From 85a9e6dcdf26c96ae360bd156b3bbf919efaf239 Mon Sep 17 00:00:00 2001 From: Peter Simons Date: Fri, 21 Apr 2017 20:00:32 +0200 Subject: [PATCH] R: update list of broken packages (and some cosmetic) --- pkgs/development/r-modules/README.md | 5 +- pkgs/development/r-modules/default.nix | 55 +++++++++++++++++++ pkgs/development/r-modules/generate-shell.nix | 3 +- 3 files changed, 59 insertions(+), 4 deletions(-) diff --git a/pkgs/development/r-modules/README.md b/pkgs/development/r-modules/README.md index 5aa839b3b5a8..fc046ed0627e 100644 --- a/pkgs/development/r-modules/README.md +++ b/pkgs/development/r-modules/README.md @@ -12,7 +12,7 @@ use by adding the following snippet to your $HOME/.config/nixpkgs/config.nix fil { rEnv = super.rWrapper.override { - packages = with self.rPackages; [ + packages = with self.rPackages; [ devtools ggplot2 reshape2 @@ -65,7 +65,7 @@ set `useRPackages` to `true`, like below: { rEnv = super.rWrapper.override { - packages = with self.rPackages; [ + packages = with self.rPackages; [ devtools ggplot2 reshape2 @@ -106,4 +106,3 @@ nix-build test-evaluation.nix --dry-run ``` If this exits fine, the expression is ok. If not, you have to edit `default.nix` - diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index ace649719c65..5c0ed284e4ae 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -694,21 +694,27 @@ let "acs" # build is broken "agRee" # depends on broken package BRugs-0.8-6 "aLFQ" # depends on broken package bio3d-2.3-1 + "anamiR" # depends on broken package RMySQL-0.10.11 + "AneuFinder" # depends on broken package Rhtslib-1.6.0 "animation" # build is broken "anim_plots" # depends on broken package animation-2.4 "annmap" # depends on broken package RMySQL-0.10.9 "apaStyle" # depends on broken package gdtools-0.1.3 "apaTables" # depends on broken package OpenMx-2.7.4 + "aptg" # depends on broken package brranching-0.2.0 "ArrayExpressHTS" # build is broken "arrayQualityMetrics" # build is broken "auRoc" # depends on broken package OpenMx-2.7.4 + "bamsignals" # depends on broken package Rhtslib-1.6.0 "BatchQC" # build is broken + "bayesCL" # build is broken "bayou" # depends on broken package animation-2.4 "bedr" # build is broken "BETS" # build is broken "BiGGR" # depends on broken package rsbml-2.30.0 "bio3d" # build is broken "bioassayR" # depends on broken package ChemmineR-2.24.2 + "bioCancer" # depends on broken package covr-2.2.2 "biomformat" # depends on broken package r-rhdf5-2.16.0 "biotools" # depends on broken package rpanel-1.1-3 "birte" # build is broken @@ -730,6 +736,8 @@ let "categoryCompare" # depends on broken package RCytoscape-1.21.1 "Causata" # depends on broken package RMySQL-0.10.9 "cdcfluview" # depends on broken package V8-1.2 + "CexoR" # depends on broken package Rhtslib-1.6.0 + "ChAMP" # depends on broken package goseq-1.26.0 "ChemmineDrugs" # depends on broken package ChemmineR-2.24.2 "ChemmineR" # build is broken "chinese_misc" # build is broken @@ -759,11 +767,13 @@ let "ctsem" # depends on broken package OpenMx-2.7.4 "cudaBayesreg" # build is broken "cytofkit" # depends on broken package flowCore-1.38.2 + "CytoML" # depends on broken package flowCore-1.40.6 "daff" # depends on broken package V8-1.2 "dagbag" # build is broken "dagitty" # depends on broken package V8-1.2 "dagLogo" # depends on broken package MotIV-1.28.0 "DAISIE" # depends on broken package animation-2.4 + "DataEntry" # build is broken "dataMaid" # build is broken "dataone" # build is broken "datapack" # build is broken @@ -772,7 +782,9 @@ let "DCM" # build is broken "DDD" # depends on broken package animation-2.4 "deBInfer" # depends on broken package PBSddesolve-1.12.2 + "debrowser" # depends on broken package V8-1.4 "DecisionCurve" # build is broken + "DeepBlueR" # build is broken "deepSNV" # build is broken "DEGraph" # depends on broken package RCytoscape-1.21.1 "DEploid" # build is broken @@ -795,11 +807,14 @@ let "euroMix" # build is broken "evobiR" # depends on broken package animation-2.4 "exifr" # build is broken + "ExperimentHubData" # build is broken "exprso" # build is broken "fastR" # build is broken + "fCCAC" # depends on broken package Rhtslib-1.6.0 "fdq" # depends on broken package gdtools-0.1.3 "Fgmutils" # depends on broken package gdtools-0.1.3 "flan" # build is broken + "flextable" # depends on broken package gdtools-0.1.4 "flowAI" # depends on broken package r-flowCore-1.38.2 "flowBeads" # depends on broken package r-flowCore-1.38.2 "flowBin" # depends on broken package r-flowCore-1.38.2 @@ -816,6 +831,7 @@ let "flowMeans" # depends on broken package r-flowCore-1.38.2 "flowMerge" # depends on broken package r-flowCore-1.38.2 "flowPeaks" # build is broken + "flowPloidy" # depends on broken package flowCore-1.40.6 "flowQB" # depends on broken package r-flowCore-1.38.2 "flowQ" # depends on broken package flowCore-1.38.2 "FlowSOM" # depends on broken package r-flowCore-1.38.2 @@ -842,6 +858,8 @@ let "gazepath" # build is broken "gdtools" # build is broken "GENE_E" # depends on broken package r-rhdf5-2.16.0 + "GenoGAM" # build is broken + "genomation" # depends on broken package Rhtslib-1.6.0 "geojson" # depends on broken package r-protolite-1.5 "geojsonio" # depends on broken package V8-1.2 "geojsonlint" # depends on broken package V8-1.2 @@ -849,18 +867,22 @@ let "gfer" # depends on broken package V8-1.2 "ggcyto" # depends on broken package r-flowCore-1.38.2 "ggghost" # depends on broken package animation-2.4 + "ggimage" # depends on broken package gridGraphics-0.1-5 "ggiraph" # depends on broken package gdtools-0.1.3 "ggiraphExtra" # depends on broken package gdtools-0.1.3 "ggseas" # build is broken + "gmapR" # build is broken "gmatrix" # depends on broken package cudatoolkit-8.0.61 "gMCP" # build is broken "gmDatabase" # depends on broken package RMySQL-0.10.9 "gmum_r" # build is broken "googleformr" # build is broken + "goseq" # build is broken "gpg" # build is broken "gpuR" # build is broken "gputools" # depends on broken package cudatoolkit-8.0.61 "GraphPAC" # build is broken + "greengenes13_5MgDb" # build is broken "gridGraphics" # build is broken "GSCA" # depends on broken package r-rhdf5-2.16.0 "GUIDE" # depends on broken package rpanel-1.1-3 @@ -870,11 +892,14 @@ let "harrietr" # build is broken "HDF5Array" # depends on broken package r-rhdf5-2.16.0 "healthyFlowData" # depends on broken package r-flowCore-1.38.2 + "hexSticker" # depends on broken package gridGraphics-0.1-5 "HierO" # build is broken "HilbertVisGUI" # build is broken "HiPLARM" # build is broken "hisse" # depends on broken package animation-2.4 + "hoardeR" # depends on broken package Rhtslib-1.6.0 "homomorpheR" # depends on broken package sodium-0.4 + "HTSeqGenie" # depends on broken package gmapR-1.16.0 "HTSSIP" # depends on broken package r-rhdf5-2.16.0 "idm" # depends on broken package animation-2.4 "ifaTools" # depends on broken package OpenMx-2.7.4 @@ -882,6 +907,7 @@ let "IHWpaper" # depends on broken package r-lpsymphony-1.0.2 "IlluminaHumanMethylation450k_db" # build is broken "immunoClust" # depends on broken package r-flowCore-1.38.2 + "imputeR" # depends on broken package ridge-2.2 "intansv" # build is broken "interactiveDisplay" # build is broken "ionicons" # depends on broken package rsvg-1.0 @@ -894,8 +920,10 @@ let "KoNLP" # build is broken "largeList" # build is broken "largeVis" # build is broken + "lavaan_shiny" # depends on broken package OpenMx-2.7.10 "lawn" # depends on broken package V8-1.2 "LCMCR" # build is broken + "LeArEst" # depends on broken package opencpu-1.6.1 "lefse" # build is broken "lfe" # build is broken "lgcp" # depends on broken package rpanel-1.1-3 @@ -918,6 +946,7 @@ let "MBESS" # depends on broken package OpenMx-2.7.4 "mBvs" # build is broken "mcaGUI" # build is broken + "mcPAFit" # build is broken "mdsr" # depends on broken package RMySQL-0.10.9 "Mediana" # depends on broken package gdtools-0.1.3 "melviewr" # build is broken @@ -928,12 +957,14 @@ let "metagear" # build is broken "MetaIntegrator" # depends on broken package RMySQL-0.10.9 "metaSEM" # depends on broken package OpenMx-2.7.4 + "methylKit" # depends on broken package Rhtslib-1.6.0 "MigClim" # build is broken "minimist" # depends on broken package V8-1.2 "miscF" # depends on broken package BRugs-0.8-6 "mixlink" # build is broken "MLSeq" # build is broken "mmnet" # build is broken + "MODIStsp" # build is broken "MonetDBLite" # build is broken "mongolite" # build is broken "monogeneaGM" # depends on broken package animation-2.4 @@ -960,7 +991,9 @@ let "ndjson" # build is broken "ndtv" # depends on broken package animation-2.4 "NetRep" # depends on broken package r-RhpcBLASctl-0.15-148 + "networkBMA" # build is broken "nlts" # build is broken + "normr" # depends on broken package Rhtslib-1.6.0 "NORRRM" # build is broken "odbc" # build is broken "officer" # depends on broken package gdtools-0.1.3 @@ -970,10 +1003,12 @@ let "OpenMx" # build is broken "optbdmaeAT" # build is broken "optBiomarker" # depends on broken package rpanel-1.1-3 + "optrcdmaeAT" # build is broken "ora" # depends on broken package ROracle-1.3-1 "OUwie" # depends on broken package animation-2.4 "PAA" # build is broken "paleotree" # depends on broken package animation-2.4 + "PathoStat" # depends on broken package BatchQC-1.2.1 "PathSelectMP" # build is broken "PatternClass" # build is broken "PBD" # depends on broken package animation-2.4 @@ -990,6 +1025,7 @@ let "PGA" # build is broken "PGPC" # depends on broken package ChemmineR-2.24.2 "ph2bye" # depends on broken package animation-2.4 + "PharmacoGx" # build is broken "PhyInformR" # depends on broken package animation-2.4 "phylocurve" # depends on broken package animation-2.4 "phyloseq" # depends on broken package r-rhdf5-2.16.0 @@ -999,6 +1035,7 @@ let "PING" # depends on broken package PICS-2.16.0 "plateCore" # depends on broken package r-flowCore-1.38.2 "plfMA" # build is broken + "plink" # build is broken "podkat" # build is broken "PottsUtils" # depends on broken package BRugs-0.8-6 "powell" # build is broken @@ -1036,8 +1073,10 @@ let "raptr" # depends on broken package PBSmapping-2.69.76 "RbioRXN" # depends on broken package ChemmineR-2.24.2 "Rblpapi" # build is broken + "RCAS" # depends on broken package Rhtslib-1.6.0 "Rchemcpp" # depends on broken package ChemmineR-2.24.2 "rchess" # depends on broken package V8-1.2 + "RchivalTag" # depends on broken package PBSmapping-2.69.76 "RchyOptimyx" # depends on broken package r-flowCore-1.38.2 "RcmdrPlugin_FuzzyClust" # build is broken "RcmdrPlugin_PcaRobust" # build is broken @@ -1050,6 +1089,7 @@ let "rcqp" # build is broken "rcrypt" # build is broken "RCytoscape" # build is broken + "rdataretriever" # build is broken "rDEA" # build is broken "RDieHarder" # build is broken "REBayes" # depends on broken package Rmosek-1.2.5.1 @@ -1065,8 +1105,10 @@ let "Rgnuplot" # build is broken "rgp" # build is broken "rgpui" # depends on broken package rgp-0.4-1 + "rgsepd" # depends on broken package goseq-1.26.0 "rhdf5" # build is broken "RhpcBLASctl" # build is broken + "Rhtslib" # build is broken "ridge" # build is broken "rjade" # depends on broken package V8-1.2 "rJPSGCS" # build is broken @@ -1079,9 +1121,12 @@ let "rmapshaper" # depends on broken package V8-1.2 "rMAT" # build is broken "Rmosek" # build is broken + "rmumps" # build is broken "RMySQL" # build is broken + "rnaturalearth" # depends on broken package sf-0.4-1 "RnavGraph" # build is broken "rnetcarto" # build is broken + "ROI_plugin_clp" # depends on broken package clpAPI-1.2.7 "ROI_plugin_cplex" # depends on broken package Rcplex-0.3-3 "ROI_plugin_symphony" # depends on broken package Rsymphony-0.1-26 "ROracle" # build is broken @@ -1092,6 +1137,7 @@ let "Rphylopars" # depends on broken package animation-2.4 "Rpoppler" # build is broken "RQuantLib" # build is broken + "Rsampletrees" # build is broken "RSAP" # build is broken "rsbml" # build is broken "RSCABS" # build is broken @@ -1110,6 +1156,7 @@ let "s2" # build is broken "sapFinder" # build is broken "sbrl" # build is broken + "SC3" # depends on broken package scater-1.2.0 "scater" # depends on broken package r-rhdf5-2.16.0 "scran" # depends on broken package r-rhdf5-2.16.0 "SDD" # depends on broken package rpanel-1.1-3 @@ -1117,6 +1164,7 @@ let "seasonalview" # build is broken "Sejong" # build is broken "SemiCompRisks" # build is broken + "semPlot" # depends on broken package OpenMx-2.7.10 "semtree" # depends on broken package OpenMx-2.7.4 "seqbias" # build is broken "SeqGrapheR" # build is broken @@ -1129,6 +1177,7 @@ let "SimInf" # build is broken "simsalapar" # build is broken "smapr" # depends on broken package r-rhdf5-2.16.0 + "SMITE" # depends on broken package goseq-1.26.0 "SnakeCharmR" # build is broken "sodium" # build is broken "soilphysics" # depends on broken package rpanel-1.1-3 @@ -1146,20 +1195,24 @@ let "subspaceMOA" # depends on broken package animation-2.4 "svglite" # depends on broken package gdtools-0.1.3 "sybilSBML" # build is broken + "SymTS" # build is broken "synthACS" # depends on broken package acs-2.0 "tcpl" # depends on broken package RMySQL-0.10.9 "TDA" # build is broken "TED" # depends on broken package animation-2.4 "tesseract" # build is broken + "texPreview" # depends on broken package magick-0.4 "textreadr" # build is broken "textTinyR" # build is broken "TFBSTools" # depends on broken package CNEr-1.8.3 + "tilegramsR" # depends on broken package sf-0.4-1 "TKF" # depends on broken package animation-2.4 "tmap" # depends on broken package V8-1.2 "tmaptools" # depends on broken package V8-1.2 "tofsims" # build is broken "toxboot" # depends on broken package RMySQL-0.10.9 "TransView" # build is broken + "treatSens" # build is broken "treeplyr" # depends on broken package animation-2.4 "TSMySQL" # depends on broken package RMySQL-0.10.9 "uaparserjs" # depends on broken package V8-1.2 @@ -1168,12 +1221,14 @@ let "umx" # depends on broken package OpenMx-2.7.4 "userfriendlyscience" # depends on broken package OpenMx-2.7.4 "V8" # build is broken + "VariantTools" # depends on broken package gmapR-1.16.0 "VBmix" # build is broken "vcfR" # build is broken "vdiffr" # depends on broken package gdtools-0.1.3 "vmsbase" # depends on broken package PBSmapping-2.69.76 "wallace" # depends on broken package V8-1.2 "wand" # build is broken + "WebGestaltR" # depends on broken package PythonInR-0.1-3 "webp" # build is broken "wordbankr" # depends on broken package RMySQL-0.10.9 "x13binary" # build is broken diff --git a/pkgs/development/r-modules/generate-shell.nix b/pkgs/development/r-modules/generate-shell.nix index 126ab7422925..beb378275087 100644 --- a/pkgs/development/r-modules/generate-shell.nix +++ b/pkgs/development/r-modules/generate-shell.nix @@ -6,7 +6,8 @@ stdenv.mkDerivation { buildCommand = "exit 1"; buildInputs = [ wget ]; - nativeBuildInputs = [ + + nativeBuildInputs = [ (rWrapper.override { packages = with rPackages; [ data_table