From e98a231af8f3d6bd70f05f588a153b9e20eaa73f Mon Sep 17 00:00:00 2001 From: Jeffrey David Johnson Date: Sat, 26 Mar 2016 11:26:29 -0700 Subject: work on fixing up bioconductor packages --- pkgs/development/r-modules/default.nix | 344 +++------------------------------ 1 file changed, 26 insertions(+), 318 deletions(-) (limited to 'pkgs/development/r-modules') diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index c2fd00c8d78e..3f0553de85ea 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -698,12 +698,35 @@ let # Packages which cannot be installed due to lack of dependencies or other reasons. brokenPackages = [ - "RareVariantVis" # broken build + "TransView" # broken build + "Starr" # broken build + "SICtools" # broken build + "ReQON" # depends on broken package seqbias + "seqbias" # broken build + "Repitools" # broken build + "QuasR" # broken build + "qrqc" # broken build + "ProteomicsAnnotationHubData" # broken build + "podkat" # broken build + "PING" # depends on broken package PICS + "PICS" # broken build + "mcaGUI" # broken build + "deepSNV" # broken build + "motifbreakR" # depends on broken package MotIV + "LowMACA" # depends on broken package MotIV + "dagLogo" # depends on broken package MotIV + "motifStack" # depends on broken package MotIV + "MotIV" # broken build + "CNEr" # broken build + "canceR" # broken build + "BubbleTree" # broken build + "arrayQualityMetrics" # broken build + "ArrayExpressHTS" # broken build + "TargetSearchData" # depends on broken package TargetSearch + "TargetSearch" # broken build "ptw" # depends on broken package nloptr - "INSPEcT" # broken build "gpuR" # broken build "erma" # broken build - "CNVPanelizer" # broken build "MBmca" # depends on broken package chipPCR "dpcR" # depends on broken package chipPCR "chipPCR" # broken build @@ -721,294 +744,9 @@ let "categoryCompare" # depends on broken package RCytoscape "preseqR" # depends on broken package polynom "permutations" # depends on broken package partitions - "yummlyr" # depends on broken package openssl - "yhatr" # depends on broken package openssl - "WufooR" # depends on broken package openssl - "WikiSocio" # depends on broken package openssl - "WikipediR" # depends on broken package openssl - "WikipediaR" # depends on broken package openssl - "WikidataR" # depends on broken package openssl - "whoapi" # depends on broken package openssl - "whoami" # depends on broken package openssl - "WHO" # depends on broken package openssl - "WaterML" # depends on broken package openssl - "vegdata" # depends on broken package openssl - "twitteR" # depends on broken package openssl - "tumblR" # depends on broken package openssl - "tuber" # depends on broken package openssl - "translateR" # depends on broken package openssl - "transcribeR" # depends on broken package openssl - "TMDb" # depends on broken package openssl - "tigris" # depends on broken package openssl - "threewords" # depends on broken package openssl - "SWMPr" # depends on broken package openssl - "swirlify" # depends on broken package openssl - "swirl" # depends on broken package openssl - "stplanr" # depends on broken package openssl - "stmBrowser" # depends on broken package openssl - "spareserver" # depends on broken package openssl - "solrium" # depends on broken package openssl - "solr" # depends on broken package openssl - "SocialMediaMineR" # depends on broken package openssl - "PogromcyDanych" # depends on broken package openssl - "SmarterPoland" # depends on broken package openssl - "slackr" # depends on broken package openssl - "sbgr" # depends on broken package openssl - "RYandexTranslate" # depends on broken package openssl - "rwunderground" # depends on broken package openssl - "rWBclimate" # depends on broken package openssl - "wikipediatrend" # depends on broken package openssl - "webchem" # depends on broken package openssl - "sejmRP" # depends on broken package openssl - "scholar" # depends on broken package openssl - "RTCGA_rnaseq" # depends on broken package openssl - "RTCGA_mutations" # depends on broken package openssl - "RTCGA_clinical" # depends on broken package openssl - "RTCGA" # depends on broken package openssl - "rNOMADS" # depends on broken package openssl - "nhanesA" # depends on broken package openssl - "MazamaSpatialUtils" # depends on broken package openssl - "gsheet" # depends on broken package openssl - "rvest" # depends on broken package openssl - "rvertnet" # depends on broken package openssl - "rusda" # depends on broken package openssl - "rtimes" # depends on broken package openssl - "rsunlight" # depends on broken package openssl - "rstatscn" # depends on broken package openssl - "RSocrata" # depends on broken package openssl - "rsnps" # depends on broken package openssl - "RSiteCatalyst" # depends on broken package openssl - "rscopus" # depends on broken package openssl - "rredlist" # depends on broken package openssl - "RPublica" # depends on broken package openssl - "RPresto" # depends on broken package openssl - "rplos" # depends on broken package openssl - "rotl" # depends on broken package openssl - "rorcid" # depends on broken package openssl - "ROptimizely" # depends on broken package openssl - "ROpenWeatherMap" # depends on broken package openssl - "robotstxt" # depends on broken package openssl - "rnoaa" # depends on broken package openssl - "RNeo4j" # depends on broken package openssl - "rnbn" # depends on broken package openssl - "Rmonkey" # depends on broken package openssl - "Rlinkedin" # depends on broken package openssl - "rinat" # depends on broken package openssl - "ridigbio" # depends on broken package openssl - "rHealthDataGov" # depends on broken package openssl - "RGoogleAnalyticsPremium" # depends on broken package openssl - "RGoogleAnalytics" # depends on broken package openssl - "heemod" # depends on broken package openssl - "rgho" # depends on broken package openssl - "rgeolocate" # depends on broken package openssl - "RGA" # depends on broken package openssl - "RForcecom" # depends on broken package openssl - "rfoaas" # depends on broken package openssl - "rfml" # depends on broken package openssl - "rfisheries" # depends on broken package openssl - "rfishbase" # depends on broken package openssl - "zoon" # depends on broken package openssl - "rfigshare" # depends on broken package openssl - "Rfacebook" # depends on broken package openssl - "rerddap" # depends on broken package openssl - "request" # depends on broken package openssl - "repmis" # depends on broken package openssl - "rentrez" # depends on broken package openssl - "REDCapR" # depends on broken package openssl - "redcapAPI" # depends on broken package openssl - "rechonest" # depends on broken package openssl - "rebird" # depends on broken package openssl - "rdrop2" # depends on broken package openssl - "rdian" # depends on broken package openssl - "RCy3" # depends on broken package openssl - "rcrossref" # depends on broken package openssl - "RCriteo" # depends on broken package openssl - "Rcolombos" # depends on broken package openssl - "rclinicaltrials" # depends on broken package openssl - "rbison" # depends on broken package openssl - "rbhl" # depends on broken package openssl - "randNames" # depends on broken package openssl - "quickmapr" # depends on broken package openssl - "qrmtools" # depends on broken package openssl - "Quandl" # depends on broken package openssl - "pxweb" # depends on broken package openssl - "pvsR" # depends on broken package openssl - "pushoverr" # depends on broken package openssl - "PSICQUIC" # depends on broken package openssl - "prism" # depends on broken package openssl - "primerTree" # depends on broken package openssl - "pollstR" # depends on broken package openssl - "plotly" # depends on broken package openssl - "pinnacle_API" # depends on broken package openssl - "pdftables" # depends on broken package openssl - "pdfetch" # depends on broken package openssl - "paxtoolsr" # depends on broken package openssl - "pageviews" # depends on broken package openssl - "packagetrackr" # depends on broken package openssl - "ores" # depends on broken package openssl - "OECD" # depends on broken package openssl - "rdryad" # depends on broken package openssl - "rdatacite" # depends on broken package openssl - "pangaear" # depends on broken package openssl - "oai" # depends on broken package openssl - "neotoma" # depends on broken package openssl - "myvariant" # depends on broken package openssl - "mygene" # depends on broken package openssl - "EMbC" # depends on broken package openssl - "move" # depends on broken package openssl - "miRLAB" # depends on broken package openssl - "AzureML" # depends on broken package openssl - "miniCRAN" # depends on broken package openssl - "markmyassignment" # depends on broken package openssl - "manifestoR" # depends on broken package openssl - "TLdating" # depends on broken package openssl - "RLumShiny" # depends on broken package openssl - "Luminescence" # depends on broken package openssl - "lumendb" # depends on broken package openssl - "lucr" # depends on broken package openssl - "longurl" # depends on broken package openssl - "lintr" # depends on broken package openssl - "LightningR" # depends on broken package openssl - "interAdapt" # depends on broken package openssl - "knitcitations" # depends on broken package openssl - "ROntoTools" # depends on broken package openssl - "RnaSeqSampleSize" # depends on broken package openssl - "CompGO" # depends on broken package openssl - "pathview" # depends on broken package openssl - "PAPi" # depends on broken package openssl - "mmnet" # depends on broken package openssl - "KEGGprofile" # depends on broken package openssl - "Hiiragi2013" # depends on broken package openssl - "gage" # depends on broken package openssl - "clusterProfiler" # depends on broken package openssl - "KEGGREST" # depends on broken package openssl - "internetarchive" # depends on broken package openssl - "SocialMediaLab" # depends on broken package openssl - "instaR" # depends on broken package openssl - "imguR" # depends on broken package openssl - "idbr" # depends on broken package openssl - "httping" # depends on broken package openssl - "httpcache" # depends on broken package openssl - "htmltab" # depends on broken package openssl - "hoardeR" # depends on broken package openssl - "googlesheets" # depends on broken package openssl - "GoogleGenomics" # depends on broken package openssl - "googleformr" # depends on broken package openssl - "searchConsoleR" # depends on broken package openssl - "googleAuthR" # depends on broken package openssl - "gmailr" # depends on broken package openssl - "gitlabr" # depends on broken package openssl - "switchrGist" # depends on broken package openssl - "spoccutils" # depends on broken package openssl - "rbokeh" # depends on broken package openssl - "mapr" # depends on broken package openssl - "gistr" # depends on broken package openssl - "geoknife" # depends on broken package openssl - "geocodeHERE" # depends on broken package openssl - "genderizeR" # depends on broken package openssl - "NLPutils" # depends on broken package openssl - "qdap" # depends on broken package openssl - "gender" # depends on broken package openssl - "GAR" # depends on broken package openssl - "flora" # depends on broken package openssl - "fitbitScraper" # depends on broken package openssl - "federalregister" # depends on broken package openssl - "eurostat" # depends on broken package openssl - "enigma" # depends on broken package openssl - "elastic" # depends on broken package openssl - "ecoengine" # depends on broken package openssl - "ecb" # depends on broken package openssl - "dpmr" # depends on broken package openssl - "distcomp" # depends on broken package openssl - "diezeit" # depends on broken package openssl - "wru" # depends on broken package openssl - "TCGAbiolinks" # depends on broken package openssl - "regionReport" # depends on broken package openssl - "rbundler" # depends on broken package openssl - "pacman" # depends on broken package openssl - "x_ent" # depends on broken package openssl - "opencpu" # depends on broken package openssl - "inpdfr" # depends on broken package openssl - "metacom" # depends on broken package openssl - "FedData" # depends on broken package openssl - "easypackages" # depends on broken package openssl - "demi" # depends on broken package openssl - "creditr" # depends on broken package openssl - "cogena" # depends on broken package openssl - "bisectr" # depends on broken package openssl - "devtools" # depends on broken package openssl - "ddeploy" # depends on broken package openssl - "EGRETci" # depends on broken package openssl - "EGRET" # depends on broken package openssl - "dataRetrieval" # depends on broken package openssl - "dataonderivatives" # depends on broken package openssl - "crunch" # depends on broken package openssl - "cranlogs" # depends on broken package openssl - "covr" # depends on broken package openssl - "couchDB" # depends on broken package openssl - "ckanr" # depends on broken package openssl - "chromer" # depends on broken package openssl - "chillR" # depends on broken package openssl - "censusr" # depends on broken package openssl - "cdcfluview" # depends on broken package openssl - "boxr" # depends on broken package openssl - "traits" # depends on broken package openssl - "TR8" # depends on broken package openssl - "SigTree" # depends on broken package openssl - "phyext2" # depends on broken package openssl - "PCPS" # depends on broken package openssl - "BMhyd" # depends on broken package openssl - "BioGeoBEARS" # depends on broken package openssl - "treescape" # depends on broken package openssl - "phylosignal" # depends on broken package openssl - "adephylo" # depends on broken package openssl - "phylobase" # depends on broken package openssl - "RNeXML" # depends on broken package openssl - "myTAI" # depends on broken package openssl - "MonoPhy" # depends on broken package openssl - "brranching" # depends on broken package openssl - "bdvis" # depends on broken package openssl - "taxize" # depends on broken package openssl - "bold" # depends on broken package openssl - "biomartr" # depends on broken package openssl - "BiocCheck" # depends on broken package openssl - "bigrquery" # depends on broken package openssl - "benchmarkme" # depends on broken package openssl - "atsd" # depends on broken package openssl - "fulltext" # depends on broken package openssl - "aRxiv" # depends on broken package openssl - "SpaDES" # depends on broken package openssl - "archivist_github" # depends on broken package openssl - "archivist" # depends on broken package openssl - "AntWeb" # depends on broken package openssl - "RefNet" # depends on broken package openssl - "pwOmics" # depends on broken package openssl - "grasp2db" # depends on broken package openssl - "EnsDb_Rnorvegicus_v79" # depends on broken package openssl - "EnsDb_Rnorvegicus_v75" # depends on broken package openssl - "EnsDb_Mmusculus_v79" # depends on broken package openssl - "EnsDb_Mmusculus_v75" # depends on broken package openssl - "EnsDb_Hsapiens_v79" # depends on broken package openssl - "EnsDb_Hsapiens_v75" # depends on broken package openssl - "REDseq" # depends on broken package openssl - "GUIDEseq" # depends on broken package openssl - "ggtut" # depends on broken package openssl - "FunciSNP" # depends on broken package openssl - "ChIPpeakAnno" # depends on broken package openssl - "ensembldb" # depends on broken package openssl - "ProteomicsAnnotationHubData" # depends on broken package openssl - "AnnotationHubData" # depends on broken package openssl - "AnnotationHub" # depends on broken package openssl - "analogsea" # depends on broken package openssl - "alm" # depends on broken package openssl - "abbyyR" # depends on broken package openssl - "httr" # depends on broken package openssl - "bcrypt" # depends on broken package openssl "GLMMRR" # depends on broken package lme4 "replicationInterval" # depends on broken package lme4 "GWASdata" # depends on broken package GWASTools - "vtpnet" # depends on broken package gQTLBase - "geuvStore" # depends on broken package gQTLBase "LLSR" # depends on broken package ggtern "ggtern" # broken build "EnsemblePCReg" # depends on broken package EnsembleBase @@ -1016,9 +754,6 @@ let "popprxl" # depends on broken package poppr "cpgen" # depends on broken package pedigreemm "mitml" # depends on broken package jomo - "gwascat" # depends on broken package gQTLBase - "gQTLstats" # depends on broken package gQTLBase - "gQTLBase" # broken build "IlluminaHumanMethylation450k_db" # broken build "gahgu95ecdf" # broken build "gahgu95dcdf" # broken build @@ -1091,7 +826,6 @@ let "abd" # depends on broken package nlopt "adabag" # depends on broken package nlopt "adhoc" # broken build - "adSplit" # build is broken "AER" # depends on broken package nlopt "afex" # depends on broken package nlopt "agRee" # depends on broken package nlopt @@ -1112,9 +846,7 @@ let "AtelieR" # broken build "auRoc" # depends on broken package rjags "AutoModel" # depends on broken package car - "BAGS" # build is broken "bamdit" # broken build - "bamsignals" # build is broken "BANOVA" # broken build "bapred" # depends on broken package lme4 "bartMachine" # depends on broken package nlopt @@ -1217,7 +949,6 @@ let "DistatisR" # depends on broken package nlopt "diveRsity" # depends on broken package nlopt "DJL" # depends on broken package car - "domainsignatures" # build is broken "doMPI" # build is broken "dpa" # depends on broken package nlopt "dpcR" # depends on broken nloptr @@ -1237,7 +968,6 @@ let "embryogrowth" # broken build "emg" # broken build "EnQuireR" # depends on broken package nlopt - "EnrichmentBrowser" # depends on broken package EDASeq "episplineDensity" # depends on broken package nlopt "epr" # depends on broken package nlopt "erer" # depends on broken package nlopt @@ -1252,10 +982,8 @@ let "FactoMineR" # depends on broken package nlopt "Factoshiny" # depends on broken package nlopt "faoutlier" # depends on broken package nlopt - "fastLiquidAssociation" # depends on broken package LiquidAssociation "fastR" # depends on broken package nlopt "FDRreg" # depends on broken package nlopt - "FEM" # build is broken "fishmethods" # depends on broken package lme4 "flipflop" # broken build "flowDensity" # depends on broken package nlopt @@ -1292,11 +1020,7 @@ let "gmatrix" # depends on broken package cudatoolkit "gMCP" # build is broken "gmum_r" # broken build - "GOFunction" # build is broken - "goProfiles" # build is broken - "goseq" # build is broken "Goslate" # depends on broken package PythonInR - "goTools" # build is broken "GPC" # broken build "gplm" # depends on broken package nlopt "gpuR" # depends on GPU-specific header files @@ -1327,7 +1051,6 @@ let "hysteresis" # depends on broken package nlopt "IATscores" # depends on broken package nlopt "ibd" # depends on broken package nlopt - "ibh" # build is broken "iccbeta" # depends on broken package nlopt "iClick" # depends on broken package rugarch "ifaTools" # depends on broken package OpenMx @@ -1352,7 +1075,6 @@ let "joda" # depends on broken package nlopt "jomo" # build is broken "js" # depends on broken package V8 - "keggorthology" # build is broken "KoNLP" # broken build "kzft" # broken build "LaplaceDeconv" # depends on broken package orthopolynom @@ -1365,10 +1087,8 @@ let "lgcp" # depends on broken package rpanel "Libra" # broken build "LinRegInteractive" # depends on broken package rpanel - "LiquidAssociation" # build is broken "lira" # broken build "littler" # broken build - "lmdme" # build is broken "lme4" # depends on broken package nlopt "LMERConvenienceFunctions" # depends on broken package nlopt "lmerTest" # depends on broken package nlopt @@ -1388,8 +1108,6 @@ let "mbest" # depends on broken package nlopt "MBmca" # depends on broken nloptr "mBvs" # build is broken - "MCRestimate" # build is broken - "mdgsa" # build is broken "meboot" # depends on broken package nlopt "medflex" # depends on broken package car "mediation" # depends on broken package lme4 @@ -1404,7 +1122,6 @@ let "metaplus" # depends on broken package nlopt "metaSEM" # depends on broken package OpenMx "Metatron" # depends on broken package nlopt - "metaX" # depends on broken package CAMERA "miceadds" # depends on broken package nlopt "micEconAids" # depends on broken package nlopt "micEconCES" # depends on broken package nlopt @@ -1413,7 +1130,6 @@ let "MigClim" # Build Is Broken "migui" # depends on broken package nlopt "minimist" # depends on broken package V8 - "mirIntegrator" # build is broken "missMDA" # depends on broken package nlopt "mitoODE" # build is broken "mixAK" # depends on broken package nlopt @@ -1427,7 +1143,6 @@ let "mlVAR" # depends on broken package nlopt "MM" # broken build "mongolite" # build is broken - "monocle" # build is broken "morse" # broken build "mosaic" # depends on broken package nlopt "mpoly" # broken build @@ -1447,7 +1162,6 @@ let "nCal" # depends on broken package nlopt "ncdfFlow" # build is broken "NCIgraph" # depends on broken package RCytoscape - "netbenchmark" # build is broken "NHPoisson" # depends on broken package nlopt "nloptr" # depends on broken package nlopt "nlsem" # broken build @@ -1462,7 +1176,6 @@ let "OpenCL" # build is broken "openCyto" # depends on broken package ncdfFlow "OpenMx" # build is broken - "openssl" # broken build "optBiomarker" # depends on broken package rpanel "ora" # depends on broken package ROracle "ordBTL" # depends on broken package nlopt @@ -1471,7 +1184,6 @@ let "OUwie" # depends on broken package nlopt "oz" # broken build "PAA" # broken build - "PADOG" # build is broken "pamm" # depends on broken package nlopt "PANDA" # build is broken "panelAR" # depends on broken package nlopt @@ -1479,14 +1191,12 @@ let "parboost" # depends on broken package nlopt "parma" # depends on broken package nlopt "partitions" # broken build - "pathRender" # build is broken "PatternClass" # build is broken "PBImisc" # depends on broken package nlopt "PBSddesolve" # build is broken "pcaBootPlot" # depends on broken FactoMineR "pcaL1" # build is broken "pcnetmeta" # broken build - "pdmclass" # build is broken "PDQutils" # broken build "pedigreemm" # depends on broken package nlopt "pedometrics" # depends on broken package nlopt @@ -1520,7 +1230,6 @@ let "PVAClone" # broken build "pvca" # depends on broken package nlopt "PythonInR" # broken build - "qcmetrics" # build is broken "QFRM" # broken build "qgraph" # depends on broken package nlopt "qtbase" # build is broken @@ -1606,7 +1315,6 @@ let "Rgnuplot" # broken build "rgp" # build is broken "rgpui" # depends on broken package rgp - "rgsepd" # depends on broken package goseq "rhdf5" # build is broken "rjade" # depends on broken package V8 "rjags" # broken build -- cgit 1.4.1