From 05fc143451639d5949bf493497febfddd29d1fa9 Mon Sep 17 00:00:00 2001 From: Jeffrey David Johnson Date: Fri, 25 Mar 2016 09:15:02 -0700 Subject: [PATCH] work on fixing up bioconductor packages --- pkgs/development/r-modules/default.nix | 334 ++++++++++++++++++++++++- 1 file changed, 331 insertions(+), 3 deletions(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 7093548a3c48..c2fd00c8d78e 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -698,6 +698,337 @@ let # Packages which cannot be installed due to lack of dependencies or other reasons. brokenPackages = [ + "RareVariantVis" # 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 + "alsace" # broken build + "rrlda" # depends on broken package VIM + "qrfactor" # depends on broken package VIM + "MVN" # depends on broken package VIM + "mvoutlier" # depends on broken package VIM + "robCompositions" # depends on broken package VIM + "DiagrammeRsvg" # depends on broken package V8 + "dagitty" # depends on broken package V8 + "remoter" # depends on broken package sodium + "Fletcher2013b" # depends on broken package RTN + "apaStyle" # depends on broken package ReporteRs + "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 + "EnsembleCV" # depends on broken package EnsembleBase + "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 + "gahgu95ccdf" # broken build + "gahgu95bcdf" # broken build + "gahgu95av2cdf" # broken build + "PREDAsampledata" # depends on broken package gahgu133plus2cdf + "gahgu133plus2cdf" # broken build + "gahgu133bcdf" # broken build + "gahgu133acdf" # broken build "annmap" # depends on broken package RMySQL "choroplethr" # depends on broken package acs "acs" # broken build @@ -956,7 +1287,6 @@ let "genridge" # depends on broken package nlopt "geojsonio" # depends on broken package V8 "GEWIST" # depends on broken package nlopt - "ggtern" # build is broken "ggtree" # broken build "gimme" # depends on broken package nlopt "gmatrix" # depends on broken package cudatoolkit @@ -971,7 +1301,6 @@ let "gplm" # depends on broken package nlopt "gpuR" # depends on GPU-specific header files "gputools" # depends on broken package cudatoolkit - "gQTLBase" # depends on broken package GenomicFiles "granova" # depends on broken package nlopt "graphicalVAR" # depends on broken package nlopt "GraphPAC" # broken build @@ -1151,7 +1480,6 @@ let "parma" # depends on broken package nlopt "partitions" # broken build "pathRender" # build is broken - "pathview" # build is broken "PatternClass" # build is broken "PBImisc" # depends on broken package nlopt "PBSddesolve" # build is broken