work on fixing up bioconductor packages

This commit is contained in:
Jeffrey David Johnson 2016-03-26 11:26:29 -07:00
parent 05fc143451
commit e98a231af8

View file

@ -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