# Never resolves in bulk recipes/mosca # freezes bulk recipes/metapop recipes/sequana recipes/phenix recipes/monocle3-cli # Resolve conflict in bulk branch, likely a python 3.9 dependency missing recipes/seidr recipes/tadbit recipes/alignlib-lite recipes/ariba recipes/concoct recipes/genomelake recipes/mockinbird recipes/openms-meta recipes/sparse-neighbors-search recipes/msaprobs recipes/mgkit recipes/vsclust recipes/starseqr recipes/desman recipes/sqt recipes/scanindel recipes/blockclust recipes/datma recipes/pasa recipes/chorus2 recipes/raxml/7.3.0 recipes/samwell recipes/quake recipes/pairsnp recipes/simlord recipes/gap2seq recipes/umis # dependency conflict recipes/probamconvert recipes/hail recipes/savage recipes/regenie 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 # uses `hts-sys v1.10.3` but rust-htslib pulls in >=1.11.1-fix1, <2.0.0 recipes/lorikeet-genome # 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::op_htrans>, arma::Mat, arma::glue_times>, arma::Mat, arma::glue_times>, arma::Mat, arma::eglue_plus>::i(bool) const' recipes/xtail # unknown c++ error recipes/bedops # patch no longer works recipes/pathracer # 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 # /Applications/Xcode_12.4.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libIntaRNA.a(InteractionEnergyIdxOffset.o) has no symbols recipes/intarna # killed during test recipes/mtsv # stl_tree.h:780:8: error: static assertion failed: comparison object must be invocable as const recipes/rmblast # 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/perl-bioperl recipes/hla-la 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/fastani recipes/coinfinder 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 # Needs the TBB repodata patch so it doesn't pull in a broken bowtie2 recipes/unicycler # 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/graphaligner recipes/crb-blast recipes/r-fastbaps recipes/paragraph recipes/selectsequencesfrommsa recipes/rappas recipes/ssake recipes/lorikeet recipes/nasp recipes/mmvc recipes/expansionhunter recipes/lumpy-sv-minimal recipes/isescan recipes/gemma recipes/roary recipes/deltabs recipes/gottcha recipes/pepnovo recipes/ea-utils recipes/nextgenmap recipes/perl-bio-automatedannotation/1.182770 recipes/mashmap recipes/extract_fullseq recipes/igor_vdj recipes/tiddit recipes/rosella recipes/pargenes recipes/emmix/1.3 recipes/porfast recipes/agg recipes/hg-color recipes/bandage recipes/prosolo recipes/ratt recipes/graphclust-wrappers recipes/perl-ensembl-io recipes/kmc recipes/swga recipes/jvarkit-bam2wig recipes/jvarkit-bam2svg recipes/jvarkit-msa2vcf recipes/rxdock recipes/cath-tools recipes/makehub recipes/phame recipes/pegasuspy recipes/goetia recipes/consel recipes/isaac4 recipes/clame recipes/perl-ensembl-funcgen recipes/sniffles recipes/tn93 recipes/prosic recipes/dms recipes/variant_tools recipes/r-phytools recipes/translig recipes/lsc recipes/rambo-k recipes/ngless recipes/mobster recipes/visceral-evaluatesegmentation recipes/perl-lockfile-simple recipes/hyphy/2.3.11 recipes/chicagotools recipes/skewer/0.1.126 recipes/skewer recipes/trim_isoseq_polya recipes/perl-ensembl-compara recipes/ra/ra-assembler recipes/pureclip recipes/hulk recipes/bolt-lmm recipes/bmfilter recipes/unitig-counter recipes/probcons recipes/spydrpick recipes/bctools recipes/genometools-genometools recipes/bayestyper recipes/blast/2.2.31 recipes/comet-ms recipes/group_humann2_uniref_abundances_to_go recipes/isonclust2 recipes/bedtools/2.26.0 recipes/bmtool recipes/fastobo recipes/sibelia recipes/var-agg recipes/t-coffee recipes/wham recipes/artic-tools recipes/percolator recipes/r-saige/0.39 # Segfaults in bulk on Linux 24.3.2021 recipes/dbgraph recipes/mira # Source code moved recipes/r-intlim 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/isoseq3 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/hmftools-isofox recipes/compalignp recipes/seq2hla recipes/reaper recipes/genie recipes/admixture recipes/ucsc-fatovcf 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}' 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/perl-bio-rna-rnaalisplit recipes/perl-bio-eutilities recipes/perl-bio-samtools 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/egglib recipes/biolite recipes/pauda recipes/hicbrowser recipes/bcftools-gtc2vcf-plugin/1.9 recipes/perl-biox-workflow-command 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 # The build string needs to be modified to account for the [nocairo] feature recipes/genometools-genometools/1.5.10-nocairo # 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 recipes/footprint # missing bioc package recipes/customprodb # runtime dep missing in Docker? recipes/bio-vcf # 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 # 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 # 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 # real long build-time recipes/perl-bio-viennangs # /boost/intrusive/list.hpp:123:22: error: ‘const bool boost::intrusive::list_impl, (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/perl-pod-coverage-trustpod/0.100003 recipes/perl-symbol-util/0.0203 recipes/perl-test-pod-coverage/1.10 recipes/oases recipes/metavelvet-sl-feature-extraction recipes/music recipes/kraken-ea recipes/gnu-getopt recipes/ghmm 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/libbambamc/0.5.00 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 recipes/zmwfilter # 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/perl-aceperl recipes/perl-acme-damn recipes/perl-algorithm-cluster recipes/perl-algorithm-dependency recipes/perl-algorithm-diff recipes/perl-algorithm-munkres recipes/perl-aliased recipes/perl-apache-test recipes/perl-appconfig recipes/perl-app-cpanminus recipes/perl-archive-extract recipes/perl-archive-tar recipes/perl-archive-tar-wrapper recipes/perl-archive-zip recipes/perl-array-compare recipes/perl-array-set recipes/perl-array-utils recipes/perl-attribute-handlers recipes/perl-authen-sasl-saslprep recipes/perl-autodie recipes/perl-autoloader recipes/perl-b recipes/perl-b-debug recipes/perl-b-hooks-endofscope recipes/perl-bignum recipes/perl-bit-vector recipes/perl-blib recipes/perl-bloom-faster recipes/perl-border-style recipes/perl-btlib recipes/perl-bundle-bioperl recipes/perl-business-isbn recipes/perl-business-isbn-data recipes/perl-cache-cache recipes/perl-cairo recipes/perl-canary-stability recipes/perl-capture-tiny recipes/perl-carp recipes/perl-carp-clan recipes/perl-cgi recipes/perl-cg-pipeline recipes/perl-class-accessor recipes/perl-class-data-inheritable recipes/perl-class-inspector recipes/perl-class-load recipes/perl-class-load-xs recipes/perl-class-methodmaker recipes/perl-class-method-modifiers recipes/perl-class-singleton recipes/perl-class-std recipes/perl-class-std-fast recipes/perl-class-xsaccessor recipes/perl-clone recipes/perl-clone-choose recipes/perl-clone-pp recipes/perl-color-theme recipes/perl-common-sense recipes/perl-compress-bgzf recipes/perl-compress-raw-bzip2 recipes/perl-compress-raw-zlib recipes/perl-config-any recipes/perl-config-autoconf recipes/perl-config-general recipes/perl-config-simple recipes/perl-config-tiny recipes/perl-constant recipes/perl-const-fast recipes/perl-convert-binary-c recipes/perl-convert-binhex recipes/perl-cpan-meta recipes/perl-cpan-meta-check recipes/perl-cpan-meta-requirements recipes/perl-cpan-meta-validator recipes/perl-cpan-meta-yaml recipes/perl-cpan-shell recipes/perl-crypt-openssl-random recipes/perl-crypt-openssl-rsa recipes/perl-crypt-rc4 recipes/perl-data-compare recipes/perl-data-dump recipes/perl-data-dumper recipes/perl-data-lock recipes/perl-data-match recipes/perl-data-munge recipes/perl-data-optlist recipes/perl-data-stag recipes/perl-data-utilities recipes/perl-data-uuid recipes/perl-data-visitor recipes/perl-data-walk recipes/perl-date-format recipes/perl-date-manip recipes/perl-datetime recipes/perl-datetime-format-strptime recipes/perl-datetime-locale recipes/perl-datetime-timezone recipes/perl-dbd-mysql recipes/perl-dbd-pg recipes/perl-dbd-sqlite recipes/perl-db-file recipes/perl-dbi recipes/perl-dbm-deep recipes/perl-devel-assert recipes/perl-devel-checkbin recipes/perl-devel-checkos recipes/perl-devel-cover recipes/perl-devel-cycle recipes/perl-devel-globaldestruction recipes/perl-devel-overloadinfo recipes/perl-devel-size recipes/perl-devel-stacktrace recipes/perl-devel-symdump recipes/perl-digest-crc32 recipes/perl-digest-hmac recipes/perl-digest-md5 recipes/perl-digest-md5-file recipes/perl-digest-perl-md5 recipes/perl-digest-sha recipes/perl-digest-sha1 recipes/perl-dist-checkconflicts recipes/perl-dumbbench recipes/perl-dynaloader recipes/perl-email-date-format recipes/perl-encode recipes/perl-encode-locale recipes/perl-env recipes/perl-env-path recipes/perl-error recipes/perl-escape-houdini recipes/perl-eval-closure recipes/perl-excel-writer-xlsx recipes/perl-exception-class recipes/perl-experimental recipes/perl-exporter recipes/perl-exporter-tidy recipes/perl-exporter-tiny recipes/perl-extutils-cbuilder recipes/perl-extutils-config recipes/perl-extutils-constant recipes/perl-extutils-cppguess recipes/perl-extutils-depends recipes/perl-extutils-helpers recipes/perl-extutils-installpaths recipes/perl-extutils-makemaker recipes/perl-extutils-manifest recipes/perl-extutils-parsexs recipes/perl-extutils-pkgconfig recipes/perl-file-chdir recipes/perl-file-compare recipes/perl-file-copy-link recipes/perl-file-copy-recursive recipes/perl-file-copy-recursive-reduced recipes/perl-file-details recipes/perl-filedirutil recipes/perl-file-fetch recipes/perl-file-find recipes/perl-file-find-rule recipes/perl-file-grep recipes/perl-file-homedir recipes/perl-file-listing recipes/perl-file-next recipes/perl-file-path recipes/perl-file-pushd recipes/perl-file-readbackwards recipes/perl-file-remove recipes/perl-file-share recipes/perl-file-sharedir recipes/perl-file-sharedir-install recipes/perl-file-slurp recipes/perl-file-slurper recipes/perl-file-slurp-tiny recipes/perl-file-sort recipes/perl-file-spec recipes/perl-filesys-df recipes/perl-file-tee recipes/perl-file-temp recipes/perl-file-touch recipes/perl-file-util recipes/perl-file-which recipes/perl-filter-simple recipes/perl-findbin recipes/perl-findbin-libs recipes/perl-findbin-real recipes/perl-font-afm recipes/perl-font-ttf recipes/perl-forks recipes/perl-gd recipes/perl-gdgraph recipes/perl-gdgraph-histogram recipes/perl-gdtextutil recipes/perl-getopt-argvfile recipes/perl-getopt-long recipes/perl-getopt-long-descriptive recipes/perl-git-wrapper recipes/perl-git-wrapper-plus recipes/perl-go-perl recipes/perl-graph recipes/perl-graphics-colornames recipes/perl-graphics-colorobject recipes/perl-graph-readwrite recipes/perl-graphviz recipes/perl-hash-merge recipes/perl-hash-util-fieldhash-compat recipes/perl-heap recipes/perl-heap-simple recipes/perl-heap-simple-perl recipes/perl-heap-simple-xs recipes/perl-hook-lexwrap recipes/perl-hpc-runner-command recipes/perl-hpc-runner-command-plugin-logger-sqlite recipes/perl-html-element-extended recipes/perl-html-entities-numbered recipes/perl-html-form recipes/perl-html-formatter recipes/perl-html-parser recipes/perl-html-tableextract recipes/perl-html-tagset recipes/perl-html-template recipes/perl-html-tidy recipes/perl-html-tree recipes/perl-html-treebuilder-xpath recipes/perl-http-cookies recipes/perl-http-daemon recipes/perl-http-date recipes/perl-http-message recipes/perl-http-negotiate recipes/perl-http-server-simple recipes/perl-http-tiny recipes/perl-image-exiftool recipes/perl-image-info recipes/perl-image-size recipes/perl-importer recipes/perl-import-into recipes/perl-indirect recipes/perl-inline recipes/perl-inline-c recipes/perl-integer recipes/perl-io-all recipes/perl-io-compress recipes/perl-io-compress-deflate recipes/perl-io-gzip recipes/perl-io-handle recipes/perl-io-html recipes/perl-io-interactive recipes/perl-io-prompt recipes/perl-io-scalar recipes/perl-io-sessiondata recipes/perl-io-socket-inet6 recipes/perl-io-socket-ssl recipes/perl-io-string recipes/perl-io-stringy recipes/perl-io-tty recipes/perl-io-uncompress-bunzip2 recipes/perl-io-uncompress-gunzip recipes/perl-io-uncompress-rawinflate recipes/perl-io-zlib recipes/perl-ipc-cmd recipes/perl-ipc-run recipes/perl-ipc-run3 recipes/perl-ipc-sharelite recipes/perl-ipc-system-simple recipes/perl-jcode recipes/perl-json recipes/perl-json-create recipes/perl-json-maybexs recipes/perl-json-parse recipes/perl-json-pp recipes/perl-json-xs recipes/perl-lib recipes/perl-libwww-perl recipes/perl-libxml-perl recipes/perl-list-compare recipes/perl-list-moreutils recipes/perl-list-moreutils-xs recipes/perl-list-someutils recipes/perl-list-uniq recipes/perl-locale recipes/perl-locale-maketext-simple recipes/perl-local-lib recipes/perl-log-any recipes/perl-logger-simple recipes/perl-log-log4perl recipes/perl-lwp-mediatypes recipes/perl-lwp-protocol-https recipes/perl-lwp-simple recipes/perl-lyve-set recipes/perl-mac-propertylist recipes/perl-mac-systemdirectory recipes/perl-mailtools recipes/perl-math-base-convert recipes/perl-math-bezier recipes/perl-math-bigint recipes/perl-math-bigrat recipes/perl-math-cdf recipes/perl-math-combinatorics recipes/perl-math-complex recipes/perl-math-derivative recipes/perl-math-random recipes/perl-math-random-mt-auto recipes/perl-math-round recipes/perl-math-spline recipes/perl-math-utils recipes/perl-math-vecstat recipes/perl-mce recipes/perl-mce-shared recipes/perl-memoize recipes/perl-mime-base64 recipes/perl-mime-lite recipes/perl-mime-quotedprint recipes/perl-mime-tools recipes/perl-mime-types recipes/perl-mixin-linewise recipes/perl-mldbm recipes/perl-mldbm-sync recipes/perl-module-build recipes/perl-module-build-tiny recipes/perl-module-corelist recipes/perl-module-extract-use recipes/perl-module-fromperlver recipes/perl-module-implementation recipes/perl-module-list recipes/perl-module-load recipes/perl-module-load-conditional recipes/perl-module-loaded recipes/perl-module-metadata recipes/perl-module-pluggable recipes/perl-module-runtime recipes/perl-module-runtime-conflicts recipes/perl-module-scandeps recipes/perl-module-util recipes/perl-moo recipes/perl-moose recipes/perl-moosex-app recipes/perl-moosex-app-role-log4perl recipes/perl-moosex-clone recipes/perl-moosex-fileattribute recipes/perl-moosex-getopt recipes/perl-moosex-nonmoose recipes/perl-moosex-object-pluggable recipes/perl-moosex-role-parameterized recipes/perl-moosex-role-withoverloading recipes/perl-moosex-singleton recipes/perl-moosex-types recipes/perl-moosex-types-path-class recipes/perl-moosex-types-path-tiny recipes/perl-moosex-types-stringlike recipes/perl-mozilla-ca recipes/perl-mro-compat recipes/perl-namespace-autoclean recipes/perl-namespace-clean recipes/perl-net-ftp recipes/perl-net-ftp-recursive recipes/perl-net-http recipes/perl-net-netrc recipes/perl-net-ssleay recipes/perl-ntlm recipes/perl-number-compare recipes/perl-number-format recipes/perl-number-misc recipes/perl-number-range recipes/perl-number-witherror recipes/perl-object-insideout recipes/perl-ole-storage_lite recipes/perl-onto-perl recipes/perl-ostype recipes/perl-package-deprecationmanager recipes/perl-package-stash recipes/perl-package-stash-xs recipes/perl-padwalker recipes/perl-par recipes/perl-parallel-forkmanager recipes/perl-parallel-iterator recipes/perl-parallel-loops recipes/perl-params-check recipes/perl-params-coerce recipes/perl-params-util recipes/perl-params-validate recipes/perl-params-validationcompiler recipes/perl-par-dist recipes/perl-parent recipes/perl-par-packer recipes/perl-parse-recdescent recipes/perl-parse-yapp recipes/perl-path-class recipes/perl-path-tiny recipes/perl-pathtools recipes/perl-pbkdf2-tiny recipes/perl-pcap recipes/perl-pdf-api2 recipes/perl-pdf-table recipes/perl-pegex recipes/perl-perl4-corelibs recipes/perl-perlio recipes/perl-perlio-encoding recipes/perl-perlio-gzip recipes/perl-perlio-utf8_strict recipes/perl-perl-osnames recipes/perl-perl-ostype recipes/perl-perl-unsafe-signals recipes/perl-perl-version recipes/perl-pod-checker recipes/perl-pod-coverage recipes/perl-pod-coverage-trustpod recipes/perl-pod-elemental recipes/perl-pod-escapes recipes/perl-pod-parser recipes/perl-pod-plaintext recipes/perl-pod-simple recipes/perl-pod-simple-text recipes/perl-pod-usage recipes/perl-posix recipes/perl-postscript recipes/perl-ppi recipes/perl-prefork recipes/perl-probe-perl recipes/perl-proc-fork recipes/perl-readonly recipes/perl-regexp-common recipes/perl-return-multilevel recipes/perl-role-tiny recipes/perl-role-tiny-with recipes/perl-safe recipes/perl-scalar-list-utils recipes/perl-scalar-util-numeric recipes/perl-scope-guard recipes/perl-sereal recipes/perl-sereal-decoder recipes/perl-sereal-encoder recipes/perl-set-intervaltree recipes/perl-set-intspan recipes/perl-set-scalar recipes/perl-slurp recipes/perl-snap recipes/perl-soap-lite recipes/perl-socket recipes/perl-socket6 recipes/perl-sort-naturally recipes/perl-sort-versions recipes/perl-specio recipes/perl-specio-exporter recipes/perl-spiffy recipes/perl-spreadsheet-parseexcel recipes/perl-spreadsheet-writeexcel recipes/perl-sql-statement recipes/perl-statistics-basic recipes/perl-statistics-caseresampling recipes/perl-statistics-descriptive recipes/perl-statistics-distributions recipes/perl-statistics-frequency recipes/perl-statistics-lite recipes/perl-statistics-r recipes/perl-statistics-ttest recipes/perl-storable recipes/perl-string-approx recipes/perl-string-diff recipes/perl-string-escape recipes/perl-string-rewriteprefix recipes/perl-string-truncate recipes/perl-string-util recipes/perl-sub-attribute recipes/perl-sub-exporter recipes/perl-sub-exporter-formethods recipes/perl-sub-exporter-progressive recipes/perl-sub-identify recipes/perl-sub-info recipes/perl-sub-install recipes/perl-sub-name recipes/perl-sub-quote recipes/perl-sub-uplevel recipes/perl-super recipes/perl-svg recipes/perl-svg-graph recipes/perl-symbol recipes/perl-symbol-util recipes/perl-sys-info recipes/perl-sys-info-base recipes/perl-sys-info-driver-linux recipes/perl-sys-info-driver-osx recipes/perl-sys-sigaction recipes/perl-tap-harness-env recipes/perl-task-weaken recipes/perl-template-toolkit recipes/perl-term-app-roles recipes/perl-term-detect-software recipes/perl-term-encoding recipes/perl-term-progressbar recipes/perl-termreadkey recipes/perl-term-table recipes/perl-test recipes/perl-test2 recipes/perl-test2-suite recipes/perl-test-base recipes/perl-test-builder-tester recipes/perl-test-classapi recipes/perl-test-class-moose recipes/perl-test-cleannamespaces recipes/perl-test-cpan-meta recipes/perl-test-deep recipes/perl-test-differences recipes/perl-test-eol recipes/perl-test-exception recipes/perl-test-exec recipes/perl-test-fatal recipes/perl-test-file recipes/perl-test-file-contents recipes/perl-test-files recipes/perl-test-fork recipes/perl-test-harness recipes/perl-test-inter recipes/perl-test-leaktrace recipes/perl-test-lectrotest recipes/perl-test-longstring recipes/perl-test-memory-cycle recipes/perl-test-mockmodule recipes/perl-test-most recipes/perl-test-needs recipes/perl-test-notabs recipes/perl-test-nowarnings recipes/perl-test-object recipes/perl-test-output recipes/perl-test-pod recipes/perl-test-pod-coverage recipes/perl-test-prereq recipes/perl-test-requires recipes/perl-test-requiresinternet recipes/perl-test-script recipes/perl-test-simple recipes/perl-test-subcalls recipes/perl-test-sys-info recipes/perl-test-toolbox recipes/perl-test-trap recipes/perl-test-unit-lite recipes/perl-test-utf8 recipes/perl-test-warn recipes/perl-test-warnings recipes/perl-test-without-module recipes/perl-test-xml recipes/perl-test-yaml recipes/perl-text-abbrev recipes/perl-text-ansitable recipes/perl-text-asciitable recipes/perl-text-balanced recipes/perl-text-csv recipes/perl-text-diff recipes/perl-text-format recipes/perl-text-glob recipes/perl-text-levenshtein recipes/perl-text-levenshteinxs recipes/perl-text-nsp recipes/perl-text-parsewords recipes/perl-text-tabs recipes/perl-text-tabs-wrap recipes/perl-text-template recipes/perl-text-template-simple recipes/perl-text-wrap recipes/perl-threaded recipes/perl-tie-cache recipes/perl-tie-cacher recipes/perl-tie-hash recipes/perl-tie-hash-indexed recipes/perl-tie-ixhash recipes/perl-tie-log4perl recipes/perl-tie-refhash recipes/perl-tie-refhash-weak recipes/perl-tie-toobject recipes/perl-timedate recipes/perl-time-hires recipes/perl-time-local recipes/perl-time-piece recipes/perl-tree-dag_node recipes/perl-try-tiny recipes/perl-try-tiny-retry recipes/perl-types-serialiser recipes/perl-type-tiny recipes/perl-unicode-map recipes/perl-unicode-normalize recipes/perl-unicode-stringprep recipes/perl-unicode-utf8 recipes/perl-uri recipes/perl-variable-magic recipes/perl-vars recipes/perl-vcftools-vcf recipes/perl-velvetoptimiser recipes/perl-version recipes/perl-version-next recipes/perl-want recipes/perl-warnings-register recipes/perl-www-mechanize recipes/perl-www-robotrules recipes/perl-xml-dom recipes/perl-xml-dom-xpath recipes/perl-xml-entities recipes/perl-xml-filter-buffertext recipes/perl-xml-libxml recipes/perl-xml-libxslt recipes/perl-xml-namespacesupport recipes/perl-xml-parser recipes/perl-xml-parser-lite recipes/perl-xml-regexp recipes/perl-xml-sax recipes/perl-xml-sax-base recipes/perl-xml-sax-expat recipes/perl-xml-sax-writer recipes/perl-xml-semanticdiff recipes/perl-xml-simple recipes/perl-xml-twig recipes/perl-xml-writer recipes/perl-xml-xpath recipes/perl-xml-xpathengine recipes/perl-xsloader recipes/perl-yaml recipes/perl-yaml-libyaml recipes/perl-yaml-tiny 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 # Tests fail, plus: "... not found in sysroot, is this binary repackaging? .. do you need to use install_name_tool/patchelf?" recipes/tophat # 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 recipes/r-boutroslabplottinggeneral recipes/r-qorts recipes/r-zerone # Missing tarball recipes/r-prestor recipes/r-ngsplot-hg19 # fails on bioconductor's side (and dependants thereof) recipes/bioconductor-animalcules recipes/bioconductor-brainstars recipes/bioconductor-browserviz recipes/bioconductor-chipseqspike recipes/bioconductor-destiny recipes/bioconductor-cytotree recipes/bioconductor-ctggem recipes/bioconductor-phemd recipes/bioconductor-envisionquery recipes/bioconductor-gramm4r recipes/bioconductor-onassis recipes/bioconductor-rawrr recipes/bioconductor-srgnet recipes/bioconductor-synapter recipes/bioconductor-synapterdata recipes/bioconductor-affyqcreport recipes/bioconductor-pcot2 recipes/bioconductor-sagx recipes/bioconductor-affyexpress recipes/bioconductor-outlierd recipes/bioconductor-yaqcaffy recipes/bioconductor-bioccasestudies recipes/bioconductor-pcpheno recipes/bioconductor-arraytools recipes/bioconductor-rnaither recipes/bioconductor-sspa recipes/bioconductor-geneanswers recipes/bioconductor-eisa recipes/bioconductor-expressionview recipes/bioconductor-rnaseqmap recipes/bioconductor-annotationfuncs recipes/bioconductor-genoset recipes/bioconductor-methyanalysis recipes/bioconductor-rchyoptimyx recipes/bioconductor-cancermutationanalysis recipes/bioconductor-keggprofile recipes/bioconductor-dbchip recipes/bioconductor-easyqpcr recipes/bioconductor-bigmemoryextras recipes/bioconductor-dexus recipes/bioconductor-rdavidwebservice recipes/bioconductor-cexor recipes/bioconductor-elbow recipes/bioconductor-edda recipes/bioconductor-polyfit recipes/bioconductor-seqplots recipes/bioconductor-simulatorz recipes/bioconductor-topaseq recipes/bioconductor-mdgsa recipes/bioconductor-rnaprobr recipes/bioconductor-encodexplorer recipes/bioconductor-xbseq recipes/bioconductor-imetagene recipes/bioconductor-metagenomefeatures recipes/bioconductor-silva128.1mgdb recipes/bioconductor-samexplorer recipes/bioconductor-post recipes/bioconductor-intramirexplorer recipes/bioconductor-cytofast recipes/bioconductor-coregflux recipes/bioconductor-hcabrowser recipes/bioconductor-crossicc recipes/bioconductor-hcaexplorer recipes/bioconductor-tbsignatureprofiler recipes/bioconductor-hcamatrixbrowser recipes/bioconductor-mousefm recipes/bioconductor-facsdorit recipes/bioconductor-hmyrib36 recipes/bioconductor-ceuhm3 recipes/bioconductor-ceu1kg recipes/bioconductor-cgdv17 recipes/bioconductor-dsqtl recipes/bioconductor-ceu1kgv recipes/bioconductor-yri1kgv recipes/bioconductor-gskb recipes/bioconductor-jctseqdata recipes/bioconductor-browserviz recipes/bioconductor-rcyjs recipes/bioconductor-compgo recipes/bioconductor-greengenes13.5mgdb recipes/bioconductor-ribosomaldatabaseproject11.5mgdb recipes/bioconductor-igvr recipes/bioconductor-biocancer recipes/r-metaboanalyst # fails test recipes/r-ngsplot recipes/r-ngsplot-hg38 # Takes hours to build recipes/bioconductor-cancer # Requires r-mpmi rebuild for R 4.1 recipes/bioconductor-metnet # compilation error and dependants recipes/bioconductor-hilbertvisgui recipes/bioconductor-chemmineob recipes/bioconductor-affypara recipes/bioconductor-travel recipes/mmult # requires root5 rebuild recipes/bioconductor-xps