build-fail-blacklist

# Never worked
recipes/multiphate

# ../../utils//fileType/FileRecordTypeChecker.h:120:21: error: 'constexpr' needed for in-class initialization of static data member 'const float FileRecordTypeChecker::PERCENTAGE_PRINTABLE' of non-integral type [-fpermissive]
recipes/bedtools/2.20.1
recipes/bedtools/2.19.1

# last-pair-probs.cc:501:10: error: cannot convert 'std::istream {aka std::basic_istream<char>}' to 'bool' in return
recipes/last/638

# Timeout downloading from sourceforge
recipes/transcomb

# compilation or other errors in bulk
recipes/xxmotif
recipes/phylip
recipes/metasnv
recipes/gqt
recipes/diamond_add_taxonomy
recipes/shapemapper
recipes/biom-format
recipes/circulator
recipes/igdiscover
recipes/rnftools
recipes/tiptoft
recipes/emboss
recipes/embassy-phylip
recipes/triform2
recipes/haploclique/1.3.1
recipes/andi
recipes/lcfit
recipes/musicc
recipes/treekin/0.4.2
recipes/blast/2.5.0
recipes/quast
recipes/w4mclassfilter
recipes/tadarida-c
recipes/w4mclstrpeakpics
recipes/rsem

# Broken due to changes in nalgebra on crates.io https://github.com/varlociraptor/prosic2/issues/1
recipes/prosic

# This seems to be the same as recipes/bioconductor-chromvar
recipes/stream_chromvar

# Requests python3, but is written for python2
recipes/ctat-mutations

# Unclear that the following old versions are still needed
recipes/augustus/3.2.3
recipes/hmmer/2.3.2
recipes/bamtools/2.3.0
recipes/bowtie/1.1.1
recipes/fastqc/0.10.1
recipes/fastqc/0.11.2
recipes/fastqc/0.11.3
recipes/fastqc/0.11.6
recipes/htseq/0.6.1.post1
recipes/htseq/0.6.1
recipes/htseq/0.7.2
recipes/htseq/0.9.1
recipes/freebayes/1.1.0.46
recipes/mothur/1.36.1
recipes/blast/2.2.21
recipes/blast-legacy/2.2.22
recipes/fwdpp/0.5.3
recipes/fwdpp/0.5.4
recipes/java-jdk/7.0.91
recipes/perl-extutils-makemaker/7.24
recipes/tabix/0.2.5
recipes/tabix/0.2.6
recipes/cyvcf2/0.7.2
recipes/rsem/1.2.21
recipes/w4mclassfilter/0.98.0
recipes/w4mclassfilter/0.98.1
recipes/w4mclassfilter/0.98.2
recipes/w4mclassfilter/0.98.3
recipes/w4mclassfilter/0.98.6
recipes/w4mclassfilter/0.98.7
recipes/w4mclassfilter/0.98.8
recipes/stringtie/1.0.3
recipes/stringtie/1.0.4
recipes/stringtie/1.2.2
recipes/stringtie/1.2.4
recipes/stringtie/1.3.0
recipes/stringtie/1.3.3
recipes/art/3.11.14
recipes/bcbiogff/0.6.2
recipes/biopet/0.8.0
recipes/metfrag/2.3.1
recipes/metfrag/2.4.2
recipes/varscan/2.4.2
recipes/bbmap/37.10
recipes/bbmap/37.17
recipes/bbmap/37.52
recipes/bbmap/37.99
recipes/gatk4/4.0.3.0
recipes/mira/3.4.1.1
recipes/mira/4.9.5
recipes/mira/4.9.6
recipes/ngmlr/0.2.3
recipes/ngmlr/0.2.4
recipes/rnastructure/5.7
recipes/rnastructure/6.0
recipes/snpeff/4.1l
recipes/snpeff/4.2

# stl_algobase.h:548:18: error: cannot bind non-const lvalue reference of type 'HitSink::batch&' to an rvalue of type 'std::remove_reference<HitSink::batch&>::type {aka HitSink::batch}'
recipes/bowtie

# Depend on dependency package versions that are no longer maintained
recipes/pysam/0.9.1

# Seems to download maven and then have java issues
recipes/megagta

# The build string needs to be modified to account for the [nocairo] feature
recipes/genometools-genometools/1.5.10-nocairo

# Unknown issues
recipes/openslide
recipes/smina
recipes/cmv
recipes/fwdpp
recipes/parafly
recipes/rdflib-jsonld
recipes/smashbenchmarking
recipes/saffrontree
recipes/slclust

# tracking master branch
recipes/frc

# OSX failures - library loading
recipes/r-pscbs/0.61.0

# CMake Error at build-common/cmake/VersionHelper.cmake:11 (list):
recipes/somatic-sniper

# need to fix the download location, the checksum changes everytime
recipes/osra/2.1.0

# needs some special treatment, shorter prefix than normal pkgs
recipes/dimspy
recipes/dimspy/1.2.0
recipes/dimspy/1.1.0
recipes/dimspy/1.0.0

# can't find file to patch at input line 3
recipes/erds

# non-standard test
recipes/fermikit

# build-error
recipes/mimodd

# error: possibly undefined macro: AM_GNU_GETTEXT
recipes/xcftools

# See https://github.com/bioconda/bioconda-recipes/pull/9458
recipes/spingo

# CMake Error: The source directory "/opt/conda/conda-bld/sqlitebrowser_1529759350498/work" does not appear to contain CMakeLists.txt.
recipes/sqlitebrowser

# no test, website down
recipes/sprinkles

# link not founds
recipes/soapcoverage

# download error
recipes/soapaligner

# missing tarball
recipes/sloika
recipes/genometools
recipes/nanonet
recipes/knot
recipes/moreutils
recipes/jali
recipes/intervalstats
recipes/mrbayes

# missing dep
recipes/oligotyping
recipes/oligotyping/2.0

# missing file
recipes/shiver

# sqt2pin missing
recipes/percolator

# missing binary
recipes/semeta

# Various C++ errors
recipes/rdock

# WARNING (talloc,lib/libpytalloc-util.so.2.1.9): did not find - or even know where to look for: /lib64/libm.so.6
recipes/talloc

# Skipped: vnl from /opt/recipe defines build/skip for this configuration ({'c_compiler': 'toolchain_c'}).
recipes/vnl

# old libc++ missing
recipes/searchgui/3.2.20

# something wrong with the test
recipes/remurna

# https://github.com/bcgsc/abyss/issues/130 and https://github.com/bioconda/bioconda-recipes/pull/6131
recipes/abyss/1.9.0
recipes/abyss/1.5.2

# Test uses a program that makes incorrect assumptions about shebangs (you can't reliably use "#!/usr/bin/env program --arguments")
recipes/amos

# aclocal error, but also downloads mauve tarballs, but there is now a mauve pkgs, is it still needed?
recipes/libmuscle

# compilation error
recipes/osra/2.0.1
recipes/lightning

# unable to access jarfile
recipes/effectivet3

# url broken
recipes/e-pcr

# linker error
recipes/discovar-denovo

# seqan errors
recipes/bowtie/1.0.0

# depends on perl-pcap
recipes/brass

# test segfaults
recipes/kat/2.3.1

# oh no TPP is failing, it was a nightmare to get it to compile in the first place :(
recipes/tpp

# perl dependency estmapper not available for 5.26
recipes/wgs-assembler

# python dep click missing
recipes/qiime/1.9.1

# requires wgs-assembler, which has a build fail
recipes/sprai

# missing dependency
recipes/genomebaser
recipes/garnet
recipes/tablet

# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml  url=https://pypi.org/simple/funcsigs/
recipes/pytest-marks
recipes/hivtrace
recipes/imfusion/0.3.0
recipes/imfusion/0.3.2
recipes/poretools/0.5.1
recipes/hubward
recipes/pasta/1.7.8
recipes/pasta/0.2
recipes/nucleoatac/0.3.1
recipes/phylotoast

# git checkout problem
recipes/pbdagcon
recipes/icqsol
recipes/pout2mzid

# checksum always fails
recipes/ms

# GL missing, needs the extended base image
recipes/emperor

# sed: can't read /opt/conda/conda-bld/idba_1530055808563/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/aclocal: No such file or directory
recipes/idba

# socket.timeout: timed out
recipes/infernal/1.0.2

# PREFIX/lib is a directory
recipes/proot

# /opt/conda/conda-bld/kat_1530056226354/test_tmp/run_test.sh: line 7:  8288 Aborted                 (core dumped) kat --version
recipes/kat/2.3.4

# bin/g++: Command not found
recipes/metavelvet/1.1.01
recipes/metavelvet-sl
recipes/metavelvet

# cp: target `/opt/conda/conda-bld/meryl_1530057980094/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/' is not a directory
recipes/meryl
recipes/metavelvet-sl-pipeline

# CMake Error: CMAKE_C_COMPILER not set, after EnableLanguage
recipes/openbabel/2.3.2

# Conflicting numpy and qiime
recipes/koeken

# no clue currently
recipes/hap.py

# cp: cannot stat `./mapsembler2_extremities/build/mapsembler2_extremities': No such file or directory
recipes/mapsembler2

# Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
recipes/primerprospector

# missing URL
recipes/intemap

# zlib missing
recipes/polymutt
recipes/prophyle/0.2.1
recipes/trimmomatic/0.35
recipes/dsk
recipes/lofreq

# /opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-redhat-linux/4.8.2/ld: cannot find -lc
recipes/piler

# no clue
recipes/portcullis/1.1.1
recipes/portcullis/1.1.0

# Skipped: guidescan from /opt/recipe defines build/skip for this configuration ({'numpy': '1.9', 'c_compiler': 'toolchain_c', 'openblas': '0.2.20'}).
recipes/guidescan

# installation error inside the container?
recipes/relocate2/2.0.1
recipes/relocate2

# ModuleNotFoundError: No module named 'model'
recipes/pyvcf/0.6.7
recipes/pyvcf

# /usr/bin/env: python -Es: No such file or directory
recipes/pizzly

# compiles its own zlib
recipes/plink2

# natsort conflicts with python
recipes/qcumber

# ModuleNotFoundError: No module named 'fasta', note that the project is deprecated in favor of pyfaidx
recipes/pyfasta

# Tests failed for spanki-0.5.1-py27h24bf2e0_1.tar.bz2 - moving package to /opt/conda/conda-bld/broken
recipes/spanki

# perl issues
recipes/vcftools/0.1.11

# broken pipe
recipes/antarna

# missing perl module
recipes/snippy/3.0

# hashFunction.c:94: Error: invalid instruction suffix for `push'
recipes/soapdenovo2

# tarball missing and should be migrated I guess
recipes/ant
recipes/ngseqbasic
recipes/footprint
recipes/mirdeep2/2.0.0.8

# missing bioc package
recipes/customprodb

# runtime dep missing in Docker?
recipes/bio-vcf

# boost missing, requires boost < 1.65
recipes/bellmans-gapc
recipes/gap2seq

# needs bellmans-gapc rebuild
recipes/pkiss

# fail in Docker test
recipes/fiji/20151222

# flexbar not found
recipes/flexbar/3.3.0

# Error: Could not find or load main class edu.duke.igsp.gkde.Main
recipes/fseq

# node error
recipes/azure-cli
recipes/arvados-cli

# takes to long to install
recipes/bcbio-rnaseq

# missing python requirements?
recipes/illuminate

# weird Docker permission error
recipes/bpipe

# perl bad interpreter
recipes/cmfinder/0.2

# dotnet not found
recipes/canvas

#ImportError: cannot import name faces
recipes/cansnper

# URL not found
recipes/bumbershoot

# /opt/conda/conda-bld/phipack_1530829563675/work/conda_build.sh: line 139: cd: src/: No such file or directory
recipes/phipack

# perl
recipes/vcftools/0.1.10

# perl wrong interpreter
recipes/prinseq

# checking whether the C compiler works... no
recipes/fastme

# perl script could not be found
recipes/rnaclust

# [javac] Caused by: java.lang.ClassNotFoundException: com.sun.tools.javac.main.OptionName
recipes/picard/1.97

# Incompatible boost and bellmans-gapc
recipes/rnashapes/3.3.0

# Unknown issues
recipes/export2graphlan
recipes/lorma
recipes/microbecensus
recipes/minialign
recipes/nspdk
recipes/dreamtools
recipes/biomaj
recipes/cas-offinder
recipes/odose

# Outdated recipe, replaced by perl-bio-samtools
recipes/perl-bio-db-sam

# bad perl interpreter, needs patching a perl script
recipes/krona/2.6
recipes/krona/2.5

# /opt/conda/conda-bld/pash_1531691261758/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in `require': cannot load such file -- brl/util/textFileUtil (LoadError)
recipes/pash

# can't open file setup.py
recipes/meneco/1.5.2

# Permission denied ESTscan
recipes/perl-estscan2/2.1

# Uses deprecated POSIX::tmpnam() function, not maintained, partially replaced by estscan 3.0
recipes/perl-btlib/0.19

# takes a long time and then fails?
recipes/kmerinshort

# chmod: cannot access `genblast_v1.0.4': No such file or directory
recipes/genblasta

# ImportError: cannot import name 'aveQual'
recipes/nanosplit

# ../short_read_connector.sh: line 299: /opt/conda/conda-bld/shortreadconnector_1531045819227/work/build/bin/SRC_linker_ram: No such file or directory
recipes/short-read-connector

# Cpp no such file or dir
recipes/genepop

# Error: Unable to access jarfile
recipes/gfinisher

# gsl missing but specified
recipes/gfold

# build errors
recipes/ghc/6.8.3

# missing python dep
recipes/hurry.filesize

# compilation error, missing boost header
recipes/k-slam

# failing
recipes/igblast/1.4.0

# missing fortran lib, will fix this upstream
recipes/ig-checkfcs

# no target specified and no make file
recipes/mreps

# np-likeness scorer no such file or directory
recipes/np-likeness-scorer

# Throws an error during testing
recipes/reago

# Error during mulled testing on circleci
recipes/ra-integrate

# real long build-time
recipes/perl-bio-viennangs

# /boost/intrusive/list.hpp:123:22: error: ‘const bool boost::intrusive::list_impl<boost::intrusive::bhtraits<dng::pileup::Node, boost::intrusive::list_node_traits<void*>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 1u>, long unsigned int, true, void>::safemode_or_autounlink’ is private
recipes/denovogear

# /opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-redhat-linux/4.8.2/ld: cannot find -lboost_system
recipes/metaprob

# Fails testing
recipes/cap-mirseq

# OSX related errors, Linux should be fine. Most of the non-perl issues are due to LLVM used as a compiler, GCC should be fine
recipes/cgat-scripts
recipes/shorah
recipes/smalt
recipes/snap
recipes/perl-pod-coverage-trustpod/0.100003
recipes/perl-symbol-util/0.0203
recipes/perl-test-pod-coverage/1.10
recipes/oases
recipes/novoplasty
recipes/metavelvet-sl-feature-extraction
recipes/music
recipes/kraken-ea
recipes/gnu-getopt
recipes/ghmm
recipes/domclust
recipes/bwa/0.6.2
recipes/disco/1.2
recipes/c-ares
recipes/cassiopee
recipes/flock
recipes/cmfinder
recipes/cortex_con
recipes/cosi2
recipes/cufflinks
recipes/dialign-tx
recipes/edlib
recipes/esimsa
recipes/fastuniq
recipes/fgap
recipes/funcannot
recipes/genepender
recipes/genometester4
recipes/ghostx
recipes/libbambamc/0.5.00
recipes/ls-gkm
recipes/mosaik
recipes/mustang
recipes/ngmerge
recipes/nlstradamus
recipes/ntcard
recipes/ocrad/0.21
recipes/panoct
recipes/perl-estscan1/1.3
recipes/pygresql
recipes/real
recipes/rmap
recipes/rnabob
recipes/sam
recipes/secimtools
recipes/sff2fastq
recipes/snpomatic
recipes/soapdenovo2-gapcloser
recipes/spectral_hk
recipes/swiftlink
recipes/tedna
recipes/transtermhp
recipes/perl-dbm-deep
recipes/carna

# R packages not in CRAN, please feel free to remove from the blacklist if you actually use any of these!
recipes/r-ampvis
recipes/r-boutroslabplottinggeneral
recipes/r-cimpl
recipes/r-DGEclustering
recipes/r-dpeak
recipes/r-genometricorr
recipes/r-george
recipes/r-ichorcna
recipes/r-intego
recipes/r-lme4qtl
recipes/r-mmgenome
recipes/r-nastiseq
recipes/r-ncbit
recipes/r-ngsplot
recipes/r-ngsplot-hg19
recipes/r-ngsplot-hg38
recipes/r-ngsplot-mm10
recipes/r-peer
recipes/r-phewas
recipes/r-pore
recipes/r-prestor
recipes/r-qorts
recipes/r-quorts
recipes/r-rBLAST
recipes/r-rubic
recipes/r-scimpute
recipes/r-soap-nmr
recipes/r-xmlrpc
recipes/r-zerone

# Deprecated/build fail in Bioconductor 3.8
recipes/bioconductor-atlasrdf
recipes/bioconductor-jmosaics
recipes/bioconductor-meshsim
recipes/bioconductor-mmdiff
recipes/bioconductor-mmnet
recipes/bioconductor-rcytoscape
recipes/bioconductor-browservizdemo
recipes/bioconductor-pannbuilder
recipes/bioconductor-splicer
recipes/bioconductor-pbcmc
recipes/bioconductor-mqtl.nmr
recipes/bioconductor-nudge
recipes/bioconductor-phenodist
recipes/bioconductor-mvgst
recipes/bioconductor-ramigo

# Old bioconductor version that's no longer available
recipes/bioconductor-edger/3.12.1
recipes/bioconductor-masigpro/1.49.4

# Old package, should we still build it?
recipes/bioconductor-dnacopy/1.48.0
recipes/bioconductor-ggbio/1.22.0
recipes/bioconductor-limma/3.28.2
recipes/bioconductor-limma/3.28.10
recipes/bioconductor-org.ce.eg.db/3.2.3
recipes/bioconductor-org.ce.eg.db/3.4.1
recipes/bioconductor-org.dm.eg.db/3.3.0
recipes/bioconductor-org.mm.eg.db/3.3.0
recipes/bioconductor-qdnaseq.mm10/1.4.0
recipes/bioconductor-rgraphviz/2.13.0
recipes/bioconductor-ropls/1.2.14
recipes/r-speaq/1.2.1
recipes/bioconductor-cummerbund/2.8.2
recipes/bioconductor-cummerbund/2.12.1
recipes/bioconductor-diffbind/2.0.9
recipes/bioconductor-diffbind/2.2.12
recipes/bioconductor-xcms/1.52.0
recipes/bioconductor-s4vectors/0.8.11

# Marked as build fails in bioconductor release 3.9
recipes/bioconductor-birte
recipes/bioconductor-dsimer
recipes/bioconductor-flipflop
recipes/bioconductor-gpumagic
recipes/bioconductor-flowq
recipes/bioconductor-procona
recipes/bioconductor-pgpc
recipes/bioconductor-appreci8r

# stringify can't find libmysqlclient.18
recipes/ucsc-overlapselect
recipes/ucsc-pslmap
recipes/ucsc-pslcdnafilter

# Source seems to have moved
recipes/discovar

# Requires GTK+
recipes/bioconductor-hilbertvisgui

# Build fails in bulk
recipes/rmblast
recipes/perl-bio-db-hts

# missing dependency r-dagitty
recipes/r-pcalg
recipes/bioconductor-mirlab
recipes/bioconductor-epinem
recipes/bioconductor-mnem

# Source no longer exists at the URL
recipes/recon

# Fails compilation everywhere, including the bioconductor build system
recipes/bioconductor-mlm4omics

# compilation errors on Linux and OSX
recipes/bioconductor-bgmix
recipes/bioconductor-grenits
recipes/bioconductor-mulcom
recipes/bioconductor-prot2d
recipes/bioconductor-genphen
recipes/bioconductor-bgx
recipes/bioconductor-netboost

# Needs a root5 rebuild
recipes/bioconductor-xps

# Needs to be patched to work with something other that gfortran
recipes/bioconductor-iclusterplus

# Needs to have the source patched to look in ${PREFIX} for zlib
recipes/bioconductor-sictools

# object ‘ebayes’ is not exported by 'namespace:limma'
recipes/bioconductor-charm
recipes/bioconductor-charmdata

# Checks for the java version incorrectly, need to patch the source
recipes/bioconductor-msgfplus
recipes/bioconductor-msgfgui

# openbabel error
recipes/bioconductor-chemmineob

# Has issues finding sbml
recipes/bioconductor-rsbml
recipes/bioconductor-biggr

# Installing package into $PREFIX/lib/R/library/00LOCK-work/00new (as "lib" is unspecified)
recipes/bioconductor-interactivedisplay

# never completes
recipes/bioconductor-cancer

# No methods found in package 'flowStats' for request: '%on%' when loading 'plateCore'
recipes/bioconductor-platecore

# Error in library("FlowSorted.CordBlood.450k") : there is no package called 'FlowSorted.CordBlood.450k'
recipes/bioconductor-flowsorted.blood.450k
recipes/bioconductor-flowsorted.cordblood.450k
recipes/bioconductor-flowsorted.cordbloodnorway.450k

# cwltool is not found
recipes/bioconductor-rcwl
recipes/bioconductor-rcwlpipelines

# unable to load shared object '$PREFIX/lib/R/library/sf/libs/sf.so': libtiledb.so.1.6.0: cannot open shared object file
recipes/bioconductor-anamir

# Compilation errors on OSX
recipes/bioconductor-rchemcpp
recipes/bioconductor-gmapr
recipes/bioconductor-flowtype
recipes/bioconductor-rchyoptimyx