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Try building bioconductor-geoquery #44726

Merged
merged 2 commits into from
Dec 10, 2023
Merged

Try building bioconductor-geoquery #44726

merged 2 commits into from
Dec 10, 2023

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@bgruening bgruening merged commit 38dfd09 into bulk Dec 10, 2023
5 checks passed
@bgruening bgruening deleted the bgruening-patch-3 branch December 10, 2023 13:01
bgruening added a commit that referenced this pull request Dec 29, 2023
* a round of fixes and build-skips

* add some build failures

* correct version for bioconductor-data-packages

* add build failure for STdeconvolve

* [ci run] trigger bulk run

* run_exports on bioconductor-data-packages

* [ci run] trigger bulk run

* build failure for omnipathr

* [ci run] trigger bulk run

* Build important packages first

* [ci run] trigger bulk run

* revert to full build

* [ci run] trigger bulk run

* build failure files

* skip iclusterplus

* skip bioconductor-lpsymphony

* bump bioconda-repodata-patches build number

* [ci run]

* build failures

* next round of high priority packages

* [ci run] trigger bulk run

* [ci run] add dependency

* [ci run] finish priority packages

* re-enable full bulk

* [ci run] trigger bulk run

* build failures

* [ci run] trigger bulk run

* next round of high priority packages

* [ci run] trigger bulk run

* build more high priority packages

* [ci run] test local channel fix

* [ci run] increase workers

* Try building bioconductor-geoquery (#44726)

* Delete recipes/bioconductor-geoquery/build_failure.linux-64.yaml

* Update meta.yaml

* try fixing parsing error

* [ci run] try rebuilding bioconductor-coregx (#44727)
* try rebuilding bioconductor-coregx
* Update meta.yaml

* add opencl loading libraries - will this work

* [ci run] remove a few build failure files

* [ci run] Bioconductor graph (#44733)

* remove build failure file
* trigger build
* Update meta.yaml
* add patch back
[ci run]

* build failures

* [ci run] high priority packages

* bulk wiki page

* [ci run] add missing packges

* build failure for bioconductor-sictools

* [ci run] missed one

* [ci run] full run

* Update build.sh

* [ci run] fix dexseq

* [ci run] next round of high priority packages

* [ci run] missing packages

* [ci run] high priority package

* [ci run] build all bioconductor-bsgenome

* [ci run] remove failures associated with bioconductor-bsgenome dependency

* full build

* use bioconda-common version

* build failures: test dev version of utils

* escape characters correctly

* build failure for bioconductor-pics

* use branch

* build failure for bioconductor-inspect

* try to fix build failure git range

* build failure for bioconductor-distinct

* use head branch

* trigger build failure wf

* [ci run] trigger bulk run

* build failures fetch depth

* build failure for biconductor-benchdamic

* build failures

* build failures with log

* don't run build failures if last commit has ci skip

* [ci skip] test build failure wiki

* test build failure wiki job

* [ci run] reenable record-build-failures

* re-add token for build failure updates

* build failures add category column

* trigger wiki update

* fix libsbml version for bioconductor-rsbml

* build failure updates

* fix bioconductor-glad

* [ci run] trigger bulk run

* [ci skip] add build failure record for recipe recipes/bioconductor-wppi

* [ci skip] add build failure record for recipe recipes/bioconductor-gars

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-metascope

* [ci skip] add build failure record for recipe recipes/bioconductor-biggr

* [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank

* [ci skip] add build failure record for recipe recipes/bioconductor-msbackendrawfilereader

* [ci skip] add build failure record for recipe recipes/bioconductor-omicsviewer

* [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr

* [ci skip] add build failure record for recipe recipes/bioconductor-micsqtl

* [ci skip] add build failure record for recipe recipes/bioconductor-fraser

* [ci skip] add build failure record for recipe recipes/bioconductor-proloc

* [ci skip] add build failure record for recipe recipes/bioconductor-psygenet2r

* [ci skip] add build failure record for recipe recipes/bioconductor-gesper

* [ci skip] add build failure record for recipe recipes/bioconductor-sctensor

* [ci skip] add build failure record for recipe recipes/bioconductor-seqcna

* [ci skip] add build failure record for recipe recipes/bioconductor-rcas

* [ci skip] add build failure record for recipe recipes/bioconductor-inpas

* [ci skip] add build failure record for recipe recipes/bioconductor-factr

* [ci skip] add build failure record for recipe recipes/bioconductor-ping

* [ci skip] add build failure record for recipe recipes/bioconductor-doubletrouble

* [ci skip] add build failure record for recipe recipes/bioconductor-phyloprofile

* [ci skip] add build failure record for recipe recipes/bioconductor-extrachips

* [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank

* [ci skip] add build failure record for recipe recipes/bioconductor-ularcirc

* [ci skip] add build failure record for recipe recipes/bioconductor-umi4cats

* [ci skip] add build failure record for recipe recipes/bioconductor-chipqc

* [ci skip] add build failure record for recipe recipes/bioconductor-outsplice

* [ci skip] add build failure record for recipe recipes/bioconductor-rlseq

* [ci skip] add build failure record for recipe recipes/bioconductor-circseqaligntk

* [ci skip] add build failure record for recipe recipes/bioconductor-ritan

* [ci skip] add build failure record for recipe recipes/bioconductor-guideseq

* [ci skip] add build failure record for recipe recipes/bioconductor-vulcan

* [ci skip] add build failure record for recipe recipes/bioconductor-singlecelltk

* [ci skip] add build failure record for recipe recipes/bioconductor-scfeatures

* [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper

* [ci skip] add build failure record for recipe recipes/bioconductor-deconvr

* [ci skip] add build failure record for recipe recipes/bioconductor-ideal

* [ci skip] add build failure record for recipe recipes/bioconductor-esatac

* [ci skip] add build failure record for recipe recipes/bioconductor-profileplyr

* [ci skip] add build failure record for recipe recipes/bioconductor-inetgrate

* [ci skip] add build failure record for recipe recipes/bioconductor-ataccogaps

* [ci skip] add build failure record for recipe recipes/bioconductor-lemur

* [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign

* [ci skip] add build failure record for recipe recipes/bioconductor-regionreport

* [ci skip] add build failure record for recipe recipes/bioconductor-motifbreakr

* [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh

* [ci skip] add build failure record for recipe recipes/bioconductor-ping

* [ci skip] add build failure record for recipe recipes/bioconductor-cageminer

* [ci skip] add build failure record for recipe recipes/bioconductor-multicrispr

* [ci skip] add build failure record for recipe recipes/bioconductor-xde

* [ci skip] add build failure record for recipe recipes/bioconductor-affycoretools

* [ci skip] add build failure record for recipe recipes/bioconductor-scpipe

* Rbowtie2 (#44856)

[ci run] fix rbowtie2 builds

* [ci run] remove build file

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-biggr

* [ci skip] add build failure record for recipe recipes/bioconductor-proloc

* [ci skip] add build failure record for recipe recipes/bioconductor-rcas

* [ci skip] add build failure record for recipe recipes/bioconductor-guideseq

* [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign

* [ci skip] remove build failure record for recipe recipes/bioconductor-affycoretools

* [ci skip] add build failure record for recipe recipes/bioconductor-fraser

* [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh

* failure for bioconda-multirnaflow

* [ci run] trigger bulk run

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-proloc

* [ci skip] add build failure record for recipe recipes/bioconductor-rcas

* [ci skip] add build failure record for recipe recipes/bioconductor-guideseq

* [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign

* [ci skip] add build failure record for recipe recipes/bioconductor-fraser

* bioconductor-lpsymphony fix from master

* remove build failures for finished dependencies

* restore skip osx-64

* fix bioconductor-rawrr

* high priority packages

* [ci run] trigger bulk run

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci skip] remove build failure record for recipe recipes/bioconductor-proloc

* fix bioconductor-chemmineob

* [ci run] remove failures for built dependencies

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci run] full build

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* remove easy build failures

* [ci run] next round of dependencies

* [ci skip] add build failure record for recipe recipes/bioconductor-pigengene

* [ci skip] add build failure record for recipe recipes/bioconductor-repitools

* [ci skip] add build failure record for recipe recipes/bioconductor-xde

* [ci skip] add build failure record for recipe recipes/bioconductor-sctensor

* [ci skip] add build failure record for recipe recipes/bioconductor-rlseq

* build failure updates

* [ci run] next batch of fixes

* [ci skip] add build failure record for recipe recipes/bioconductor-mitoclone2

* [ci skip] add build failure record for recipe recipes/bioconductor-rlseq

* [ci run] full build

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci run]remove failures for built dependencies

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci skip] add build failure record for recipe recipes/bioconductor-rlseq

* [ci skip] add build failure record for recipe recipes/bioconductor-gatom

* [ci run] set failures to skip

* [ci run] reduce resources that are wasted

* [ci skip] add build failure record for recipe recipes/bioconductor-pd.barley1

* fix accidental reverts

* add GSL to bioconductor-pics

* add back fix from master for omnipathr

* remove build failure

* [ci run] skip root nodes to spread out builds

* [ci run] include more root nodes in blacklist

* update build failures

* [ci run] add more blacklist items and do osx build

* [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh

* [ci skip] add build failure record for recipe recipes/bioconductor-ping

* [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes

* [ci skip] add build failure record for recipe recipes/bioconductor-mumosa

* [ci skip] add build failure record for recipe recipes/bioconductor-chromscape

* [ci skip] add build failure record for recipe recipes/bioconductor-scmerge

* [ci skip] add build failure record for recipe recipes/bioconductor-tadcompare

* fix build errors

* [ci run] more skipped builds

* [ci skip] add build failure record for recipe recipes/bioconductor-cghmcr

* [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper

* [ci skip] add build failure record for recipe recipes/bioconductor-ccpromise

* [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh

* [ci skip] add build failure record for recipe recipes/bioconductor-interactivedisplay

* [ci run] reduce workers

* [ci skip] add build failure record for recipe recipes/bioconductor-cepo

* [ci skip] add build failure record for recipe recipes/bioconductor-tbsignatureprofiler

* [ci run] manually distribute packages

* [ci skip] add build failure record for recipe recipes/bioconductor-cocoa

* [ci skip] add build failure record for recipe recipes/bioconductor-condiments

* [ci skip] add build failure record for recipe recipes/bioconductor-scclassify

* [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf

* [ci skip] add build failure record for recipe recipes/bioconductor-gcapc

* [ci skip] add build failure record for recipe recipes/bioconductor-cepo

* [ci skip] add build failure record for recipe recipes/bioconductor-traviz

* remove build failures

* remove colon that breaks yaml parsing

* remove temporary bioconductor bulk skips

* [ci run] remaining packages

* [ci skip] add build failure record for recipe recipes/bioconductor-distinct

* [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf

* [ci skip] add build failure record for recipe recipes/bioconductor-promise

* [ci skip] add build failure record for recipe recipes/bioconductor-otubase

* [ci skip] add build failure record for recipe recipes/bioconductor-cocoa

* [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes

* retry http error

* [ci run] full bulk build

* [ci skip] add build failure record for recipe recipes/bioconductor-deepbluer

* [ci skip] remove build failure record for recipe recipes/bioconductor-meb

* [ci skip] add build failure record for recipe recipes/bioconductor-distinct

* [ci run] categorize failures

* add bioconductor-cdi

* remove old failure files

* update bioconductor-reusedata to 3.18

* remove failures for dependencies that have been built

* [ci run] build certain packages

* bulk: update bioconductor-ccfindr and bioconductor-rjmcmcnucleosomes with gsl (#44986)

* update bioconductor-ccfindr with gsl

* update bioconductor-rjmcmcnucleosomes with gsl

* [ci run] build updated recipes

* [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr

* [ci skip] add build failure record for recipe recipes/bioconductor-reusedata

* remove temporary changes from workflows

* build got bumped in merge

* remove temp files

---------

Co-authored-by: Ryan Dale <ryan.dale@nih.gov>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Bjoern Gruening <bjoern.gruening@gmail.com>
Co-authored-by: BiocondaBot <BiocondaBot@users.noreply.github.com>
erikrikarddaniel pushed a commit to erikrikarddaniel/bioconda-recipes that referenced this pull request Jan 10, 2024
* a round of fixes and build-skips

* add some build failures

* correct version for bioconductor-data-packages

* add build failure for STdeconvolve

* [ci run] trigger bulk run

* run_exports on bioconductor-data-packages

* [ci run] trigger bulk run

* build failure for omnipathr

* [ci run] trigger bulk run

* Build important packages first

* [ci run] trigger bulk run

* revert to full build

* [ci run] trigger bulk run

* build failure files

* skip iclusterplus

* skip bioconductor-lpsymphony

* bump bioconda-repodata-patches build number

* [ci run]

* build failures

* next round of high priority packages

* [ci run] trigger bulk run

* [ci run] add dependency

* [ci run] finish priority packages

* re-enable full bulk

* [ci run] trigger bulk run

* build failures

* [ci run] trigger bulk run

* next round of high priority packages

* [ci run] trigger bulk run

* build more high priority packages

* [ci run] test local channel fix

* [ci run] increase workers

* Try building bioconductor-geoquery (bioconda#44726)

* Delete recipes/bioconductor-geoquery/build_failure.linux-64.yaml

* Update meta.yaml

* try fixing parsing error

* [ci run] try rebuilding bioconductor-coregx (bioconda#44727)
* try rebuilding bioconductor-coregx
* Update meta.yaml

* add opencl loading libraries - will this work

* [ci run] remove a few build failure files

* [ci run] Bioconductor graph (bioconda#44733)

* remove build failure file
* trigger build
* Update meta.yaml
* add patch back
[ci run]

* build failures

* [ci run] high priority packages

* bulk wiki page

* [ci run] add missing packges

* build failure for bioconductor-sictools

* [ci run] missed one

* [ci run] full run

* Update build.sh

* [ci run] fix dexseq

* [ci run] next round of high priority packages

* [ci run] missing packages

* [ci run] high priority package

* [ci run] build all bioconductor-bsgenome

* [ci run] remove failures associated with bioconductor-bsgenome dependency

* full build

* use bioconda-common version

* build failures: test dev version of utils

* escape characters correctly

* build failure for bioconductor-pics

* use branch

* build failure for bioconductor-inspect

* try to fix build failure git range

* build failure for bioconductor-distinct

* use head branch

* trigger build failure wf

* [ci run] trigger bulk run

* build failures fetch depth

* build failure for biconductor-benchdamic

* build failures

* build failures with log

* don't run build failures if last commit has ci skip

* [ci skip] test build failure wiki

* test build failure wiki job

* [ci run] reenable record-build-failures

* re-add token for build failure updates

* build failures add category column

* trigger wiki update

* fix libsbml version for bioconductor-rsbml

* build failure updates

* fix bioconductor-glad

* [ci run] trigger bulk run

* [ci skip] add build failure record for recipe recipes/bioconductor-wppi

* [ci skip] add build failure record for recipe recipes/bioconductor-gars

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-metascope

* [ci skip] add build failure record for recipe recipes/bioconductor-biggr

* [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank

* [ci skip] add build failure record for recipe recipes/bioconductor-msbackendrawfilereader

* [ci skip] add build failure record for recipe recipes/bioconductor-omicsviewer

* [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr

* [ci skip] add build failure record for recipe recipes/bioconductor-micsqtl

* [ci skip] add build failure record for recipe recipes/bioconductor-fraser

* [ci skip] add build failure record for recipe recipes/bioconductor-proloc

* [ci skip] add build failure record for recipe recipes/bioconductor-psygenet2r

* [ci skip] add build failure record for recipe recipes/bioconductor-gesper

* [ci skip] add build failure record for recipe recipes/bioconductor-sctensor

* [ci skip] add build failure record for recipe recipes/bioconductor-seqcna

* [ci skip] add build failure record for recipe recipes/bioconductor-rcas

* [ci skip] add build failure record for recipe recipes/bioconductor-inpas

* [ci skip] add build failure record for recipe recipes/bioconductor-factr

* [ci skip] add build failure record for recipe recipes/bioconductor-ping

* [ci skip] add build failure record for recipe recipes/bioconductor-doubletrouble

* [ci skip] add build failure record for recipe recipes/bioconductor-phyloprofile

* [ci skip] add build failure record for recipe recipes/bioconductor-extrachips

* [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank

* [ci skip] add build failure record for recipe recipes/bioconductor-ularcirc

* [ci skip] add build failure record for recipe recipes/bioconductor-umi4cats

* [ci skip] add build failure record for recipe recipes/bioconductor-chipqc

* [ci skip] add build failure record for recipe recipes/bioconductor-outsplice

* [ci skip] add build failure record for recipe recipes/bioconductor-rlseq

* [ci skip] add build failure record for recipe recipes/bioconductor-circseqaligntk

* [ci skip] add build failure record for recipe recipes/bioconductor-ritan

* [ci skip] add build failure record for recipe recipes/bioconductor-guideseq

* [ci skip] add build failure record for recipe recipes/bioconductor-vulcan

* [ci skip] add build failure record for recipe recipes/bioconductor-singlecelltk

* [ci skip] add build failure record for recipe recipes/bioconductor-scfeatures

* [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper

* [ci skip] add build failure record for recipe recipes/bioconductor-deconvr

* [ci skip] add build failure record for recipe recipes/bioconductor-ideal

* [ci skip] add build failure record for recipe recipes/bioconductor-esatac

* [ci skip] add build failure record for recipe recipes/bioconductor-profileplyr

* [ci skip] add build failure record for recipe recipes/bioconductor-inetgrate

* [ci skip] add build failure record for recipe recipes/bioconductor-ataccogaps

* [ci skip] add build failure record for recipe recipes/bioconductor-lemur

* [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign

* [ci skip] add build failure record for recipe recipes/bioconductor-regionreport

* [ci skip] add build failure record for recipe recipes/bioconductor-motifbreakr

* [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh

* [ci skip] add build failure record for recipe recipes/bioconductor-ping

* [ci skip] add build failure record for recipe recipes/bioconductor-cageminer

* [ci skip] add build failure record for recipe recipes/bioconductor-multicrispr

* [ci skip] add build failure record for recipe recipes/bioconductor-xde

* [ci skip] add build failure record for recipe recipes/bioconductor-affycoretools

* [ci skip] add build failure record for recipe recipes/bioconductor-scpipe

* Rbowtie2 (bioconda#44856)

[ci run] fix rbowtie2 builds

* [ci run] remove build file

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-biggr

* [ci skip] add build failure record for recipe recipes/bioconductor-proloc

* [ci skip] add build failure record for recipe recipes/bioconductor-rcas

* [ci skip] add build failure record for recipe recipes/bioconductor-guideseq

* [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign

* [ci skip] remove build failure record for recipe recipes/bioconductor-affycoretools

* [ci skip] add build failure record for recipe recipes/bioconductor-fraser

* [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh

* failure for bioconda-multirnaflow

* [ci run] trigger bulk run

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-proloc

* [ci skip] add build failure record for recipe recipes/bioconductor-rcas

* [ci skip] add build failure record for recipe recipes/bioconductor-guideseq

* [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign

* [ci skip] add build failure record for recipe recipes/bioconductor-fraser

* bioconductor-lpsymphony fix from master

* remove build failures for finished dependencies

* restore skip osx-64

* fix bioconductor-rawrr

* high priority packages

* [ci run] trigger bulk run

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci skip] remove build failure record for recipe recipes/bioconductor-proloc

* fix bioconductor-chemmineob

* [ci run] remove failures for built dependencies

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci run] full build

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* remove easy build failures

* [ci run] next round of dependencies

* [ci skip] add build failure record for recipe recipes/bioconductor-pigengene

* [ci skip] add build failure record for recipe recipes/bioconductor-repitools

* [ci skip] add build failure record for recipe recipes/bioconductor-xde

* [ci skip] add build failure record for recipe recipes/bioconductor-sctensor

* [ci skip] add build failure record for recipe recipes/bioconductor-rlseq

* build failure updates

* [ci run] next batch of fixes

* [ci skip] add build failure record for recipe recipes/bioconductor-mitoclone2

* [ci skip] add build failure record for recipe recipes/bioconductor-rlseq

* [ci run] full build

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci run]remove failures for built dependencies

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci skip] add build failure record for recipe recipes/bioconductor-rlseq

* [ci skip] add build failure record for recipe recipes/bioconductor-gatom

* [ci run] set failures to skip

* [ci run] reduce resources that are wasted

* [ci skip] add build failure record for recipe recipes/bioconductor-pd.barley1

* fix accidental reverts

* add GSL to bioconductor-pics

* add back fix from master for omnipathr

* remove build failure

* [ci run] skip root nodes to spread out builds

* [ci run] include more root nodes in blacklist

* update build failures

* [ci run] add more blacklist items and do osx build

* [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh

* [ci skip] add build failure record for recipe recipes/bioconductor-ping

* [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes

* [ci skip] add build failure record for recipe recipes/bioconductor-mumosa

* [ci skip] add build failure record for recipe recipes/bioconductor-chromscape

* [ci skip] add build failure record for recipe recipes/bioconductor-scmerge

* [ci skip] add build failure record for recipe recipes/bioconductor-tadcompare

* fix build errors

* [ci run] more skipped builds

* [ci skip] add build failure record for recipe recipes/bioconductor-cghmcr

* [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper

* [ci skip] add build failure record for recipe recipes/bioconductor-ccpromise

* [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh

* [ci skip] add build failure record for recipe recipes/bioconductor-interactivedisplay

* [ci run] reduce workers

* [ci skip] add build failure record for recipe recipes/bioconductor-cepo

* [ci skip] add build failure record for recipe recipes/bioconductor-tbsignatureprofiler

* [ci run] manually distribute packages

* [ci skip] add build failure record for recipe recipes/bioconductor-cocoa

* [ci skip] add build failure record for recipe recipes/bioconductor-condiments

* [ci skip] add build failure record for recipe recipes/bioconductor-scclassify

* [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf

* [ci skip] add build failure record for recipe recipes/bioconductor-gcapc

* [ci skip] add build failure record for recipe recipes/bioconductor-cepo

* [ci skip] add build failure record for recipe recipes/bioconductor-traviz

* remove build failures

* remove colon that breaks yaml parsing

* remove temporary bioconductor bulk skips

* [ci run] remaining packages

* [ci skip] add build failure record for recipe recipes/bioconductor-distinct

* [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf

* [ci skip] add build failure record for recipe recipes/bioconductor-promise

* [ci skip] add build failure record for recipe recipes/bioconductor-otubase

* [ci skip] add build failure record for recipe recipes/bioconductor-cocoa

* [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes

* retry http error

* [ci run] full bulk build

* [ci skip] add build failure record for recipe recipes/bioconductor-deepbluer

* [ci skip] remove build failure record for recipe recipes/bioconductor-meb

* [ci skip] add build failure record for recipe recipes/bioconductor-distinct

* [ci run] categorize failures

* add bioconductor-cdi

* remove old failure files

* update bioconductor-reusedata to 3.18

* remove failures for dependencies that have been built

* [ci run] build certain packages

* bulk: update bioconductor-ccfindr and bioconductor-rjmcmcnucleosomes with gsl (bioconda#44986)

* update bioconductor-ccfindr with gsl

* update bioconductor-rjmcmcnucleosomes with gsl

* [ci run] build updated recipes

* [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr

* [ci skip] add build failure record for recipe recipes/bioconductor-reusedata

* remove temporary changes from workflows

* build got bumped in merge

* remove temp files

---------

Co-authored-by: Ryan Dale <ryan.dale@nih.gov>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Bjoern Gruening <bjoern.gruening@gmail.com>
Co-authored-by: BiocondaBot <BiocondaBot@users.noreply.github.com>
apeltzer added a commit that referenced this pull request Jan 24, 2024
* Updated sativa build, incl. test case

* Update meta.yaml with new Sativa release

* Linting

* Update keggcharter to 1.0.2 (#44992)

* Update keggcharter to 1.0.2

* Update meta.yaml

Now put all TXTs and TSVs from "resources" folder into "share" folder.

---------

Co-authored-by: João Sequeira <maildosequeira@gmail.com>

* Update hictk to v0.0.5 (#44988)

* Update conanfile.txt.patch

* Bump version

* Update perl-minion to 10.28 (#44495)

* bugfix: strand deprecated and removed in BioPython 1.82 (#44987)

- see: chapmanb/bcbb#138

* bugfix: breaking API change between ruamel.yaml 0.17.x and 0.18 (#44989)

* Update tsebra to 1.1.2.2 (#45000)

* Update sylph to 0.5.1 (#45001)

* add r-misha 3.7.0 (history version) (#44981)

* add misha version 3.7.0 (history version)

* fix hash

* fix compiler settings

* use template variable to specify name

* add run_export to lock version

* add r-misha 3.7.1 (history version) (#44984)

* add r-misha 3.7.1 (history version)

* fix: incorrect commit and hash

* Update viguno to 0.2.0 (#44996)

* Update viguno to 0.2.0

* run_exports

---------

Co-authored-by: Thanh Lee <thanh.le-viet@quadram.ac.uk>

* Update annonars to 0.32.0 (#45013)

* Fix recognizer (#45012)

* Update recognizer to 1.10.0

* Update meta.yaml

No more build.sh file

* Update meta.yaml

Forgot about the other TSV files

* Removed build.sh

---------

Co-authored-by: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>

* Update last to 1522 (#45011)

* Update pcaone to 0.4.1 (#45009)

* genoflu version 1.02 (#44995)

* genoflu version 1.02

* Update meta.yaml

* Update meta.yaml

* https://spdx.org/licenses/GPL-3.0-or-later.html

---------

Co-authored-by: Thanh Lee <thanh.le-viet@quadram.ac.uk>

* Update chromhmm to 1.25 (#45016)

* Update chromhmm to 1.25

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

---------

Co-authored-by: Christian Brueffer <christian@brueffer.io>

* Update ColabFold to 1.5.5 (#45008)

* Update ColabFold to 1.5.4

* Use 1.5.5 instead, 1.5.4 had a bug

* OpenMM 8.1 causes issues

* Update expam to 1.2.2.4 (#45007)

* Update expam to 1.2.2.4

* add run_exports

---------

Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com>

* Update upimapi to 1.13.1 (#45019)

Co-authored-by: João Sequeira <maildosequeira@gmail.com>

* Update raptor (#44952)

multiple binaries and a wrapper scripts depending on available instruction sets.

* add AnnoSINE2 recipes (#44980)

* add strainscan recipes

* add annosine2 recipes

* Delete recipes/strainscan/meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Bulk (#45014)

* a round of fixes and build-skips

* add some build failures

* correct version for bioconductor-data-packages

* add build failure for STdeconvolve

* [ci run] trigger bulk run

* run_exports on bioconductor-data-packages

* [ci run] trigger bulk run

* build failure for omnipathr

* [ci run] trigger bulk run

* Build important packages first

* [ci run] trigger bulk run

* revert to full build

* [ci run] trigger bulk run

* build failure files

* skip iclusterplus

* skip bioconductor-lpsymphony

* bump bioconda-repodata-patches build number

* [ci run]

* build failures

* next round of high priority packages

* [ci run] trigger bulk run

* [ci run] add dependency

* [ci run] finish priority packages

* re-enable full bulk

* [ci run] trigger bulk run

* build failures

* [ci run] trigger bulk run

* next round of high priority packages

* [ci run] trigger bulk run

* build more high priority packages

* [ci run] test local channel fix

* [ci run] increase workers

* Try building bioconductor-geoquery (#44726)

* Delete recipes/bioconductor-geoquery/build_failure.linux-64.yaml

* Update meta.yaml

* try fixing parsing error

* [ci run] try rebuilding bioconductor-coregx (#44727)
* try rebuilding bioconductor-coregx
* Update meta.yaml

* add opencl loading libraries - will this work

* [ci run] remove a few build failure files

* [ci run] Bioconductor graph (#44733)

* remove build failure file
* trigger build
* Update meta.yaml
* add patch back
[ci run]

* build failures

* [ci run] high priority packages

* bulk wiki page

* [ci run] add missing packges

* build failure for bioconductor-sictools

* [ci run] missed one

* [ci run] full run

* Update build.sh

* [ci run] fix dexseq

* [ci run] next round of high priority packages

* [ci run] missing packages

* [ci run] high priority package

* [ci run] build all bioconductor-bsgenome

* [ci run] remove failures associated with bioconductor-bsgenome dependency

* full build

* use bioconda-common version

* build failures: test dev version of utils

* escape characters correctly

* build failure for bioconductor-pics

* use branch

* build failure for bioconductor-inspect

* try to fix build failure git range

* build failure for bioconductor-distinct

* use head branch

* trigger build failure wf

* [ci run] trigger bulk run

* build failures fetch depth

* build failure for biconductor-benchdamic

* build failures

* build failures with log

* don't run build failures if last commit has ci skip

* [ci skip] test build failure wiki

* test build failure wiki job

* [ci run] reenable record-build-failures

* re-add token for build failure updates

* build failures add category column

* trigger wiki update

* fix libsbml version for bioconductor-rsbml

* build failure updates

* fix bioconductor-glad

* [ci run] trigger bulk run

* [ci skip] add build failure record for recipe recipes/bioconductor-wppi

* [ci skip] add build failure record for recipe recipes/bioconductor-gars

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-metascope

* [ci skip] add build failure record for recipe recipes/bioconductor-biggr

* [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank

* [ci skip] add build failure record for recipe recipes/bioconductor-msbackendrawfilereader

* [ci skip] add build failure record for recipe recipes/bioconductor-omicsviewer

* [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr

* [ci skip] add build failure record for recipe recipes/bioconductor-micsqtl

* [ci skip] add build failure record for recipe recipes/bioconductor-fraser

* [ci skip] add build failure record for recipe recipes/bioconductor-proloc

* [ci skip] add build failure record for recipe recipes/bioconductor-psygenet2r

* [ci skip] add build failure record for recipe recipes/bioconductor-gesper

* [ci skip] add build failure record for recipe recipes/bioconductor-sctensor

* [ci skip] add build failure record for recipe recipes/bioconductor-seqcna

* [ci skip] add build failure record for recipe recipes/bioconductor-rcas

* [ci skip] add build failure record for recipe recipes/bioconductor-inpas

* [ci skip] add build failure record for recipe recipes/bioconductor-factr

* [ci skip] add build failure record for recipe recipes/bioconductor-ping

* [ci skip] add build failure record for recipe recipes/bioconductor-doubletrouble

* [ci skip] add build failure record for recipe recipes/bioconductor-phyloprofile

* [ci skip] add build failure record for recipe recipes/bioconductor-extrachips

* [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank

* [ci skip] add build failure record for recipe recipes/bioconductor-ularcirc

* [ci skip] add build failure record for recipe recipes/bioconductor-umi4cats

* [ci skip] add build failure record for recipe recipes/bioconductor-chipqc

* [ci skip] add build failure record for recipe recipes/bioconductor-outsplice

* [ci skip] add build failure record for recipe recipes/bioconductor-rlseq

* [ci skip] add build failure record for recipe recipes/bioconductor-circseqaligntk

* [ci skip] add build failure record for recipe recipes/bioconductor-ritan

* [ci skip] add build failure record for recipe recipes/bioconductor-guideseq

* [ci skip] add build failure record for recipe recipes/bioconductor-vulcan

* [ci skip] add build failure record for recipe recipes/bioconductor-singlecelltk

* [ci skip] add build failure record for recipe recipes/bioconductor-scfeatures

* [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper

* [ci skip] add build failure record for recipe recipes/bioconductor-deconvr

* [ci skip] add build failure record for recipe recipes/bioconductor-ideal

* [ci skip] add build failure record for recipe recipes/bioconductor-esatac

* [ci skip] add build failure record for recipe recipes/bioconductor-profileplyr

* [ci skip] add build failure record for recipe recipes/bioconductor-inetgrate

* [ci skip] add build failure record for recipe recipes/bioconductor-ataccogaps

* [ci skip] add build failure record for recipe recipes/bioconductor-lemur

* [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign

* [ci skip] add build failure record for recipe recipes/bioconductor-regionreport

* [ci skip] add build failure record for recipe recipes/bioconductor-motifbreakr

* [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh

* [ci skip] add build failure record for recipe recipes/bioconductor-ping

* [ci skip] add build failure record for recipe recipes/bioconductor-cageminer

* [ci skip] add build failure record for recipe recipes/bioconductor-multicrispr

* [ci skip] add build failure record for recipe recipes/bioconductor-xde

* [ci skip] add build failure record for recipe recipes/bioconductor-affycoretools

* [ci skip] add build failure record for recipe recipes/bioconductor-scpipe

* Rbowtie2 (#44856)

[ci run] fix rbowtie2 builds

* [ci run] remove build file

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-biggr

* [ci skip] add build failure record for recipe recipes/bioconductor-proloc

* [ci skip] add build failure record for recipe recipes/bioconductor-rcas

* [ci skip] add build failure record for recipe recipes/bioconductor-guideseq

* [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign

* [ci skip] remove build failure record for recipe recipes/bioconductor-affycoretools

* [ci skip] add build failure record for recipe recipes/bioconductor-fraser

* [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh

* failure for bioconda-multirnaflow

* [ci run] trigger bulk run

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-proloc

* [ci skip] add build failure record for recipe recipes/bioconductor-rcas

* [ci skip] add build failure record for recipe recipes/bioconductor-guideseq

* [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign

* [ci skip] add build failure record for recipe recipes/bioconductor-fraser

* bioconductor-lpsymphony fix from master

* remove build failures for finished dependencies

* restore skip osx-64

* fix bioconductor-rawrr

* high priority packages

* [ci run] trigger bulk run

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci skip] remove build failure record for recipe recipes/bioconductor-proloc

* fix bioconductor-chemmineob

* [ci run] remove failures for built dependencies

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci run] full build

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* remove easy build failures

* [ci run] next round of dependencies

* [ci skip] add build failure record for recipe recipes/bioconductor-pigengene

* [ci skip] add build failure record for recipe recipes/bioconductor-repitools

* [ci skip] add build failure record for recipe recipes/bioconductor-xde

* [ci skip] add build failure record for recipe recipes/bioconductor-sctensor

* [ci skip] add build failure record for recipe recipes/bioconductor-rlseq

* build failure updates

* [ci run] next batch of fixes

* [ci skip] add build failure record for recipe recipes/bioconductor-mitoclone2

* [ci skip] add build failure record for recipe recipes/bioconductor-rlseq

* [ci run] full build

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci run]remove failures for built dependencies

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci skip] add build failure record for recipe recipes/bioconductor-rlseq

* [ci skip] add build failure record for recipe recipes/bioconductor-gatom

* [ci run] set failures to skip

* [ci run] reduce resources that are wasted

* [ci skip] add build failure record for recipe recipes/bioconductor-pd.barley1

* fix accidental reverts

* add GSL to bioconductor-pics

* add back fix from master for omnipathr

* remove build failure

* [ci run] skip root nodes to spread out builds

* [ci run] include more root nodes in blacklist

* update build failures

* [ci run] add more blacklist items and do osx build

* [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh

* [ci skip] add build failure record for recipe recipes/bioconductor-ping

* [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes

* [ci skip] add build failure record for recipe recipes/bioconductor-mumosa

* [ci skip] add build failure record for recipe recipes/bioconductor-chromscape

* [ci skip] add build failure record for recipe recipes/bioconductor-scmerge

* [ci skip] add build failure record for recipe recipes/bioconductor-tadcompare

* fix build errors

* [ci run] more skipped builds

* [ci skip] add build failure record for recipe recipes/bioconductor-cghmcr

* [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper

* [ci skip] add build failure record for recipe recipes/bioconductor-ccpromise

* [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh

* [ci skip] add build failure record for recipe recipes/bioconductor-interactivedisplay

* [ci run] reduce workers

* [ci skip] add build failure record for recipe recipes/bioconductor-cepo

* [ci skip] add build failure record for recipe recipes/bioconductor-tbsignatureprofiler

* [ci run] manually distribute packages

* [ci skip] add build failure record for recipe recipes/bioconductor-cocoa

* [ci skip] add build failure record for recipe recipes/bioconductor-condiments

* [ci skip] add build failure record for recipe recipes/bioconductor-scclassify

* [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf

* [ci skip] add build failure record for recipe recipes/bioconductor-gcapc

* [ci skip] add build failure record for recipe recipes/bioconductor-cepo

* [ci skip] add build failure record for recipe recipes/bioconductor-traviz

* remove build failures

* remove colon that breaks yaml parsing

* remove temporary bioconductor bulk skips

* [ci run] remaining packages

* [ci skip] add build failure record for recipe recipes/bioconductor-distinct

* [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf

* [ci skip] add build failure record for recipe recipes/bioconductor-promise

* [ci skip] add build failure record for recipe recipes/bioconductor-otubase

* [ci skip] add build failure record for recipe recipes/bioconductor-cocoa

* [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes

* retry http error

* [ci run] full bulk build

* [ci skip] add build failure record for recipe recipes/bioconductor-deepbluer

* [ci skip] remove build failure record for recipe recipes/bioconductor-meb

* [ci skip] add build failure record for recipe recipes/bioconductor-distinct

* [ci run] categorize failures

* add bioconductor-cdi

* remove old failure files

* update bioconductor-reusedata to 3.18

* remove failures for dependencies that have been built

* [ci run] build certain packages

* bulk: update bioconductor-ccfindr and bioconductor-rjmcmcnucleosomes with gsl (#44986)

* update bioconductor-ccfindr with gsl

* update bioconductor-rjmcmcnucleosomes with gsl

* [ci run] build updated recipes

* [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr

* [ci skip] add build failure record for recipe recipes/bioconductor-reusedata

* remove temporary changes from workflows

* build got bumped in merge

* remove temp files

---------

Co-authored-by: Ryan Dale <ryan.dale@nih.gov>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Bjoern Gruening <bjoern.gruening@gmail.com>
Co-authored-by: BiocondaBot <BiocondaBot@users.noreply.github.com>

* Update deeplc to 2.2.26 (#44238)

* Update deeplc to 2.2.23

* Update deeplc to 2.2.24

* add pyopenms

* Update deeplc to 2.2.25

* Update deeplc to 2.2.26

* try extended base

* revert extended base

---------

Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>

* Add recipe for CellBender v0.3.0 (#45024)

* Add recipe for CellBender v0.3.0

* add run_exports

* Fix nrpys to build on python 3.8+ (#45025)

* Update oakvar to 2.9.83 (#45026)

* Update foldcomp to 0.0.6 (#45018)

* Update foldcomp to 0.0.6

* add run_exports

---------

Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com>

* Update antismash-lite to 7.1.0 (#45027)

* Update jcvi to 1.3.9 (#45029)

* Update jcvi to 1.3.9

* Update meta.yaml

---------

Co-authored-by: Christian Brueffer <christian@brueffer.io>

* Update recognizer to 1.10.1 (#45031)

Co-authored-by: João Sequeira <maildosequeira@gmail.com>

* Update midsv to 0.11.0 (#45028)

* Update midsv to 0.11.0

* Update meta.yaml

* Update meta.yaml

---------

Co-authored-by: Christian Brueffer <christian@brueffer.io>

* Update meta.yaml (#45041)

Snakemake refactored in newer version.

* Rebuild unitig caller for new bifrost version (#45035)

* Rebuild unitig caller for new bifrost version

* Add run_exports

* Fix string interpolation in pinning

* Update annosine2 build (#45033)

* Update meta.yaml

* Update meta.yaml

* Update rasusa to 0.8.0 (#45042)

* Update rasusa to 0.8.0

* add run_export

* bump msrv

---------

Co-authored-by: Michael Hall <michael@mbh.sh>

* Update annonars to 0.33.0 (#45043)

* patch viroconstrictor snakemake requirements to not use version 8.x (#45036)

* Add Deepmei version 1.0.0 recipes (#45005)

* Update keggcharter to 1.1.0 (#45046)

* Update mosca to 2.2.0 (#45054)

* Update mosca to 2.2.0

* Update meta.yaml

Added run_exports
Added pandas as dependency
Fixed python version to <3.12
Fixed snakemake version to <8

---------

Co-authored-by: João Sequeira <maildosequeira@gmail.com>

* Update fgbio to 2.2.1 (#45050)

* Update fgbio-minimal to 2.2.1 (#45051)

* Update viralmsa to 1.1.41 (#45047)

* Update ndex2 to 3.7.0 (#45049)

* Update expam to 1.2.2.5 (#45053)

* Update bustools to 0.43.2 (#45055)

* Update kb-python to 0.28.1 (#45056)

* Update xengsort to 2.0.5 (#44888)

* Update xengsort to 2.0.4

* pin python to 3.11

* Update xengsort to 2.0.5

---------

Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com>

* Update ena-webin-cli to 6.8.0 (#45059)

* Update zol to 1.3.17 (#45067)

* Update pybiolib to 1.1.1673 (#45057)

* Update pybiolib to 1.1.1682 (#45072)

* Update adam to 1.0.1 (#45069)

* Update adam to 1.0.1

* add pin_subpackage

* Update cannoli to 1.0.1 (#45070)

* Update cannoli to 1.0.1.

* add pin_subpackage

* Update keggcharter to 1.1.1 (#45079)

* Update galaxy-objectstore to 23.1.4 (#45061)

* Update galaxy-files to 23.1.4 (#45062)

* Update mashmap to 3.1.3 (#45064)

* Update rosella to 0.5.3 (#45075)

* Update snakemake-executor-plugin-googlebatch to 0.2.0 (#45039)

* Update snakemake-executor-plugin-googlebatch to 0.2.0

* add summary

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>

* Update hifihla to 0.2.3 (#45066)

* Update micom to 0.33.1 (#45071)

* Update flight-genome to 1.6.3 (#45073)

* Update bioframe to 0.6.0 (#45076)

* Update metdatamodel to 0.5.5 (#45082)

* Update odgi to 0.8.4 (#45077)

* Update odgi to 0.8.4

* run_exports

---------

Co-authored-by: Thanh Lee <thanh.le-viet@quadram.ac.uk>

* Update nanovar to 1.5.1 (#45084)

* Update r-ldweaver to 1.4 (#45058)

* Update r-ldweaver to 1.4

* drop genbankr dependency

* it seems genbankr is still needed

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>

* Update ncbi-datasets-pylib to 16.1.1 (#45090)

* Update dbcan to 4.1.0 (#45088)

* Update dbcan to 4.1.0

* fix bug

* add hatchling and other fixes

* edit sha256

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>

* Update perl-math-bigint to 2.003002 (#45096)

* Update nf-test to 0.8.3 (#45098)

* Update foldcomp to 0.0.7 (#45097)

* Update meta.yaml (#45086)

* Update ltr_retriever to 2.9.8 (#45006)

* Update ltr_retriever to 2.9.8

* add run_exports

* revert channel specifications

* remove channels section

---------

Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com>

* prodigal: include upstream patches fixing critical bugs (#45091)

* prodigal: freshen up

* prodigal: include patches for critical bugs fixed upstream but unreleased

The developer has accepted these changes, but no new release has been made
in over a year.

* Add vcfphasesets (#45092)

* Add vcfphasesets.

* Change meta.yaml for run exports.

* Complexcgr (#45089)

* Add complexcgr v0.8.0

* Add complexcgr v0.8.0

* Add complexcgr v0.8.0

* Update ribowaltz to 2.0 (#45065)

* Update ribowaltz to 2.0

* add run_exports

---------

Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>

* Update vcf2variants (#45083)

* Update to version 1.0.

* Add run_exports.

* Extra dependency.

* Bump version.

* Bump version and test import.

* Fix import test.

* Add additional requirement.

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>

* Update snapatac2 to 2.5.2 (#45078)

* Update snapatac2 to 2.5.2

* add typing_extensions to run section

---------

Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com>

* Update breseq to 0.38.2 (#45103)

* Update breseq to 0.38.2

* add run_exports

---------

Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com>

* Update mitos to 2.1.6 (#45104)

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>

* Update harmony-pytorch to 0.1.8 (#45106)

* Update harmony-pytorch to 0.1.8

* add run_exports

---------

Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com>

* Update snakemake to 8.1.0 (#45108)

* Update ltr_retriever to 2.9.9 (#45107)

* Update tn93 to 1.0.13 (#45109)

* Update hyphy to 2.5.59 (#45111)

* Update pyfaidx to 0.8.0 (#45113)

* Depend on gcc; new sha256

* Finally a sativa recipe that puts sativa.py in PATH

* Update mitgard to 1.1 (#45101)

* Update mitgard to 1.1

* add run_exports

---------

Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com>

* Update bioframe to 0.6.1 (#45120)

* Add virusrecom (#45099)

* add virusrecom recipes

* add virusrecom recipes xx

* Update meta.yaml

* add python to run section and use SPDX identifier

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>

* bump mitos1 (#45112)

* bump mitos1

* repin blast-legacy .. add tests first

* Update pybiolib to 1.1.1685 (#45119)

* Update ncbi-datasets-pylib to 16.1.2 (#45124)

* Update das_tool to 1.1.7 (#45123)

* Update das_tool to 1.1.7

* add run_exports

---------

Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com>

* Update virusrecom to 1.1.3 (#45122)

* Update severus to 0.1.2 (#45135)

* Update virusrecom (#45130)

* add virusrecom recipes

* Update meta.yaml

* edit recipe-maintainer

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>

* Update hybracter to 0.5.0 (#45128)

* Update dnaapler to 0.5.1 (#45129)

* Update recentrifuge to 1.13.1 (#45132)

* Update tissuumaps to 3.2.0.3 (#45137)

* mitos: add tests for R packages (#44971)

* mitos: add tests for R packages

In test with the container I got:

Exception: b"Warning message:\npackage \xe2\x80\x98ggplot2\xe2\x80\x99 was built under R version 3.6.3 \nError: package or namespace load failed for \xe2\x80\x98reshape2\xe2\x80\x99 in dyn.load(file, DLLpath = DLLpath, ...):\n unable to load shared object '/usr/local/lib/R/library/stringi/libs/stringi.so':\n  libicui18n.so.64: cannot open shared object file: No such file or directory\nIn addition: Warning message:\npackage \xe2\x80\x98reshape2\xe2\x80\x99 was built under R version 3.6.3 \nExecution halted\n"

* try to use R directly in tests

* try R > 3

* bump and unpin vienna

* retry R>3

* another try

* try to pin r-stringi

* bump

* cnt

* unpin some more requirements

* remove stringi

* repin infernal

* repin hmmer

* repin blast

* Revert "repin blast"

This reverts commit 6a5717a.

* Update kb-python to 0.28.2 (#45138)

* Update ena-webin-cli to 6.9.0 (#45139)

* Update r-seqmagick to 0.1.7 (#45131)

* Update r-seqmagick to 0.1.7

* Update meta.yaml

---------

Co-authored-by: Christian Brueffer <christian@brueffer.io>

* Update snakefmt to 0.9.0 (#45134)

* remove static compilation (#45141)

* Update dajin2 to 0.3.6 (#45143)

* Update jbrowse2 to 2.10.1 (#45145)

* Update ncbi-datasets-pylib to 16.2.0 (#45144)

* Add ACI (#45121)

* adding aci recipe

* fixed entry point typo

* fix typo

* matplotlib-base

* url

* revert url

* underscore

* version

---------

Co-authored-by: Thanh Lee <thanh.le-viet@quadram.ac.uk>

* Update ngs-chew to 0.9.0 (#45140)

* Update vcfpy to 0.13.7 (#45150)

* Avoid building on OS X

---------

Co-authored-by: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Co-authored-by: João Sequeira <maildosequeira@gmail.com>
Co-authored-by: Roberto Rossini <71787608+robomics@users.noreply.github.com>
Co-authored-by: DrYak <ivan.topolsky@sib.swiss>
Co-authored-by: TPOB <19909103+TTTPOB@users.noreply.github.com>
Co-authored-by: Thanh Lee <thanh.le-viet@quadram.ac.uk>
Co-authored-by: stuber <tod.p.stuber@usda.gov>
Co-authored-by: Christian Brueffer <christian@brueffer.io>
Co-authored-by: Milot Mirdita <milot@mirdita.de>
Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com>
Co-authored-by: Enrico Seiler <eseiler@users.noreply.github.com>
Co-authored-by: Ray <851836818@qq.com>
Co-authored-by: Alicia A. Evans <108547992+aliciaaevans@users.noreply.github.com>
Co-authored-by: Ryan Dale <ryan.dale@nih.gov>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Bjoern Gruening <bjoern.gruening@gmail.com>
Co-authored-by: BiocondaBot <BiocondaBot@users.noreply.github.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Co-authored-by: Carl Mathias Kobel <carl.mathias.kobel@nmbu.no>
Co-authored-by: John Lees <lees.john6@gmail.com>
Co-authored-by: Michael Hall <michael@mbh.sh>
Co-authored-by: Florian Zwagemaker <49153065+florianzwagemaker@users.noreply.github.com>
Co-authored-by: Kanglu123 <64641114+Kanglu123@users.noreply.github.com>
Co-authored-by: Michael L Heuer <heuermh@acm.org>
Co-authored-by: Le (Lena) Huang <lehuang@unc.edu>
Co-authored-by: Jens Luebeck <jluebeck@ucsd.edu>
Co-authored-by: Afif Elghraoui <aelghraoui@sdsu.edu>
Co-authored-by: Mark Santcroos <m.a.santcroos@lumc.nl>
Co-authored-by: Koke <49822617+jorgeavilacartes@users.noreply.github.com>
Co-authored-by: Zhou ZJ <43747306+ZhijianZhou01@users.noreply.github.com>
Co-authored-by: M Bernt <m.bernt@ufz.de>
Co-authored-by: boukn <boukn@ncbi.nlm.nih.gov>
Co-authored-by: Young <erin.olde@gmail.com>
Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
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