sorted-r-blacklist

# TODO: cap-mirseq has test error. Perhaps just needs a fix on expected exit
# code
recipes/cap-mirseq


# recipes/r-multitaper
# recipes/r-readbrukerflexdata


# TODO: rsem is giving zlib errors. probably needs patching
recipes/rsem

# recipes/bioconductor-protgenerics
# recipes/bioconductor-hpar
# recipes/r-lambda.r
# recipes/r-matrixstats
# recipes/r-globals
# recipes/r-bh
# recipes/r-abind
# recipes/bioconductor-gagedata
# recipes/r-cghflasso
# recipes/bioconductor-limma

# TODO: older limma packages should stay blacklisted until we can track down stable
# URLs for these versions.
recipes/bioconductor-limma/3.26.7
recipes/bioconductor-limma/3.28.6
recipes/bioconductor-limma/3.28.2

# recipes/bioconductor-marray
# recipes/r-bio3d
# recipes/r-fdrtool
# recipes/r-compute.es
# recipes/r-pcapp
# recipes/r-hwriter
# recipes/r-bigmemory.sri
# recipes/r-svgui
# recipes/bioconductor-seqlogo
# recipes/r-deoptimr
# recipes/r-mba
# recipes/r-rsm
# recipes/r-nor1mix
# recipes/r-runit
# recipes/r-pracma
# recipes/r-spam
# recipes/r-nozzle.r1
# recipes/r-seqinr
# recipes/r-corrplot
# recipes/bioconductor-zlibbioc
# recipes/r-idr
# recipes/r-batch
# recipes/bioconductor-biocstyle
# recipes/bioconductor-ropls
# recipes/bioconductor-ropls/1.2.14
# recipes/bioconductor-biocinstaller
# recipes/r-xnomial
# recipes/r-writexls
# recipes/r-pmcmr
# recipes/r-svdialogs
# recipes/r-permute
# recipes/r-futile.options
# recipes/bioconductor-edger
#recipes/bioconductor-edger/3.12.1
# recipes/bioconductor-dnacopy
# recipes/bioconductor-preprocesscore
# recipes/r-magrittr
# recipes/r-futile.logger
# recipes/r-venndiagram
# recipes/r-listenv
# recipes/r-future
# recipes/r-rcircos
# recipes/r-params
# recipes/r-rpmg
# recipes/r-rseis
# recipes/r-dunn.test
# recipes/r-docopt
# recipes/bioconductor-rhdf5
# recipes/r-scatterplot3d
# recipes/r-optparse
# recipes/r-ellipse
# recipes/r-splancs
# recipes/r-findpython
# recipes/bioconductor-tximport
# recipes/r-polynom
# recipes/r-calibrate
# recipes/r-fitdistrplus
# recipes/r-checkmate
# recipes/r-maldiquant
# recipes/r-png
# recipes/r-amap
# recipes/r-locfit
# recipes/r-bit
# recipes/r-bigmemory
# recipes/r-preseqr
# recipes/r-bbmisc
# recipes/r-fail
# recipes/r-base64
# recipes/r-jsonlite
# recipes/bioconductor-biomformat
# recipes/r-biasedurn/1.07
# recipes/r-ore
# recipes/r-bit64
# recipes/r-rappdirs
# recipes/r-signal
# recipes/r-robustrankaggreg
# recipes/r-corpcor
# recipes/r-statmod
# recipes/r-mclust
# recipes/jamm
# recipes/jamm/1.0.7.2
# recipes/r-fastcluster
# recipes/r-blockmodeling
# recipes/r-pheatmap
# recipes/r-globaloptions
# recipes/r-getoptlong
# recipes/r-digest
# recipes/r-testthat
# recipes/r-ggplot2
# recipes/r-ggrepel
# recipes/r-upsetr
# recipes/r-ggally
# recipes/r-ggdendro
# recipes/r-dendextend
# recipes/r-snow
# recipes/r-snowfall
# recipes/bioconductor-biocparallel
# recipes/r-beanplot
# recipes/r-fields
# recipes/r-geomap
# recipes/r-rfoc
# recipes/r-argparse
# recipes/macs2
# recipes/r-proj4
# recipes/r-ggalt
# recipes/r-multicool


# TODO: r-ks has error related to rgl
recipes/r-ks


# TODO: r-hrdcde depends on r-ash which has unresolved issues, and on r-ks
# which has rgl issues
recipes/r-hdrcde


# recipes/r-chbutils
# recipes/bioconductor-rsubread
# recipes/bioconductor-dupradar
# recipes/r-lsd
# recipes/nonpareil
# recipes/r-robustbase
# recipes/r-longitudinal
# recipes/r-genenet
# recipes/r-r.methodss3
# recipes/r-r.oo
# recipes/r-r.utils
# recipes/r-r.cache
# recipes/r-readmzxmldata
# recipes/r-sparql
# recipes/r-xmlrpc
# recipes/r-funr
# recipes/bioconductor-qvalue
# recipes/r-shape
# recipes/r-diagram
# recipes/r-circlize
# recipes/bioconductor-complexheatmap
# recipes/r-yaml
# recipes/metilene


# TODO: r-rainbow depends on r-ash which has unresolved issues, and on r-ks
# which has rgl issues
recipes/r-rainbow


# recipes/r-sleuth
# recipes/r-pore
# recipes/r-wasabi
# recipes/r-pscbs
# recipes/r-viridis
# recipes/r-fftwtools
# recipes/r-tiff
# recipes/bioconductor-biocgenerics
# recipes/bioconductor-biobase
# recipes/bioconductor-cghbase
# recipes/bioconductor-cghcall
# recipes/bioconductor-biosigner
# recipes/bioconductor-multtest


# TODO: r-mutoss has the same problem as r-phonr: it loops indefinitely on osx.
recipes/r-mutoss


# recipes/bioconductor-siggenes
# recipes/bioconductor-ebimage
# recipes/bioconductor-mzr
# recipes/bioconductor-degreport
# recipes/bioconductor-pcamethods
# recipes/bioconductor-xcms
# recipes/bioconductor-xcms/1.44.0
# recipes/bioconductor-xcms/1.46.0
# recipes/bioconductor-graph
# recipes/bioconductor-rbgl
# recipes/bioconductor-rgraphviz
# recipes/bioconductor-rgraphviz/2.13.0
# recipes/bioconductor-flowcl
# recipes/bioconductor-camera
# recipes/bioconductor-camera/1.22.0
# recipes/bioconductor-camera/1.26.0
# recipes/bioconductor-metams
# recipes/r-ipo
# recipes/bioconductor-kegggraph
# recipes/bioconductor-rcytoscape
# recipes/r-probmetab/1.1
# recipes/r-probmetab/1.0
# recipes/bioconductor-s4vectors


# TODO: older s4vectors should stay blacklisted until we can track down stable
# version for 0.8.7
recipes/bioconductor-s4vectors/0.8.7


# recipes/r-changepoint
# recipes/bioconductor-iranges


# TODO: older versions o bioconductor-iranges need stable URLS
recipes/bioconductor-iranges/2.4.7
recipes/bioconductor-iranges/2.4.6


# recipes/bioconductor-annotationdbi
# recipes/bioconductor-biomart
# recipes/bioconductor-annotate
# recipes/bioconductor-org.hs.eg.db
# recipes/bioconductor-org.ce.eg.db
# recipes/bioconductor-genefilter
# recipes/bioconductor-sva
# recipes/bioconductor-kegg.db
# recipes/bioconductor-graphite
# recipes/bioconductor-do.db
# recipes/bioconductor-annotationforge
# recipes/bioconductor-org.dm.eg.db
# recipes/bioconductor-gseabase
# recipes/bioconductor-category
# recipes/bioconductor-org.mm.eg.db
# recipes/bioconductor-illuminamousev2.db
# recipes/bioconductor-mgug4122a.db
# recipes/bioconductor-geneplotter
# recipes/bioconductor-deseq
# recipes/r-dbchip
# recipes/bioconductor-go.db
# recipes/bioconductor-gostats
# recipes/bioconductor-gosemsim
# recipes/bioconductor-topgo
# recipes/bioconductor-xvector
# recipes/bioconductor-biostrings
# recipes/bioconductor-ggtree
# recipes/bioconductor-keggrest
# recipes/bioconductor-gage
# recipes/bioconductor-pathview
# recipes/r-rBLAST
# recipes/r-maldiquantforeign
# recipes/bioconductor-geoquery
# recipes/bioconductor-sradb
# recipes/r-htmltools
# recipes/r-htmlwidgets
# recipes/r-plotly
# recipes/r-dt
# recipes/r-googlevis
# recipes/r-biom
# recipes/r-rrcov
# recipes/r-bma
# recipes/r-coloc
# recipes/bioconductor-flowcore
# recipes/bioconductor-flowai
# recipes/bioconductor-flowdensity
# recipes/bioconductor-illuminaio
# recipes/r-rniftyreg
# recipes/bioconductor-affyio
# recipes/bioconductor-affy
# recipes/bioconductor-vsn
# recipes/r-nanostringnorm
# recipes/r-flowr
# recipes/bioconductor-genomeinfodb
# recipes/bioconductor-genomicranges
#recipes/bioconductor-seqpattern
#recipes/bioconductor-summarizedexperiment
recipes/bioconductor-summarizedexperiment/1.0.2
#recipes/bioconductor-deseq2
recipes/bioconductor-deseq2/1.10.1
#recipes/r-empiricalfdr.deseq2
#recipes/bioconductor-rsamtools
#recipes/bioconductor-cn.mops
#recipes/bioconductor-genomicalignments
#recipes/bioconductor-rtracklayer
#recipes/bioconductor-ballgown
#recipes/bioconductor-bsgenome
#recipes/bioconductor-bsgenome.ecoli.ncbi.20080805
#recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3
#recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9
#recipes/bioconductor-bsgenome.celegans.ucsc.ce6
#recipes/r-dpeak
#recipes/bioconductor-regioner
#recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19
#recipes/bioconductor-motifrg
# recipes/bioconductor-genomicfeatures
# recipes/bioconductor-organismdbi
recipes/bioconductor-rhtslib
recipes/bioconductor-csaw
# recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene
# recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene
# recipes/bioconductor-genelendatabase
recipes/bioconductor-genelendatabase/1.6.0
# recipes/bioconductor-goseq/1.22.0
# recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene


# TODO: bioconductor-qdnaseq depends on bioconductor-dnacopy which has some
# gfortran issues
recipes/bioconductor-qdnaseq


# TODO: no url for DEXSeq 1.16. bioarchive has 1.21.0, but the latest available
# on bioconductor site v3.4 is 1.20. Need to resolve version issues.
recipes/bioconductor-dexseq

# recipes/bioconductor-chipcomp
# recipes/bioconductor-variantannotation
# recipes/r-mutationalpatterns
# recipes/bioconductor-biovizbase


# depends on r-rainbow, which has r-rgl issues
recipes/bioconductor-bubbletree


recipes/bioconductor-ggbio
# recipes/bioconductor-gviz
recipes/bioconductor-cummerbund
recipes/bioconductor-mosaics
recipes/bioconductor-jmosaics
recipes/r-dorng
recipes/bioconductor-bumphunter
recipes/r-knitr
recipes/r-sartools/1.2.0
recipes/bioconductor-flowai
recipes/r-sendmailr
recipes/r-batchjobs
recipes/r-readr
recipes/bioconductor-genomation
recipes/bioconductor-cexor
recipes/r-gsalib
recipes/bioconductor-shortread
recipes/bioconductor-dada2
recipes/bioconductor-systempiper

# TODO: r-phonr seems to loop indefinitely when trying to build.
recipes/r-phonr

# recipes/r-catools

# spp looks to be having boost issues
recipes/r-spp

recipes/bioconductor-basic4cseq
recipes/r-rmarkdown
recipes/r-knitrbootstrap
recipes/r-gplots
recipes/r-gmd
recipes/bioconductor-chipseeker
recipes/bioconductor-isomirs
recipes/bioconductor-made4
recipes/bioconductor-piano
recipes/bioconductor-diffbind
recipes/bioconductor-mmdiff




# TODO: depends on r-blockmodeling which has some gfortran issues
recipes/bioconductor-ebseq


recipes/bioconductor-fourcseq
recipes/bioconductor-dose
recipes/bioconductor-clusterprofiler
recipes/bcbio-rnaseq
recipes/r-vegan/2.3_4
recipes/r-vegan/2.3_0
recipes/r-vegan/2.3_3
recipes/bioconductor-phyloseq
recipes/rpy2
recipes/triform2
recipes/lefse
# recipes/poretools
recipes/poretools/0.5.0
recipes/poretools/0.5.1
recipes/mgkit
recipes/r-mixomics
recipes/bioconductor-minfi