build-fail-blacklist

# breaks nightly build, see https://github.com/bioconda/bioconda-recipes/issues/55909
recipes/pixelator

# ----- 2023-12-02 problematic on bulk -----
r-ramclustr
# ------------------------------------------

# Currently kills bulk, and dependants
recipes/bioconductor-conumee
recipes/r-shazam
recipes/r-scoper
recipes/r-dowser
recipes/bioconductor-chipxpressdata
recipes/bioconductor-chipxpress
recipes/bioconductor-meal
recipes/bioconductor-methylgsa
recipes/bioconductor-champ
recipes/bioconductor-appreci8r
recipes/bioconductor-mirsm

# Allegedly requires ancient gatb
recipes/lordec

# Uses all the RAM/time on github actions
recipes/octopus
recipes/bttcmp
recipes/bttoxin_scanner
recipes/monocle3-cli
recipes/phenix

# Fills the disk on the CI
recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5
recipes/bioconductor-mafdb.gnomad.r2.1.grch38
recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch37
recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch38
recipes/bioconductor-trena

# x86_64-conda-linux-gnu-cc: error: unrecognized command-line option '-R'
recipes/ncbi-util-legacy

# HDF5 compatibility, https://github.com/mateidavid/nanocall/issues/38
recipes/nanocall

# source code no longer available
recipes/bugseq-porechop

# move to conda-forge. After moving, the recipe directory can be deleted and the blacklist entry removed.
recipes/autolog
recipes/avro-python2
recipes/elasticluster
recipes/epydoc
recipes/esmre
recipes/forked-path
recipes/justbackoff
recipes/kid
recipes/myriad
recipes/nose-capturestderr
recipes/perl-digest-md5-file
recipes/perl-getopt-argvfile
recipes/perl-hpc-runner-command-plugin-logger-sqlite
recipes/perl-pcap
recipes/perl-pdf-api2
recipes/perl-probe-perl
recipes/perl-rest-client
recipes/perl-soap-lite
recipes/perl-test-xml
recipes/perl-util-properties
recipes/perl-xml-dom
recipes/perl-xml-dom-xpath
recipes/perl-xml-twig
recipes/pyasp
recipes/pyexcelerator
recipes/pyhashxx
recipes/pyopt
recipes/rdfextras
recipes/scala
recipes/sharedmem
recipes/stacks_summary
recipes/workspace
recipes/wtforms-alchemy
recipes/wtforms-components
recipes/xmlbuilder

# the following packages have open PRs labeled with "Move to conda-forge"
recipes/gecode
recipes/perl-unicode-utf8
recipes/perl-test-files
recipes/perl-bio-cigar
recipes/perl-mime-lite

# perl package with no proper installation method
recipes/feelnc

# Maven no longer accepts http connections https://github.com/rdpstaff/ReadSeq/issues/2
recipes/rdp-readseq

# Only specific versions are failing
recipes/emmix/1.3
recipes/hyphy/2.3.11
recipes/skewer/0.1.126
recipes/blast/2.2.31
recipes/bedtools/2.26.0
recipes/opsin/1.4.0
recipes/opsin/2.1.0
recipes/meme/4.11.1
recipes/meme/4.8.1
recipes/bcftools-gtc2vcf-plugin/1.9
recipes/panx/1.6.0
recipes/panx/1.5.0
recipes/blast/2.5.0

# Unclear that the following old version is still needed, but the main recipe has an older version?!?
recipes/mira/4.9.6

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

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

# Permission denied ESTscan
recipes/perl-estscan2/2.1

# Source code no longer easily available
recipes/strip_it/1.0.2
recipes/shape_it/1.0.1
recipes/tqdist/1.0.0
recipes/ocrad/0.21
recipes/perl-estscan1/1.3
recipes/bwa/0.6.2

# reprocessed to here
# fails compilation in bulk on Linux
recipes/paragraph
recipes/selectsequencesfrommsa
recipes/mmvc
recipes/deltabs
recipes/gottcha
recipes/ea-utils
recipes/nextgenmap
recipes/igor_vdj
recipes/pargenes
recipes/porfast
recipes/agg
recipes/hg-color
recipes/prosolo
recipes/graphclust-wrappers
recipes/swga
recipes/jvarkit-bam2wig
recipes/jvarkit-bam2svg
recipes/jvarkit-msa2vcf
recipes/cath-tools
recipes/goetia
recipes/isaac4
recipes/prosic
recipes/translig
recipes/lsc
recipes/rambo-k
recipes/mobster
recipes/chicagotools
recipes/trim_isoseq_polya
recipes/ra/ra-assembler
recipes/hulk
recipes/spydrpick
recipes/bctools
recipes/group_humann2_uniref_abundances_to_go
recipes/isonclust2
recipes/sibelia
recipes/var-agg
recipes/wham

# Source code moved
recipes/astalavista
recipes/kggseq
recipes/coral
recipes/ngsep
recipes/rnabridge-denovo
recipes/eval
recipes/minorseq
recipes/methylextract
recipes/blasr
recipes/asn2gb
recipes/maaslin
recipes/micropita
recipes/pblaa
recipes/translatorx
recipes/meme/4.11.1
recipes/meme/4.8.1
recipes/bax2bam
recipes/break-point-inspector
recipes/embl-api-validator
recipes/readseq
recipes/smcounter2
recipes/compalignp
recipes/genie
recipes/admixture
recipes/mace
recipes/riboseq-rust

# vendors bzip2, samtools, etc.
recipes/rvtests

# Source URL no longer exists
recipes/python-mailund-newick

# Requires obsolete matplotlib versions incompatible with our gfortran pinnings
recipes/riboplot

# Requires libXext.so.6 in the container
recipes/samsifter

# Mulled test never completes
recipes/comparative-annotation-toolkit

# compilation or other errors in bulk
recipes/transcomb
recipes/detonate
recipes/bmtagger

# Packages failing in bulk that haven't yet received more attention
recipes/ig-checkflowtypes
recipes/bufet
recipes/qtip
recipes/strainest
recipes/t_coffee
recipes/shannon_cpp
recipes/ecopy
recipes/qiimetomaaslin
recipes/biolite
recipes/pauda
recipes/hicbrowser
recipes/vqsr_cnn
recipes/mqc
recipes/roprofile
recipes/chanjo
recipes/gqt
recipes/triform2
recipes/lcfit
recipes/tadarida-c
recipes/w4mclstrpeakpics

# KeyError: '>=1.0.6'
# (apparently due to bzip2 constraint)
recipes/sgcocaller
recipes/sscocaller

# numba import fails with no exception
recipes/sparse-neighbors-search

# needs specific clusterprofiler and enrichplot versions that are not currently available
recipes/vsclust

# make: common": No such file or directory
recipes/conduit-assembler

# configure: error: cannot find required auxiliary files: config.guess config.sub
recipes/bcftools-snvphyl-plugin

# rnamoves.c:(.text.RNA2_move_noLP_bpshift+0x1f): undefined reference to `close_bp'
recipes/kinsimriboswitch

# configure: error: R package gtools not found.
# (even though r-gtools is in host: and run:
recipes/footprint

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

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

# Unknown issues
recipes/cmv
recipes/smashbenchmarking

# tracking master branch
recipes/frc

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

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

# 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/jali
recipes/intervalstats

# missing dep
recipes/oligotyping
recipes/oligotyping/2.0

# missing binary
recipes/semeta

# 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

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

# compilation error
recipes/lightning

# unable to access jarfile
recipes/effectivet3

# url broken
recipes/e-pcr

# linker error
recipes/discovar-denovo

# depends on perl-pcap
recipes/brass

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

# 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/hubward
recipes/phylotoast

# git checkout problem
recipes/icqsol
recipes/pout2mzid

# checksum always fails
recipes/ms

# PREFIX/lib is a directory
recipes/proot

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

# Conflicting numpy and qiime
recipes/koeken

# 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

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

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

# natsort conflicts with python
recipes/qcumber

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

# broken pipe
recipes/antarna

# missing bioc package
recipes/customprodb

# 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

# perl script could not be found
recipes/rnaclust

# Unknown issues
recipes/lorma
recipes/nspdk
recipes/dreamtools
recipes/biomaj
recipes/odose

# /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

# 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

# Error: Unable to access jarfile
recipes/gfinisher

# gsl missing but specified
recipes/gfold

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

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

# 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

# /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
recipes/graphprot

# 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/metavelvet-sl-feature-extraction
recipes/music
recipes/gnu-getopt
recipes/flock
recipes/cmfinder
recipes/cortex_con
recipes/cufflinks
recipes/esimsa
recipes/funcannot
recipes/genepender
recipes/mosaik
recipes/nlstradamus
recipes/pygresql
recipes/real
recipes/rmap
recipes/rnabob
recipes/sam
recipes/sff2fastq
recipes/snpomatic
recipes/swiftlink
recipes/carna

# Source seems to have moved
recipes/discovar

# Requirements pinned down so much that rebuilds are prevented. (Some old deps may only be available on the old pks/free defaults channel.)
recipes/oncotator

# Depends on rdfextras with depends old pyparsing not available on conda-forge and pkgs/main (only on pkgs/free)
recipes/pacbio_falcon

# Depends on old matplotlib <1.5.0 not available on conda-forge and pkgs/main (only on pkgs/free)
recipes/pymix

# Depends on pymix, see above
recipes/ale

# Pinned to biopython=1.65 which is only availble through pkgs/free. If it doesn't break the package, the requirement should be set to biopython=1.70 or higher.
recipes/breakseq2

# Depends on r-base and mentalist. The latter has has pinned down dependencies preventing the installation alongside other packages like r-base. Need to fix mentalist!
recipes/pathogist

# Uses binary wheel that have been deleted upstream (and are not available from depot.galaxyproject.org). To fix it, build from source
recipes/python-consensuscore2

# Pinned to older Bioconductor package version that is not build for current R
recipes/scater-scripts
recipes/sc3-scripts

# Warning: replacing previous import ‘BiocGenerics::combine’ by ‘gridExtra::combine’ when loading ‘RiboseQC’\nWarning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘RiboseQC’\nERROR: lazy loading failed for package ‘RiboseQC’\n* removing ‘$PREFIX/lib/R/library/RiboseQC’\nError: object ‘DEFAULT_CIRC_SEQS’ is not exported by 'namespace:GenomicFeatures'
recipes/riboseqc

# Some UnsatisfiableError
recipes/music-deconvolution

# Bulk times out while solving environment
recipes/mercat
recipes/panpasco

# Needs a bunch of fixes (remove outdated conda-forge::perl workaround, not symlinking compiler/linker, linker fixes, etc.).
recipes/arb-bio

# Source needs patching ("degree()" definition is ambiguous):
# BWTIL/data_structures/../common/../extern/bitvector/include/internal/bitvector.hpp:815:43: error: expression cannot be used as a function
#                     t.ranks(child, degree()) -= 1;
recipes/erne

# Uses pyinstaller (why??) but doesn't run: "Cannot open self $PREFIX/bin/taco_run or archive $PREFIX/bin/taco_run.pkg"
recipes/taco

# Unknown issues
recipes/cnvetti
recipes/bibliospec

# OCaml/opam build fails
recipes/phylocsf

# Ruby build failes
recipes/protk

# Does not link include -lGL -lGLU when linking, might require libOSMesa.
recipes/connectome-workbench

# Build fails during boostrap of vendored Boost.
recipes/gvcftools
recipes/seer

# Can't compile
recipes/gplas

# compilation error and dependants
recipes/mmult
recipes/bioconductor-hilbertvisgui
recipes/bioconductor-travel
recipes/bioconductor-netboost

# some missing perl dependency
recipes/perl-biox-workflow-command

# python 2-only with C requiring graphiv. No longer supportable
recipes/sshmm

# Source code no longer easily available
recipes/cap3
recipes/bumbershoot
recipes/gerp
recipes/turbocor

# tool renamed
recipes/titan-gc

# failing in bulk for now
recipes/cmip
recipes/cesm
recipes/minnow
recipes/conterminator
recipes/apoc
recipes/quorum
recipes/noresm
recipes/callstate
recipes/pb-falcon-phase
recipes/hiline
recipes/eqtlbma

# Takes hours to solve the environment
recipes/rop

# Above v1.0.5 there are licensing restrictions and it cannot be distributed
# via bioconda. See https://github.com/bioconda/bioconda-recipes/pull/23476.
recipes/fishtaco

# no matching package named `quickersort` found
recipes/mudskipper

# md5 mismatch when downloading source
recipes/komb

# duplicate recipe
recipes/treeqmc

# migrated to conda-forge to be windows-friendly
recipes/pygenomeviz

# migrated to conda-forge
recipes/grep
recipes/logomaker
recipes/dockq
recipes/hesslab-gambit


# Bioconductor rebuild 2026-02
recipes/smcpp


recipes/cytocad
recipes/pydnase
recipes/genblastg
recipes/cnv_facets

# strict-repo-priority mess
r-alakazam

recipes/bioconductor-gpumagic # binary packages only
recipes/bioconductor-nearbynding # filter function not available
recipes/bioconductor-singlemoleculefootprinting # filter function not available
recipes/bioconductor-rsbml # compile error

# unsupported T character
recipes/bioconductor-hmp2data
recipes/aodp

# outdated
recipes/jbrowse

# has a non-numeric version "MKV"
recipes/privateer
# has a deprecated dependency "bioconductor-suprahex"
recipes/r-dnet
recipes/r-xgr

# some mismatch with data packages
recipes/bioconductor-systempiperdata
# no source package
recipes/bioconductor-beadarray
recipes/bioconductor-beadarrayusecases

# compile errors
recipes/bioconductor-gmapr

# fails with newer compiler
recipes/augustus/3.3.3
# needs maybe older version of numpy and pysam in runtime? mantis-msi2 exist
recipes/mantis-msi

# strict pins and too old
recipes/sensv

# cp: cannot stat 'lib/*.h': No such file or directory
recipes/sonlib

# ... $SRC_DIR/genoiser/src/genoiser.nim(75, 20) Error: invalid indentation
recipes/duphold