build-fail-blacklist

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

recipes/mothur/1.36.1

# more temporary blacklisting to get other packages to run

recipes/transcomb

# tracking master branch
recipes/frc

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

recipes/openslide

# warning: spurious network error (1 tries remaining): [12/-2] [77] Problem with the SSL CA cert (path? access rights?) (error setting certificate verify locations:
# also failing due to a missing trait bound: the trait `rand::distributions::Distribution<N>` is not implemented for `rand::distributions::Standard`
#   |
#   = help: consider adding a `where rand::distributions::Standard: rand::distributions::Distribution<N>` bound
#   = note: required by `rand::random`
recipes/prosic

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

# Make file needs to be patched to find newer zlib?
recipes/samtools/1.1

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

# osx failures
recipes/smalt
recipes/perl-file-homedir

# 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

# The following recipes are also found in other channels (notably conda-forge).
# They are placed here on the blacklist until we can deal with them further.
recipes/aenum
recipes/intervaltree
recipes/jemalloc
recipes/jq
recipes/lapack
recipes/libdb
recipes/mysql-connector-c
recipes/nasm
recipes/netifaces
#Exists in conda-forge - getting rid of this
#recipes/perl-text-soundex
recipes/popt
recipes/pysftp
recipes/pytest-timeout
recipes/python-levenshtein
recipes/r-argumentcheck
recipes/r-bio3d
recipes/r-biomark
recipes/r-cnogpro
recipes/r-data.table/1.10.4
recipes/r-deoptimr
recipes/r-diptest
recipes/r-diptest/0.75_7
recipes/r-drc
recipes/r-dynamictreecut
recipes/r-gam
recipes/r-gbm
recipes/r-genabel
recipes/r-genabel.data
recipes/r-genenet
recipes/r-giant
recipes/r-gprofiler
recipes/r-gpseq
recipes/r-grimport
recipes/r-gsalib
recipes/r-gsmoothr
recipes/r-haplo.stats
recipes/r-ic10trainingdata
recipes/r-icluster
recipes/r-idr
recipes/r-inlinedocs
recipes/r-km.ci
recipes/r-kmsurv
recipes/r-kriging
recipes/r-lsd
recipes/r-maldiquant
recipes/r-matrixeqtl
recipes/r-metarnaseq
recipes/r-microseq
recipes/r-mixomics
recipes/r-mlgt
recipes/r-mqtl
recipes/r-pamr
recipes/r-patpro
recipes/r-phangorn
recipes/r-pinfsc50
recipes/r-plasmidprofiler
recipes/r-precrec
recipes/r-propcis
recipes/r-purbayes
recipes/r-qiimer
recipes/r-qtl
recipes/r-rcircos
recipes/r-readbrukerflexdata
recipes/r-readmzxmldata
recipes/r-rematch2
recipes/r-rentrez
recipes/r-robustrankaggreg
recipes/r-rphylip
recipes/r-seqinr
recipes/r-smvar
recipes/r-snpassoc
recipes/r-solarius
recipes/r-tfmpvalue
recipes/r-xnomial
recipes/regex
recipes/scikit-bio
recipes/xdg

#  error: possibly undefined macro: AM_GNU_GETTEXT
recipes/xcftools

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

# According to output of CI in https://github.com/bioconda/bioconda-recipes/pull/9524
# It seems that the compiler build flags specified in the CMake files are out of date
# https://github.com/medvedevgroup/TwoPaCo/search?q=c%2B%2B0x&unscoped_q=c%2B%2B0x
# E.g., I think the recipe needs to move from -std=c++0x to -std=c++11x
# See https://gcc.gnu.org/projects/cxx-status.html
# https://gcc.gnu.org/gcc-4.5/cxx0x_status.html
# And https://gcc.gnu.org/gcc-4.8/cxx0x_status.html

# 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

# unknown
recipes/smina

# missing tarball
recipes/metagene_annotator
recipes/sloika
recipes/pycoqc

# missing dep
recipes/sistr_cmd
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
# Warning: Unrecognized source format. Source file will be copied to the SRC_DIR
recipes/smoove
# 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

# unable to access jarfile
recipes/effectivet3

# url broken
recipes/e-pcr

# linker error
recipes/discovar-denovo

recipes/blast/2.2.21
recipes/blast-legacy/2.2.22

# seqan errors
recipes/bowtie/1.0.0

recipes/cmv

# tarball missing
recipes/mrbayes

# error in BucketCache setup command: 'install_requires' must be a string or list of strings containing valid project/version requirement specifiers; Unordered types are not allowed
recipes/bucketcache

# depends on perl-pcap
recipes/brass

recipes/fwdpp
recipes/fwdpp/0.5.3
recipes/fwdpp/0.5.4

# 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 perl dep
recipes/perl-text-ansitable/0.48

# missing tarballs
recipes/genometools
recipes/nanonet

#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

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

# checksum always fails
recipes/ms

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

# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml  url=https://pypi.org/simple/HyPhy/
recipes/hivtrace

# 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

recipes/java-jdk/7.0.91
# /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
# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml  url=https://pypi.org/simple/click/
recipes/onto2nx

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

recipes/parafly

# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml  url=https://files.pythonhosted.org/packages/source/c/certifi/certifi-2016.9.26.tar.gz#md5=baa81e951a29958563689d868ef1064d
recipes/imfusion/0.3.0
recipes/imfusion/0.3.2
recipes/poretools/0.5.1

# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml  url=https://pypi.org/simple/pyaml/#
recipes/hubward

#failed to get install actions, retrying.  exception was: The following specifications were found to be in conflict:
#  - numpy=1.9
#  - qiime -> numpy=1.12
recipes/koeken

# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml  url=https://files.pythonhosted.org/packages/source/c/certifi/certifi-2016.9.26.tar.gz#md5=baa81e951a29958563689d868ef1064d
recipes/nucleoatac/0.3.1


# no clue currently
recipes/hap.py
# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml  url=https://pypi.org/simple/click/
recipes/phylotoast

# takes hours to build
recipes/plastid

# 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

# compilation error
recipes/lightning

# zlib missing
recipes/polymutt
recipes/prophyle/0.2.1

# /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

recipes/rdflib-jsonld
recipes/smashbenchmarking

#failed to get install actions, retrying.  exception was: The following specifications were found to be in conflict:
#  - natsort[version='<4.0.0'] -> python=2.6
#  - python=3.5
recipes/qcumber

recipes/saffrontree
recipes/slclust

# /opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-redhat-linux/4.8.2/ld: cannot find -lz
recipes/samtools/0.1.19
# 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

# zlib
recipes/trimmomatic/0.35

# https://github.com/conda-forge/cairo-feedstock/issues/31
recipes/rdkit/2015.09.2
recipes/rdkit/2016.03.3

# broken pipe
recipes/antarna

#gff.h missing
recipes/gffcompare

# perl errors
recipes/snvphyl-tools

# missing perl module
recipes/snippy/3.0

# is running forever?
recipes/amptk

# 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

# no such file or directory (bin/classifier.jar')
recipes/frogs

# post-link error
recipes/antismash

# zlib
recipes/megahit

recipes/dreamtools

# 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

# compiler error
recipes/fwdpy11

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

# takes to long to install
recipes/bcbio-rnaseq

# cannot open file

recipes/expansionhunter

recipes/biomaj
# missing python requirements?
recipes/illuminate

# wired Docker permission error
recipes/bpipe

# perl bad interpreter
recipes/cmfinder/0.2

# conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {'perl-graphics-colorobject'}
recipes/circos-tools


recipes/cas-offinder

# 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

# zlib
recipes/dsk

# perl
recipes/vcftools/0.1.10

# perl wrong interpreter
recipes/prinseq


recipes/locarna/1.8.7
recipes/locarna/1.9.1
recipes/locarna/1.8.11
recipes/locarna/1.8.12
recipes/locarna/1.8.10
recipes/locarna/1.9.0
recipes/locarna/1.8.9
recipes/intarna/2.1.0

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

# but ['zlib'] not in reqs/run, i.e. it is overlinked (likely) or a missing dependency (less likely)
recipes/lofreq

# perl script could not be found
recipes/rnaclust

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

#conda.exceptions.UnsatisfiableError: The following specifications were found to be in conflict:
#  - bellmans-gapc -> boost=1.61 -> icu=56
#  - boost=1.66.0 -> boost-cpp==1.66.0
recipes/rnashapes/3.3.0


recipes/export2graphlan
recipes/lorma
recipes/microbecensus
recipes/minialign
recipes/nspdk
recipes/visceral-evaluatesegmentation


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

# tarball missing
recipes/igvtools

recipes/odose

# missing module
recipes/perl-statistics-ttest
recipes/perl-module-fromperlver/0.008002

# test failed:
recipes/perl-locale-maketext-simple/0.21
recipes/perl-mldbm-sync
recipes/perl-pod-checker/1.60

recipes/perl-bio-db-sam

# /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

# chmod: cannot access `/opt/conda/conda-bld/pantools_1531691214490/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/pantools': No such file or directory
recipes/pantools

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

# Permission denied ESTscan
recipes/perl-estscan2/2.1

recipes/perl-sql-statement

# test failed
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

# missing tarball
recipes/knot
recipes/moreutils

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

# missing tarball
recipes/jali
recipes/intervalstats

# failing
recipes/igblast/1.4.0

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

# I got far with desmon but not it fails inside Docker with a missing perl module
recipes/desman

# fortran missing :(
recipes/fastspar

# build error
recipes/mapsplice

# 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

recipes/perl-pcap
recipes/perl-hpc-runner-command/3.2.13
recipes/perl-biox-workflow-command

recipes/perl-hpc-runner-command-plugin-logger-sqlite/0.0.3

# /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

# TODO: cap-mirseq has test error. Perhaps just needs a fix on expected exit
# code
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/perl-file-homedir
recipes/snap
recipes/perl-mixin-linewise
recipes/perl-pod-coverage-trustpod/0.100003
recipes/perl-symbol-util/0.0203
recipes/oases
recipes/novoplasty
recipes/metavelvet-sl-feature-extraction
recipes/locarna
recipes/music
recipes/kraken
recipes/kraken-ea
recipes/gnu-getopt
recipes/ghmm
recipes/domclust
recipes/bwa/0.6.2
recipes/metilene
recipes/disco/1.2
recipes/c-ares
recipes/cassiopee
recipes/check-sort-order
recipes/flock
recipes/cmfinder
recipes/cortex_con
recipes/cosi2
recipes/cufflinks
recipes/dialign-tx
recipes/edlib
recipes/esimsa
recipes/fastuniq
recipes/fgap
recipes/gclib
recipes/funcannot
recipes/genepender
recipes/genometester4
recipes/ghostx
recipes/ghostz
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-pod-elemental
recipes/perl-dbm-deep
recipes/perl-set-intervaltree
recipes/carna
recipes/perl-moosex-app/1.39


# clang

####################### OSX errors above ###############

############### R packages not in CRAN #################
recipes/r-ampvis
recipes/r-annotables
recipes/r-basejump
recipes/r-bcbiobase
recipes/r-bcbiornaseq
recipes/r-biodb
recipes/r-boutroslabplottinggeneral
recipes/r-chbutils
recipes/r-cimpl
recipes/r-DGEclustering
recipes/r-dpeak
recipes/r-genometricorr
recipes/r-george
recipes/r-histonehmm
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-probmetab
recipes/r-qorts
recipes/r-quorts
recipes/r-raceid3
recipes/r-rBLAST
recipes/r-rubic
recipes/r-scimpute
recipes/r-soap-nmr
recipes/r-spieceasi
recipes/r-wasabi
recipes/r-workflowscriptscommon
recipes/r-xmlrpc
recipes/r-zerone
########### End R packages not in CRAN #################

# recipes/bioconductor-dbchip already exists
recipes/r-dbchip

# Removed from CRAN
recipes/r-asics
recipes/r-biom

# Deprecated in Bioconductor
recipes/bioconductor-atlasrdf
recipes/bioconductor-jmosaics
recipes/bioconductor-meshsim
recipes/bioconductor-mmdiff
recipes/bioconductor-mmnet
recipes/bioconductor-rcytoscape

# 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-org.dm.eg.db/3.3.0
recipes/bioconductor-ggbio/1.22.0

# Errors with bioconductor-skeleton
recipes/bioconductor-mvgst

# bioconductor-mzr has compilation problems and the others depend on it
recipes/bioconductor-mzr
recipes/bioconductor-camera
recipes/bioconductor-cosmiq
recipes/bioconductor-faahko
recipes/bioconductor-flagme
recipes/bioconductor-ipo
recipes/bioconductor-lobstahs
recipes/bioconductor-metab
recipes/bioconductor-metams
recipes/bioconductor-msmseda
recipes/bioconductor-msnbase
recipes/bioconductor-msnid
recipes/bioconductor-mspurity
recipes/bioconductor-pbase
recipes/bioconductor-profia
recipes/bioconductor-proloc
recipes/bioconductor-prolocgui
recipes/bioconductor-proteomicsannotationhubdata
recipes/bioconductor-risa
recipes/bioconductor-simat
recipes/bioconductor-synapter
recipes/bioconductor-xcms
recipes/bioconductor-yamss
recipes/r-george
recipes/r-msqrob
recipes/r-probmetab

# Not actually bioconductor packages

# post-link error
recipes/bioconductor-jaspar2018