:01 +1100 Subject: [PATCH 10/21] rPackages.keyring: fix build --- pkgs/development/r-modules/default.nix | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 500cdf5a0d8..f81cfb22ef7 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -1034,6 +1034,12 @@ let buildInputs = [ libsodium.dev ] ++ attrs.buildInputs; }); + keyring = old.keyring.overrideDerivation (attrs: { + preConfigure = '' + patchShebangs configure + ''; + }); + Rhtslib = old.Rhtslib.overrideDerivation (attrs: { preConfigure = '' substituteInPlace R/zzz.R --replace "-lcurl" "-L${pkgs.curl.out}/lib -lcurl" From 83ada1edeef94564acafab0cd4a5ea0569ceb1a4 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Tue, 12 Oct 2021 08:12:49 +1100 Subject: [PATCH 11/21] rPackages: mark R.cache depenencies as requiring home --- pkgs/development/r-modules/default.nix | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index f81cfb22ef7..8dca60120de 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -706,7 +706,23 @@ let ]; packagesRequiringHome = [ + "aroma_affymetrix" + "aroma_cn" + "aroma_core" + "csodata" + "DiceView" + "MSnID" "OmnipathR" + "precommit" + "PSCBS" + "repmis" + "R_filesets" + "RKorAPClient" + "R_rsp" + "scholar" + "stepR" + "styler" + "TreeTools" ]; packagesToSkipCheck = [ From 403bcccbb3a5f5faaeada2c54e83d0b9a8e0ec35 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Tue, 12 Oct 2021 08:18:04 +1100 Subject: [PATCH 12/21] rPackages.R_cache: shift override to requiring home framework --- pkgs/development/r-modules/default.nix | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 8dca60120de..7daed4c781d 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -716,6 +716,7 @@ let "precommit" "PSCBS" "repmis" + "R_cache" "R_filesets" "RKorAPClient" "R_rsp" @@ -1030,12 +1031,6 @@ let ''; }); - R_cache = old.R_cache.overrideDerivation (attrs: { - preConfigure = '' - export R_CACHE_ROOTPATH=$TMP - ''; - }); - lpsymphony = old.lpsymphony.overrideDerivation (attrs: { preConfigure = '' patchShebangs configure From 09730dc3997247bf624f19389a355aefad26d2e1 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Tue, 12 Oct 2021 08:37:18 +1100 Subject: [PATCH 13/21] rPackages.av: mark as broken --- 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 7daed4c781d..f7592837204 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -734,6 +734,7 @@ let # Packages which cannot be installed due to lack of dependencies or other reasons. brokenPackages = [ + "av" "rgl" "NetLogoR" "x13binary" From 7af21117921c5d7ce77f122ba8975782022fd3c5 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Tue, 12 Oct 2021 09:05:10 +1100 Subject: [PATCH 14/21] rPackages.proj4: mark as broken --- pkgs/development/r-modules/default.nix | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index f7592837204..1669162c529 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -737,6 +737,7 @@ let "av" "rgl" "NetLogoR" + "proj4" "x13binary" ]; @@ -1064,6 +1065,7 @@ let sha256 = "sha256-3UI60n49xuX6LniHpTLOUSsHCEAQ7f1FMBVH0jNlW60="; }) ]; }); + }; in self From a644e88ab4f997879e5d9d0dfd9213e125be9973 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Wed, 13 Oct 2021 06:51:43 +1100 Subject: [PATCH 15/21] 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 1669162c529..c714d9a571f 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 16/21] 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 c714d9a571f..5053d951767 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 17/21] 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 5053d951767..09d18dcb6b9 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 afc9de3a95a..00000000000 --- 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 18/21] 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 09d18dcb6b9..d1309024613 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 = [ From e26f35b8cedbf072ef5003c8b3a9d9e2cda487ec Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Tue, 7 Sep 2021 14:34:15 +1000 Subject: [PATCH 19/21] rPackages.h2o: disable JAR fetching while in nix build --- pkgs/development/r-modules/default.nix | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index d1309024613..6bd4ada845f 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -1065,6 +1065,18 @@ let }) ]; }); + h2o = old.h2o.overrideDerivation (attrs: { + preConfigure = '' + # prevent download of jar file during install and postpone to first use + sed -i '/downloadJar()/d' R/zzz.R + + # during runtime the package directory is not writable as it's in the + # nix store, so store the jar in the user's cache directory instead + substituteInPlace R/connection.R --replace \ + 'dest_file <- file.path(dest_folder, "h2o.jar")' \ + 'dest_file <- file.path("~/.cache/", "h2o.jar")' + ''; + }); }; in self From b1d8a801a0ae8de0a292e1cdd5fc91e8255b47f7 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Wed, 13 Oct 2021 15:32:30 +1100 Subject: [PATCH 20/21] rPackages.mzR: fix aarch64-linux build --- pkgs/development/r-modules/default.nix | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 6bd4ada845f..d1bd608f7c7 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -324,7 +324,7 @@ let ModelMetrics = lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp; mvabund = [ pkgs.gsl ]; mwaved = [ pkgs.fftw.dev ]; - mzR = [ pkgs.zlib ]; + mzR = with pkgs; [ zlib boost159.dev netcdf ]; ncdf4 = [ pkgs.netcdf ]; nloptr = with pkgs; [ nlopt pkg-config ]; n1qn1 = [ pkgs.gfortran ]; @@ -479,7 +479,6 @@ let tikzDevice = with pkgs; [ which texlive.combined.scheme-medium ]; gridGraphics = [ pkgs.which ]; adimpro = with pkgs; [ which xorg.xdpyinfo ]; - mzR = [ pkgs.netcdf ]; cluster = [ pkgs.libiconv ]; KernSmooth = [ pkgs.libiconv ]; nlme = [ pkgs.libiconv ]; From 3a0bdda3d91ca750f9be08e93bb37cc45b814357 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Sun, 17 Oct 2021 08:41:58 +1100 Subject: [PATCH 21/21] R: add myself to maintainers --- pkgs/applications/science/math/R/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/applications/science/math/R/default.nix b/pkgs/applications/science/math/R/default.nix index a8fdfe8571a..7d3f73228fc 100644 --- a/pkgs/applications/science/math/R/default.nix +++ b/pkgs/applications/science/math/R/default.nix @@ -120,6 +120,6 @@ stdenv.mkDerivation rec { platforms = platforms.all; hydraPlatforms = platforms.linux; - maintainers = with maintainers; [ peti ] ++ teams.sage.members; + maintainers = with maintainers; [ jbedo peti ] ++ teams.sage.members; }; }