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build-fail-blacklist
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# Recipe tests fail with "Error in library("spatialLIBD") there is no package called spatialLIBD".
recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5
recipes/bioconductor-mafdb.gnomad.r2.1.grch38
recipes/bioconductor-spatiallibd# Building tries to install 1.1.27 for some reason (despite meta.yaml
# Need perl-net-ssleay to be migrated in conda-forge
recipes/srax
recipes/irida-linker
recipes/quantwiz-iq
recipes/hotspot3d
recipes/perl-bioperl-core
recipes/perl-bio-searchio-hmmer
recipes/perl-bio-featureio
recipes/perl-bio-phylo
recipes/perl-bio-procedural
recipes/perl-bio-tools-run-remoteblast
recipes/perl-metabolomics-fragment-annotation
recipes/perl-bio-automatedannotation
recipes/perl-sanger-cgp-battenberg
recipes/perl-bio-eutilities
recipes/perl-ensembl-api
recipes/perl-bio-asn1-entrezgene
recipes/perl-bio-phylo-cipres
recipes/perl-bio-db-refseq
recipes/perl-bio-db-embl
recipes/perl-bio-coordinate
recipes/perl-bio-db-swissprot
recipes/perl-ensembl-compara
# move to conda-forge
recipes/perl-net-ssleay
recipes/perl-io-socket-ssl
recipes/perl-carp-clan
recipes/perl-bit-vector
recipes/perl-ipc-system-simple
recipes/perl-text-csv
recipes/perl-mozilla-ca
recipes/perl-io-null
recipes/perl-test
recipes/perl-pcap
recipes/perl-text-levenshteinxs
recipes/perl-getopt-argvfile
recipes/perl-data-dump
recipes/perl-text-csv_xs
recipes/perl-probe-perl
recipes/perl-svg
recipes/perl-lwp-protocol-https
recipes/perl-libwww-perl
recipes/perl-test-xml
recipes/perl-www-mechanize
recipes/perl-io-socket-ssl
recipes/perl-rest-client
recipes/perl-net-http
recipes/perl-lwp-simple
recipes/perl-soap-lite
recipes/perl-xml-twig
recipes/perl-digest-md5-file
recipes/perl-graphviz
recipes/perl-xml-dom-xpath
recipes/perl-xml-dom
recipes/perl-util-properties
# needs perl-svg in conda-forge:
reipces/ldblockshow
# sha256 mismatch, needs review
recipes/3seq
recipes/last
# these depend on last, which needs sha256 review
recipes/nanosim-h
recipes/lamassemble
recipes/dnarrange
# depend on python-bioext:
recipes/python-hivclustering
recipes/hivtrace
# conda_build.source:Error: HTTP 503 SERVICE TEMPORARILY UNAVAILABLE for url
# <https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/2.8.0/OpenMS-2.8.0-src.tar.gz>
recipes/pyopenms
# compiler errors
recipes/pylibseq
recipes/medicc2
recipes/ggcaller
# compiler errors. Also seems to vendor in samtools
recipes/gembs
# seems unable to find hdf5?
recipes/genomedata
# depend on genomedata:
recipes/segtools
recipes/segway
# dlopen error upon import
recipes/pyrodigal
# depends on auspice
recipes/nextstrain
#
# solver seems to want alignlib-lite for py27, even when building for py310.
# Recipe currently skipped for py2k, py39, and py36 so maybe not the first time
# it's been problematic.
recipes/cgat-apps
# source no longer available
recipes/bugseq-porechop
# Never resolves in bulk
recipes/mosca
# freezes bulk
recipes/metapop
recipes/phenix
recipes/monocle3-cli
recipes/coinfinder
recipes/pysam/0.9.1
recipes/hatchet
recipes/tobias
recipes/strainge
recipes/jcvi
# Resolve conflict in bulk branch, likely a python 3.9 dependency missing
recipes/seidr
recipes/tadbit
recipes/alignlib-lite
recipes/genomelake
recipes/mockinbird
recipes/sparse-neighbors-search
recipes/msaprobs
recipes/mgkit
recipes/starseqr
recipes/sqt
recipes/scanindel
recipes/blockclust
recipes/datma
recipes/chorus2
recipes/raxml/7.3.0
recipes/quake
recipes/simlord
recipes/gap2seq
recipes/umis
# dependency conflict
recipes/probamconvert
recipes/hail
recipes/savage
recipes/pb-falcon
# incompatible with modern htslib
recipes/vt/2015.11.10
# incorrectly merged, test segfaults
recipes/docking_py
# uses too much memory
recipes/anise_basil
# incompatible with c++ 17
recipes/bsmap
# needs tweaking on osx
recipes/bcftools/1.3.1
# fitBeta2.cpp:158:93: error: no matching function for call to 'arma::eGlue<arma::Glue<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::eglue_plus>::i(bool) const'
recipes/xtail
# needs patching for compilers
recipes/logol
# fails mulled test
recipes/ribotaper
# sketch/include/sketch/mh.h:993:15: error: no viable overloaded '='
recipes/dashing
# Prebuilt binaries no longer work
recipes/msms
recipes/omssa
# killed during test
recipes/mtsv
# make: *** No rule to make target 'common"'. Stop.
recipes/conduit-assembler
# ./gecode/set/int/weights.hpp:131:35: error: no viable overloaded '='
recipes/gecode
recipes/gecode/4.4.0
# binary missing after installation
recipes/scrappie
# error while loading shared libraries: libblis.so.3: cannot open shared object file: No such file or directory
recipes/andi
# unknown type name 'ptrdiff_t'
recipes/centrifuge
# prior.c:102:12: error: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)' [-Werror,-Wimplicit-function-declaration]
recipes/wise2
# fails subtests
recipes/perl-bio-das
recipes/kinsimriboswitch
# needs rebuild or perl-gd
recipes/feelnc
recipes/bttoxin_scanner
recipes/perl-bio-mlst-check
recipes/snmf
recipes/perl-bio-bigfile
recipes/bttcmp
recipes/perl-sanger-cgp-vagrent
recipes/gaas
recipes/mashtree
recipes/aodp
recipes/perl-sanger-cgp-allelecount
recipes/gcluster
recipes/fastx_toolkit
recipes/perl-ensembl-variation
# Can't find boost (looking for static libraries?)
recipes/metabat2
recipes/hap.py
recipes/kat
# Controller/../Reader/../Graph/pre_graph/../flow_graph/../../Datatype_Templates/boost_bitset_hash.h:27:17: error: redefinition of 'hash_value'
recipes/ryuto
# Unable to initialize nextflow environment
recipes/illumina-cleanup
# pulls in non-existent static boost library, needs to switch to using the shared library
recipes/metamaps
# test now fails
recipes/rnasnp
# Uses too much memory during test?
recipes/megahit
# requires patching around "invalid suffix on literal; C++11 requires a space between literal and identifier "
recipes/atac
# ldc requires a rebuild
recipes/sambamba/0.5.9
# incompatible with htslib >1.10
recipes/popscle
# fails test, Can't locate Bio/EnsEMBL/TaxonomyNode.pm in @INC (you may need to install the Bio::EnsEMBL::TaxonomyNode module) (@INC contains: /usr/local/lib/site_perl/5.26.2/x86_64-linux-thread-multi /usr/local/lib/site_perl/5.26.2 /usr/local/lib/5.26.2/x86_64-linux-thread-multi /usr/local/lib/5.26.2 .)
recipes/perl-ensembl-genomes
# fails compilation in bulk on Linux
recipes/beast2
recipes/stride
recipes/catch_chimera
recipes/rdp-readseq
recipes/crb-blast
recipes/paragraph
recipes/selectsequencesfrommsa
recipes/rappas
recipes/ssake
recipes/lorikeet
recipes/nasp
recipes/mmvc
recipes/expansionhunter
recipes/lumpy-sv-minimal
recipes/gemma
recipes/roary
recipes/deltabs
recipes/gottcha
recipes/pepnovo
recipes/ea-utils
recipes/nextgenmap
recipes/extract_fullseq
recipes/igor_vdj
recipes/pargenes
recipes/emmix/1.3
recipes/porfast
recipes/agg
recipes/hg-color
recipes/bandage
recipes/prosolo
recipes/ratt
recipes/graphclust-wrappers
recipes/swga
recipes/jvarkit-bam2wig
recipes/jvarkit-bam2svg
recipes/jvarkit-msa2vcf
recipes/rxdock
recipes/cath-tools
recipes/makehub
recipes/phame
recipes/goetia
recipes/consel
recipes/isaac4
recipes/clame
recipes/prosic
recipes/dms
recipes/variant_tools
recipes/r-phytools
recipes/translig
recipes/lsc
recipes/rambo-k
recipes/mobster
recipes/visceral-evaluatesegmentation
recipes/hyphy/2.3.11
recipes/chicagotools
recipes/skewer/0.1.126
recipes/skewer
recipes/trim_isoseq_polya
recipes/ra/ra-assembler
recipes/pureclip
recipes/hulk
recipes/bolt-lmm
recipes/bmfilter
recipes/unitig-counter
recipes/probcons
recipes/spydrpick
recipes/bctools
recipes/bayestyper
recipes/blast/2.2.31
recipes/group_humann2_uniref_abundances_to_go
recipes/isonclust2
recipes/bedtools/2.26.0
recipes/bmtool
recipes/sibelia
recipes/var-agg
recipes/t-coffee
recipes/wham
recipes/percolator
recipes/r-saige/0.39
# Segfaults in bulk on Linux 24.3.2021
recipes/dbgraph
recipes/mira
# Source code moved
recipes/astalavista
recipes/kggseq
recipes/hts-nim-tools
recipes/pbmarkdup
recipes/oligoarrayaux
recipes/coral
recipes/ngsep
recipes/rnabridge-denovo
recipes/eval
recipes/minorseq
recipes/prosampler
recipes/methylextract
recipes/opsin/1.4.0
recipes/opsin/2.1.0
recipes/blasr
recipes/asn2gb
recipes/skesa
recipes/orfm
recipes/maaslin
recipes/seqmap
recipes/micropita
recipes/assemblytics
recipes/nemo
recipes/pblaa
recipes/translatorx
recipes/meme/4.11.1
recipes/meme/4.11.2
recipes/meme/4.8.1
recipes/bax2bam
recipes/break-point-inspector
recipes/embl-api-validator
recipes/readseq
recipes/smcounter2
recipes/compalignp
recipes/seq2hla
recipes/reaper
recipes/genie
recipes/admixture
recipes/mace
recipes/riboseq-rust
# ../../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
# This vendors bowtie2, which breaks the noarch: python setting
recipes/humann2
# vendors bzip2, samtools, etc.
recipes/rvtests
# Source URL no longer exists
recipes/python-mailund-newick
recipes/piret
# Requires obsolete matplotlib versions incompatible with our gfortran pinnings
recipes/riboplot
# Requires libXext.so.6 in the container
recipes/samsifter
# C++ syntax error: ../../lib/srprism/query_acct.hpp:118:51: error: expected primary-expression before ')' token { return query_info_[qn].MaxErr< paired >(); }
recipes/srprism
# Mulled test never completes
recipes/comparative-annotation-toolkit
# compilation or other errors in bulk
recipes/transcomb
recipes/detonate
recipes/bmtagger
# Killing bulk
recipes/rsat-core
# Packages failing in bulk that haven't yet received more attention
recipes/ig-checkflowtypes
recipes/bufet
recipes/mapsplice
recipes/pasta
recipes/moods
recipes/halla
recipes/qtip
recipes/tagger
recipes/compare-reads
recipes/strainest
recipes/r-peer
recipes/methylpy
recipes/openslide-python
recipes/t_coffee
recipes/shannon_cpp
recipes/ecopy
recipes/qiimetomaaslin
recipes/glimmerhmm
recipes/groopm
recipes/biolite
recipes/pauda
recipes/hicbrowser
recipes/bcftools-gtc2vcf-plugin/1.9
recipes/vqsr_cnn
recipes/bam-readcount
recipes/mqc
recipes/panx/1.6.0
recipes/panx/1.5.0
recipes/roprofile
recipes/chanjo
recipes/xxmotif
recipes/phylip
recipes/gqt
recipes/diamond_add_taxonomy
recipes/shapemapper
recipes/rnftools
recipes/embassy-phylip
recipes/triform2
recipes/haploclique/1.3.1
recipes/lcfit
recipes/blast/2.5.0
recipes/tadarida-c
recipes/w4mclstrpeakpics
# 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/bamtools/2.3.0
recipes/bowtie/1.1.1
recipes/freebayes/1.1.0.46
recipes/blast-legacy/2.2.22
recipes/perl-extutils-makemaker/7.24
recipes/tabix/0.2.5
recipes/tabix/0.2.6
recipes/rsem/1.2.21
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/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
# Seems to download maven and then have java issues
recipes/megagta
# Unknown issues
recipes/smina
recipes/cmv
recipes/fwdpp
recipes/parafly
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
# 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
# missing dep
recipes/oligotyping
recipes/oligotyping/2.0
# missing file
recipes/shiver
# 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
# 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
# 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
# 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/imfusion/0.3.0
recipes/imfusion/0.3.2
recipes/poretools/0.5.1
recipes/hubward
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
# PREFIX/lib is a directory
recipes/proot
# 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/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
# 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
# /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
# perl issues
recipes/vcftools/0.1.11
# broken pipe
recipes/antarna
# hashFunction.c:94: Error: invalid instruction suffix for `push'
recipes/soapdenovo2
# tarball missing and should be migrated I guess
recipes/ant
recipes/ngseqbasic
# missing bioc package
recipes/customprodb
# fail in Docker test
recipes/fiji/20151222
recipes/fiji/20170530
# 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
# perl bad interpreter
recipes/cmfinder/0.2
# dotnet not found
recipes/canvas
# perl
recipes/vcftools/0.1.10
# perl script could not be found
recipes/rnaclust
# Unknown issues
recipes/lorma
recipes/microbecensus
recipes/minialign
recipes/nspdk
recipes/dreamtools
recipes/biomaj
recipes/cas-offinder
recipes/odose
# 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
# missing python dep
recipes/hurry.filesize
# 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/smalt
recipes/oases
recipes/metavelvet-sl-feature-extraction
recipes/music
recipes/kraken-ea
recipes/gnu-getopt
recipes/domclust
recipes/bwa/0.6.2
recipes/c-ares
recipes/flock
recipes/cmfinder
recipes/cortex_con
recipes/cosi2
recipes/cufflinks
recipes/edlib
recipes/esimsa
recipes/fastuniq
recipes/fgap
recipes/funcannot
recipes/genepender
recipes/ghostx
recipes/ls-gkm
recipes/mosaik
recipes/mustang
recipes/ngmerge
recipes/nlstradamus
recipes/ocrad/0.21
recipes/panoct
recipes/perl-estscan1/1.3
recipes/pygresql
recipes/real
recipes/rmap
recipes/rnabob
recipes/sam
recipes/sff2fastq
recipes/snpomatic
recipes/soapdenovo2-gapcloser
recipes/spectral_hk
recipes/swiftlink
recipes/tedna
recipes/transtermhp
recipes/carna
# stringify can't find libmysqlclient.18
recipes/ucsc-overlapselect
recipes/ucsc-pslmap
recipes/ucsc-pslcdnafilter
# Source seems to have moved
recipes/discovar
# source code no longer available at URL
recipes/r-genometricorr
# (binary) source no longer available at URL
recipes/extracthifi
# Packages that should be moved to conda-forge
recipes/autolog
recipes/avro-python2
recipes/avro-python3
recipes/bitstring
recipes/cityhash
recipes/collectl
recipes/elasticluster
recipes/epydoc
recipes/esmre
recipes/forked-path
recipes/gcs-oauth2-boto-plugin
recipes/gnuplot-py
recipes/justbackoff
recipes/kid
recipes/minimock
recipes/myriad
recipes/nose-capturestderr
recipes/pdfkit
recipes/pyasp
recipes/pyexcelerator
recipes/pyhashxx
recipes/pyopt
recipes/pysvg
recipes/pyx
recipes/rdfextras
recipes/sbt
recipes/scala
recipes/sharedmem
recipes/stacks_summary
recipes/tgt
recipes/udocker
recipes/workspace
recipes/wtforms-alchemy
recipes/wtforms-components
recipes/xmlbuilder
recipes/yaggo
# License prevents distribution on Bioconda
recipes/extractpirs
recipes/shapeit
# Dependency bioconductor-rcytoscape removed from Bioconductor
recipes/r-probmetab
recipes/r-probmetab/1.0/
# 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
# R package build segfaults: [2020-07-28 05:38:00] Plotting genome...\n\n*** caught segfault ***\naddress (nil), cause 'memory not mapped'\n\nTraceback:\n 1: cairoVersion()\n 2: grSoftVersion()\n 3: symbolType1support()\n 4: optionSymbolFont(d$symbolfamily)\n 5: png(paste0(xargs$out, ".cnv.png"), units = "px", width = 1600, height = 1600, res = 300)
recipes/cnv_facets
# 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/maaslin2
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
# Vendors gsl but fails to compile it.
recipes/rseg
# 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/proteowizard
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
# GSL linking problem (-lgsl not used?): "undefined reference to `gsl_ran_multinomial_pdf'"
recipes/merfishtools
# Build fails during boostrap of vendored Boost.
recipes/gvcftools
recipes/seer
# Can't compile