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Packages breaking the nightly upload job #15196

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58 tasks done
dpryan79 opened this issue May 9, 2019 · 2 comments
Closed
58 tasks done

Packages breaking the nightly upload job #15196

dpryan79 opened this issue May 9, 2019 · 2 comments
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@dpryan79
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dpryan79 commented May 9, 2019 •
edited

The following recipes have meta.yaml files that are breaking the nightly upload job. The order for sections in a meta.yaml should be package, source, build, requirements, test, about, extras. Usually these start with about.

  • recipes/2pg_cartesian
  • recipes/weblogo/2.8.2
  • recipes/trimmomatic/0.32
  • recipes/trimmomatic/0.33
  • recipes/trimmomatic/0.35
  • recipes/tophat2
  • recipes/tophat2/2.0.13
  • recipes/rnashapes/2.1.6
  • recipes/rnashapes/3.3.0
  • recipes/trinotate
  • recipes/metavelvet-annois
  • recipes/meme/4.11.1
  • recipes/meme/4.11.2
  • recipes/mafft/7.305
  • recipes/mafft/7.310
  • recipes/samtools/0.1.19
  • recipes/samtools/1.1
  • recipes/last/490
  • recipes/last/638
  • recipes/last/874
  • recipes/kat/2.0.8
  • recipes/kat/2.3.1
  • recipes/gromacs
  • recipes/braker
  • recipes/bowtie2/2.2.1
  • recipes/bowtie2/2.2.4
  • recipes/bowtie2/2.2.5
  • recipes/bedtools/2.19.1
  • recipes/bedtools/2.20.1
  • recipes/bedtools/2.22
  • recipes/bedtools/2.23.0
  • recipes/bcftools
  • recipes/bcftools/1.3.1
  • recipes/sqt
  • recipes/tepid
  • recipes/aragorn/1.2.38
  • recipes/art/3.11.14
  • recipes/autodock-vina
  • recipes/bcbiogff/0.6.2
  • recipes/bcbiogff
  • recipes/biopet/0.8.0
  • recipes/biopet
  • recipes/blockbuster
  • recipes/metfrag
  • recipes/metfrag/2.3.1
  • recipes/metfrag/2.4.2
  • recipes/varscan/2.4.2
  • recipes/discovar
  • recipes/ccat/3.0
  • recipes/transabyss
  • recipes/opsin/1.4.0
  • recipes/opsin/2.1.0
  • recipes/opsin/2.4.0
  • recipes/cluster-picker
  • recipes/soapdenovo2-prepare
  • recipes/damidseq_pipeline
  • recipes/repeatmodeler
  • recipes/detonate
@dpryan79
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dpryan79 commented May 9, 2019 •
edited

I have these blacklisted in bulk (where I'm doing the bioconductor 3.9 release) at the moment, but we should really fix these in master.

@dpryan79 dpryan79 mentioned this issue May 9, 2019
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@npavlovikj npavlovikj mentioned this issue May 10, 2019
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@dpryan79 dpryan79 mentioned this issue May 10, 2019
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@npavlovikj npavlovikj mentioned this issue May 11, 2019
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dpryan79 added a commit that referenced this issue May 12, 2019
@dpryan79
more from #15196
5ebb51f
dpryan79 added a commit that referenced this issue May 13, 2019
@dpryan79
more from #15196 (#15326)
16b0b30 
* more from #15196

* bump build numbers

* updates

* updates

* old bedtools versions won't build, fix bcftools/1.3.1

* group blacklist items a bit

* Try to fix braker and bowtie2

* a few updates

* Update meta.yaml
dpryan79 added a commit that referenced this issue May 15, 2019
@dpryan79
update blacklist from #15196
5117261
@dpryan79
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I'm working on these in the bulk branch now.

kpalin pushed a commit to kpalin/bioconda-recipes that referenced this issue Aug 7, 2019
@dpryan79 @kpalin
more from bioconda#15196 (bioconda#15326)
2f97adb 
* more from bioconda#15196

* bump build numbers

* updates

* updates

* old bedtools versions won't build, fix bcftools/1.3.1

* group blacklist items a bit

* Try to fix braker and bowtie2

* a few updates

* Update meta.yaml
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