Overview

As part of the recent migration that re-built many packages for Python 3.10, we encountered issues with recipes that either haven't been re-built in a while or that specifically had issues with Python 3.10. These were dealt with in one of two ways. If there was an obvious specific issue (e.g., an issue unique to Python 3.10 or unique to Mac OSX, for example), then a preprocessing selector with skip: True was used. E.g.:

build:
  skip: True  # [osx]

Otherwise, the recipe was added to the build-fail-blacklist at the top of the repo.

If we didn't do this, then it would hold up the building of other packages, and further delay the process of migrating to Python 3.10.

What we need help with

Pick a package from the list below. Try to get it working.
If you can get it working, great -- create a PR that passes, check the box here, and edit the issue description to include the PR (see example below).
If you can't get it working, then add a description somewhere -- either in the blacklist or in the recipe itself. Open a PR with those changes (which will probably just be comments/documentation). And similarly edit this issue with the PR and cross it off the list.
On your PR, add the addressed-bulk-skip label so we can easily filter and keep track of which PRs are specifically addressing this issue. You can reference this issue in your PR as well if you want.

While editing this issue, a package that has been addressed should look like this in the issue text entry box:

   - [X] pkgname #123

which will show up like this:

[X] pkgname #123

Recently blacklisted packages

These packages were blacklisted in the latest re-build. Remove them from the build-fail-blacklist, and then try building them.

auspice has error about symlink of python3 within node dir; nextstrain depends on auspice

[ ] auspice
[ ] nextstrain

These have a sha256 mismatch, so they need review to figure out if that is expected.

[x] 3seq #37220
[ ] last

These depend on last, which needs sha256 review above:

[ ] nanosim-h
[ ] lamassemble
[ ] dnarrange

Compiler errors for python-bioexp; python-hivclustering and hivtrace depend on python-bioext:

[X] python-bioext #36907
[ ] python-hivclustering
[ ] 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>

[ ] pyopenms

compiler errors

[X] atropos #36914
[ ] pylibseq
[ ] medicc2
[ ] ggcaller
[ ] gembs

Genomedata seems unable to find hdf5; segtools and segway depend on genomedata.

[ ] genomedata #36902
[ ] segtools
[ ] segway

dlopen error upon import

[ ] pyrodigal

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.

[ ] cgat-apps

source no longer available

[ ] bugseq-porechop

misc

[ ] coinfinder
[ ] pysam/0.9.1 #36905
[ ] hatchet
[ ] tobias
[ ] strainge #37237
[ ] jcvi

Building tries to install 1.1.27 for some reason (despite meta.yaml specifying 1.1.25), but 1.1.27 URL does not exist:

[ ] illumina-interop #37139

Recipes that need to be migrated to conda-forge

These should be moved to conda-forge rather than be re-built on bioconda as they are legacy packages from back when only bioconda supported perl. As these are not directly related to biomedical research, we want to move them to conda-forge.

Note that perl-net-ssleay is a major dependency (see reverse-dependency list below) so it should be done first.

[X] perl-net-ssleay
[X] perl-io-socket-ssl
[X] perl-carp-clan
[ ] perl-bit-vector
[ ] perl-ipc-system-simple
[X] perl-text-csv
[ ] perl-mozilla-ca
[ ] perl-io-null
[X] perl-test
[ ] perl-pcap
[X] perl-text-levenshteinxs
[ ] perl-getopt-argvfile
[ ] perl-data-dump
[ ] perl-text-csv_xs
[ ] perl-probe-perl
[X] perl-svg
[ ] perl-lwp-protocol-https
[ ] perl-libwww-perl
[ ] perl-test-xml
[ ] perl-www-mechanize
[ ] perl-rest-client
[ ] perl-net-http
[ ] perl-lwp-simple
[ ] perl-soap-lite
[ ] perl-xml-twig
[ ] perl-digest-md5-file
[ ] perl-graphviz
[ ] perl-xml-dom-xpath
[ ] perl-xml-dom
[ ] perl-util-properties

Work on these after perl packages migrated

These need perl-net-ssleay to be migrated in conda-forge before they can be removed from the blacklist to attempt building.

[ ] srax
[ ] irida-linker
[ ] quantwiz-iq
[ ] hotspot3d
[ ] perl-bioperl-core
[ ] perl-bio-searchio-hmmer
[ ] perl-bio-featureio
[ ] perl-bio-phylo
[ ] perl-bio-procedural
[ ] perl-bio-tools-run-remoteblast
[ ] perl-metabolomics-fragment-annotation
[ ] perl-bio-automatedannotation
[ ] perl-sanger-cgp-battenberg
[ ] perl-bio-eutilities
[ ] perl-ensembl-api
[ ] perl-bio-asn1-entrezgene
[ ] perl-bio-phylo-cipres
[ ] perl-bio-db-refseq
[ ] perl-bio-db-embl
[ ] perl-bio-coordinate
[ ] perl-bio-db-swissprot
[ ] perl-ensembl-compara

This needs perl-svg in conda-forge:

[ ] ldblockshow

Recipes that are conditionally skipped

Rather than completely blacklist a recipe, some were able to be selectively skipped with a preprocessing selector. Edit the preprocessing selector on the skip: True line to see if any restrictions can be removed:

[ ] ariba
[ ] bamm
[ ] bbknn Investigating in #37172
[ ] cistrome_beta
[ ] clever-toolkit
[ ] cogent
[ ] cooltools/0.3.2
[ ] cooltools
[ ] cortexpy
[ ] cpat
[ ] crispritz
[ ] deltapd
[x] unifrac (skipped on osx due to unifrac-binaries dependency) #37162
[ ] unitig-caller (see https://github.com/bioconda/bioconda-recipes/issues/36884#issuecomment-1262092115 below)
[ ] yahmm

bioconda / bioconda-recipes

HELP NEEDED: cleaning up the build-fail-blacklist #36884