work on fixing up bioconductor packages

1 files changed, 26 insertions, 318 deletions

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