R rebuild against R 3.3.2 #4972

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merged 130 commits into from Jun 15, 2017

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bgruening commented Jun 15, 2017 edited by xguse

  • I have read the guidelines for bioconda recipes.
  • This PR adds a new recipe.
  • This PR updates an existing recipe.
  • This PR does something else (explain below).

This PR has all changes that were necessary to rebuild all* R packages against R 3.3.2. Moreover, we migrated all packages from the r-channel to conda-forge (build against 3.2.2.).
This means we can drop the r-channel completely from you build-infrastructure. Which is done here: bioconda/bioconda-utils#122

Please note that if you want to run against R3.3.1 you still need the r-channel.

Additionally, this means we changed the channel priority to prefer conda-forge over defaults.
Overall, a large change and we want to make you aware of these and we hope it does not break too many packages. We do think it is worth the effort to drop the r-channel.

ping @bioconda/all

* a few packages are still on the sorted-r-blacklist and I would appreciate some help from R experts or OSX experts.

mdehollander and others added some commits Jun 2, 2017

@mdehollander mdehollander Add R package micropan 145b70b
@mdehollander mdehollander Add R package microseq fcead0a
@bgruening bgruening start rebuilding for R 3.3.2 without the r-channel 2dead83
@bgruening bgruening change channel order c5e5241
@bgruening bgruening various fixes e2288cc
@bgruening bgruening Merge branch 'bulk' of https://github.com/bioconda/bioconda-recipes i…
…nto bulk
8492427
@bgruening bgruening various fixes a620427
@bgruening bgruening fixes to bioc packages e9bf5a8
@bgruening bgruening fixes 593cf9b
@bgruening bgruening remove blacklist 25a406b
@bgruening bgruening multiple fixes 4003cf3
@bgruening bgruening multiple fixes 53d2853
@bgruening bgruening fixes 7dbaa18
@bgruening bgruening r fixes 1be8468
@bgruening bgruening change r to r-base 776d5d7
@bgruening bgruening change r to r-base 3f26602
@bgruening bgruening change r to r-base 68c9157
@bgruening bgruening url fix 90bac3b
@bgruening bgruening r fixes 490a3fb
@bgruening bgruening r fixes 4994c6b
@bgruening bgruening remove irganes 2.4.7 f1f1ea1
@bgruening bgruening r fixes b2a42d6
@bgruening bgruening r fixes 14e163e
@bgruening bgruening r fixes 326996e
@bgruening bgruening remove older version 9d5969e
@bgruening bgruening r fixes 7690318
@bgruening bgruening r fixes 0ee3573
@bgruening bgruening r fixes 7a4c142
@bgruening bgruening r fixes 01bfa64
@bgruening bgruening r fixes c7d25ac
@bgruening bgruening r fixes 5c168b4
@bgruening bgruening r fixes 4f1c4db
@bgruening bgruening r fixes c48873e
@bgruening bgruening rename folder 787f73f
@bgruening bgruening remove recipe 019c04e
@daler daler update bioc skeleton; fix tximport & biomformat ee1ca56
@bgruening bgruening Merge branch 'bulk' of https://github.com/bioconda/bioconda-recipes i…
…nto bulk
cae8391
@bgruening bgruening r fixes 4d13b01
@bgruening bgruening fix syntax b01ced2
@bgruening bgruening r fixes dd80b6b
@bgruening bgruening r fixes a9087c4
@daler daler update flowViz recipe 4901b63
@daler daler fix BiocStyle recipe 46f3140
@daler daler fix org.Hs.eg.db 9119a10
@daler daler fix bioconductor_skeleton to auto-find data packages d29079a
@daler daler Merge branch 'bulk' of github.com:/bioconda/bioconda-recipes into bulk f21ae4a
@daler daler fix SummarizedExperiment 4df9903
@daler daler fix BiocParallel fb2a6c2
@daler daler fix fastseg ef810b7
@daler daler fix org.Dm.eg.db 515f4f1
@daler daler R 3.3.2 has a different set of default packages ecfc84b
@daler daler fix bioconductor-biomformat 1236dd7
@bgruening bgruening r fixes d52b572
@daler daler bioconductor_skeleton handles typos in DESCRIPTION 8450bb5
@daler daler fix DEGreport d49a66b
@daler daler fix flowViz again d555d1d
@daler daler fix multtest 888f077
@bgruening bgruening r fixes 629acff
@daler daler Merge branch 'bulk' of github.com:/bioconda/bioconda-recipes into bulk f8ee2a6
@daler daler more fixes to bioconductor_skeleton da7fdbe
@daler daler fix org.{Hs,Dm}.eg.db 6e72cd4
@daler daler update the update_bioconductor_packages script to build topsorted dag 113e4a0
@daler daler fix Category f072eaf
@daler daler fix genefilter 01d4e6d
@daler daler add matrix to summarizedexperiment 789fd61
@daler daler add urls for gostats 5bd4737
@daler daler fix MotIV 6c3b20b
@daler daler urls for rGADEM abf70a6
@daler daler urls and built-ins for Ringo cc38fe2
@daler daler urls for zlibbioc 3f968e4
@bgruening bgruening r fixes f354f92
@bgruening bgruening r fixes 233eb44
@bgruening bgruening remove old package 2eac640
@bgruening bgruening r fixes b899b52
@bgruening bgruening r-fixes da3e393
@bgruening bgruening r fixes e054a6c
@bgruening bgruening rpy e55adf5
@bgruening bgruening r fixes f4f9fe8
@mdehollander mdehollander Minor formatting 1ed5175
@daler daler add readline to some failing R packages cd4ed38
@bgruening bgruening remove old recipe 305a211
@bgruening bgruening Merge branch 'bulk' of https://github.com/bioconda/bioconda-recipes i…
…nto bulk
46affc3
@mdehollander mdehollander Remove micropan from this branch b4d84a4
@bgruening bgruening remove libffi 9427284
@bgruening bgruening remove old recipe ddfa916
@bgruening bgruening r fixes ede4153
@bgruening bgruening pin rpy to conda-forge version dd754a3
@mdehollander mdehollander Apply comments bgruening f725875
@bgruening bgruening Merge branch 'microseq' of https://github.com/mdehollander/bioconda-r…
…ecipes into mdehollander-microseq
562b389
@bgruening bgruening Merge branch 'mdehollander-microseq' into bulk 5ec2f26
@bgruening bgruening r fixes c2e4f48
@bgruening bgruening enable more debug output 79a92cd
@bgruening bgruening merge 17ef11c
@bgruening bgruening Merge branch 'master' into bulk 7f9c5a2
@johanneskoester johanneskoester Disable debug logging. 75d7684
@johanneskoester johanneskoester Fix zifa source. fcd5f80
@johanneskoester johanneskoester Imrpove cap-mirseq recipe. 57db684
@bgruening bgruening Merge branch 'master' into bulk 92a96fa
@bgruening bgruening r fixes 0ec1c75
@bgruening bgruening remove rpy2 a462be1
@bgruening bgruening r fixes c518586
@bgruening bgruening Merge branch 'bulk' of https://github.com/bioconda/bioconda-recipes i…
…nto bulk
1e2e320
@bgruening bgruening r fixes c0a2b7b
@bgruening bgruening r fixes 50d85c5
@bgruening bgruening r fixes 89c4bad
@bgruening bgruening remove old version adbfed8
@bgruening bgruening add new version ca32ab2
@bgruening bgruening r fixes ce84fee
@bgruening bgruening try some fixes d5f1ec1
@bgruening bgruening remove old package d8c9252
@bgruening bgruening r fixes 1951ae7
@bgruening bgruening r fixes 6f9a239
@bgruening bgruening skip this recipe, as it has to strict pinning 347b980
@bgruening bgruening r fixes b868cee
@bgruening bgruening cMerge branch 'master' into bulk 861c469
@bgruening bgruening remove old nanoraw package 0d360e5
@bgruening bgruening fix osx version a4a5ab9
@bgruening bgruening r fixes 6d44bf5
@bgruening bgruening r fixes e298891
@bgruening bgruening remove older releases c2a6e0a
@bgruening bgruening this pkg is a bioc package c3edb34
@bgruening bgruening r fixes 022751a
@bgruening bgruening Merge branch 'master' into bulk 810bb68
@bgruening bgruening remove old r-ggally version 5b786d2
@bgruening bgruening readd older version 6f62239
@bgruening bgruening add R blacklist again 117c834
@bgruening bgruening update blacklist 02d8eef
@bgruening bgruening Merge branch 'master' into bulk 3b3f88d
@bgruening bgruening blacklist the rest of the packages
3f2eca2
@bgruening bgruening Change back to master branch
53a22e3

@johanneskoester johanneskoester merged commit fd2ecba into master Jun 15, 2017

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sebastian-luna-valero referenced this pull request in CGATOxford/cgat Jun 19, 2017

Open

Conda installation broken #301

Contributor

rvalieris commented Jun 19, 2017

r-ggally is on the blacklist but apparently it built on 3.3.2 successfully (https://anaconda.org/bioconda/r-ggally/files), am I missing something ?

Contributor

bgruening commented Jun 19, 2017

@rvalieris can you remove it from the blacklist?

Contributor

rvalieris commented Jun 19, 2017

sure, I just wanted to double check :)

rvalieris referenced this pull request Jun 19, 2017

Merged

clean blacklist #4993

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