Bioconductior upgrades to 3.12

[zimoun <zimon.toutoune@gmail.com>]

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Hi,

I am updating to the last Bioconductor release v3.12.  Please fetch the
branch ’wip-r’ from:

    https://github.com/zimoun/guix

There is remaining work to do.  See below.


Here, I am describing the workflow.  Maybe it could help as basis for
future updates.  Ricardo provided helpful tips:

   <http://logs.guix.gnu.org/guix-hpc/2020-10-28.log#201611>

First, I create a local branch name ’wip-r’ with the convention that
’wip’ means “could be rewritten and/or rebased”.  Then I update to
"3.12":

--8<---------------cut here---------------start------------->8---
modified   guix/import/cran.scm
@@ -143,7 +143,7 @@ package definition."

 ;; The latest Bioconductor release is 3.11.  Bioconductor packages should be
 ;; updated together.
-(define %bioconductor-version "3.11")
+(define %bioconductor-version "3.12")
--8<---------------cut here---------------end--------------->8---

and run “./pre-inst-env guix refresh -t bioconductor -u” inside an Emacs
shell and then save the buffer.  Depending on the network, it takes some
time.  Then the previous change to 3.12 is stashed.  Now let commit all
the changes –– thank you so much Ricardo for having written the
tool. :-)

  ./etc/committer.scm

and done.  The next step is to check.  Using the saved output buffer, I
use some Emacs tricks. :-)

 1. M-x keep-lines ^r-
 2. Macro with 2 buffers: the one of #1 and “git-rebase-todo” doing:
  C-x ( C-a C-SPC C-s : RET M-w C-x o M-< C-s C-y RET e C-x o C-n C-x )
  C-x C-e eee…

Warning, Magit will be slow.


Second, I review each of these ’edit’ changes.  Some are skipped,
because of missing dependencies or because I am not sure (for instance
’zlib’ removal).  Below what I did.

The commit messages are not always accurate because some item as:

    [propagate-inputs]: Remove ’foo’.
    [propagate-inputs]: Adding ’bar’.

are missing.


All the best,
simon
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$ ./pre-inst-env guix refresh -t bioconductor -u

# NOT DONE
r-bamsignals: consider removing this input: zlib

# NOT DONE
r-rsamtools: consider removing this input: zlib
r-rsamtools: consider adding this propagated input: r-zlibbioc

# NOT DONE
r-methylkit: consider removing this input: zlib

# NOT DONE
r-variantannotation: consider removing this input: zlib
r-variantannotation: consider adding this propagated input: r-matrixgenerics

# NOt DONE
r-rhdf5: consider removing this input: zlib
r-rhdf5: consider adding this propagated input: r-rhdf5filters

# NOT DONE
r-gdsfmt: consider removing this input: lz4
r-gdsfmt: consider removing this input: xz
r-gdsfmt: consider removing this input: zlib

# NOT DONE
r-rbowtie2: consider removing this input: zlib

# NOT DONE
r-seqbias: consider removing this input: zlib

# NOT DONE
r-cytolib: consider removing this input: zlib
r-cytolib: consider adding this native input: pkg-config

# NOT DONE
r-ncdfflow: consider removing this input: zlib
r-hdf5array: consider removing this input: zlib

# DEP but added (my bad)
r-annaffy: consider adding this propagated input: r-kegg-db

# DEP
r-flowworkspace: consider adding this propagated input: r-aws-s3
r-flowworkspace: consider adding this propagated input: r-aws-signature
r-flowworkspace: consider removing this propagated input: r-stringr

# DEP
r-scater: consider adding this propagated input: r-gridextra
r-scater: consider adding this propagated input: r-scuttle
r-scater: consider removing this propagated input: r-beachmat
r-scater: consider removing this propagated input: r-rcpp

# DEP
r-biocset: consider adding this propagated input: r-biocio
r-biocset: consider adding this propagated input: r-ontologyindex
r-biocset: consider adding this propagated input: r-s4vectors
r-biocset: consider adding this propagated input: r-tidyr
r-biocset: consider removing this propagated input: r-rtracklayer

# DEP
r-scran: consider adding this propagated input: r-bluster
r-scran: consider adding this propagated input: r-scuttle
r-scran: consider removing this propagated input: r-iranges
r-scran: consider removing this propagated input: r-scater

# DEP
r-xcms: consider adding this propagated input: r-mscoreutils

# DEP
r-webbioc: consider adding this input: unix

# DEP
r-biocpkgtools: consider adding this input: mailsend-go

# DEP
r-enrichplot: consider adding this propagated input: r-shadowtext
r-enrichplot: consider removing this propagated input: r-annotationdbi
r-enrichplot: consider removing this propagated input: r-europepmc
r-enrichplot: consider removing this propagated input: r-ggplotify
r-enrichplot: consider removing this propagated input: r-ggridges
r-enrichplot: consider removing this propagated input: r-gridextra

# DEP
r-delayedarray: consider adding this propagated input: r-matrixgenerics
r-delayedarray: consider removing this propagated input: r-matrixstats

# DEP
r-genomicfiles: consider adding this propagated input: r-matrixgenerics

# DEP
r-diffbind: consider removing this input: zlib
r-diffbind: consider adding this propagated input: r-apeglm
r-diffbind: consider adding this propagated input: r-ashr
r-diffbind: consider adding this propagated input: r-greylistchip
r-diffbind: consider removing this propagated input: r-edger

# DEP
r-delayedmatrixstats: consider adding this propagated input: r-matrixgenerics
r-delayedmatrixstats: consider adding this propagated input: r-sparsematrixstats

# NOT DONE
r-complexheatmap: consider adding this propagated input: r-cairo
r-complexheatmap: consider adding this propagated input: r-digest
r-complexheatmap: consider adding this propagated input: r-iranges
r-complexheatmap: consider adding this propagated input: r-matrixstats
r-complexheatmap: consider adding this propagated input: r-s4vectors

# NOT DONE
r-gwascat: consider adding this propagated input: r-biocfilecache
r-gwascat: consider adding this propagated input: r-readr
r-gwascat: consider adding this propagated input: r-snpstats
r-gwascat: consider adding this propagated input: r-variantannotation
r-gwascat: consider removing this propagated input: r-biocgenerics
r-gwascat: consider removing this propagated input: r-ggplot2
r-gwascat: consider removing this propagated input: r-rsamtools
r-gwascat: consider removing this propagated input: r-rtracklayer

# NOT DONE
r-rcas: consider adding this input: pandoc
r-rcas: consider adding this propagated input: r-knitr
r-rcas: consider removing this propagated input: pandoc

# NOT DONE
r-mutationalpatterns: consider adding this native input: r-knitr
r-mutationalpatterns: consider adding this propagated input: r-bsgenome
r-mutationalpatterns: consider adding this propagated input: r-dplyr
r-mutationalpatterns: consider adding this propagated input: r-ggalluvial
r-mutationalpatterns: consider adding this propagated input: r-magrittr
r-mutationalpatterns: consider adding this propagated input: r-purrr
r-mutationalpatterns: consider adding this propagated input: r-stringr
r-mutationalpatterns: consider adding this propagated input: r-tibble
r-mutationalpatterns: consider adding this propagated input: r-tidyr
r-mutationalpatterns: consider removing this propagated input: r-bsgenome-hsapiens-1000g
r-mutationalpatterns: consider removing this propagated input: r-bsgenome-hsapiens-ucsc-hg19
r-mutationalpatterns: consider removing this propagated input: r-plyr
r-mutationalpatterns: consider removing this propagated input: r-reshape2
r-mutationalpatterns: consider removing this propagated input: r-summarizedexperiment

# NOT DONE
r-msnid: consider adding this propagated input: r-annotationdbi
r-msnid: consider adding this propagated input: r-annotationhub
r-msnid: consider adding this propagated input: r-biocgenerics
r-msnid: consider adding this propagated input: r-biocstyle
r-msnid: consider adding this propagated input: r-biostrings
r-msnid: consider adding this propagated input: r-ggplot2
r-msnid: consider adding this propagated input: r-msmstests
r-msnid: consider adding this propagated input: r-purrr
r-msnid: consider adding this propagated input: r-rlang
r-msnid: consider adding this propagated input: r-runit
r-msnid: consider adding this propagated input: r-stringr
r-msnid: consider adding this propagated input: r-tibble
r-msnid: consider adding this propagated input: r-xtable

# NOT DONE
r-rhtslib: consider removing this propagated input: curl

# NOT DONE
r-mzr: consider removing this input: boost

# NOT DONE
r-pcamethods: consider adding this input: rcpp

# NOT DONE
r-mzid: consider removing this propagated input: r-rcpp

# NOT DONE
r-edger: consider removing this propagated input: r-statmod

# NOT DONE
r-flowclust: consider removing this input: gsl

# NOT DONE
r-cytoml: consider adding this input: xml2
r-cytoml: consider removing this input: libxml2

# NOT DONE
r-roc: consider adding this native input: r-knitr

# NOT DONE
r-rhdf5lib: consider removing this native input: hdf5-source
r-rhdf5lib: consider removing this propagated input: hdf5

# MISSED what had be done
r-abseqr: consider removing this input: pandoc-citeproc

# MISSED what had be done
r-rbowtie: consider removing this input: zlib

#
# DONE
#

r-shortread: consider adding this propagated input: r-rhtslib
r-summarizedexperiment: consider adding this propagated input: r-matrixgenerics
r-biomart: consider adding this propagated input: r-xml2

r-a4preproc: consider adding this native input: r-knitr
r-a4preproc: consider adding this propagated input: r-biobase
r-a4preproc: consider adding this propagated input: r-biocgenerics
r-a4preproc: consider removing this propagated input: r-annotationdbi

r-a4classif: consider adding this native input: r-knitr
r-a4classif: consider adding this propagated input: r-biobase
r-a4classif: consider removing this propagated input: r-mlinterfaces

r-a4core: consider adding this native input: r-knitr

r-a4base: consider removing this propagated input: r-annotationdbi
r-destiny: consider removing this native input: r-nbconvertr
r-destiny: consider removing this propagated input: r-nbconvertr
r-yapsa: consider adding this propagated input: r-limsolve
r-yapsa: consider removing this propagated input: r-lsei

r-annotate: consider adding this propagated input: r-httr
r-annotate: consider removing this propagated input: r-rcurl

r-wavcluster: consider removing this propagated input: r-wmtsa

r-depecher: consider adding this propagated input: r-gmodels
r-mixomics: consider adding this propagated input: r-ggrepel

r-motifstack: consider removing this propagated input: r-grimport2
r-motifstack: consider removing this propagated input: r-motiv
r-motifstack: consider removing this propagated input: r-scales

r-genomicscores: consider adding this propagated input: r-biocfilecache
r-genomicscores: consider adding this propagated input: r-biocmanager

r-a4reporting: consider adding this native input: r-knitr
r-a4reporting: consider removing this propagated input: r-annaffy

r-chippeakanno: consider adding this propagated input: r-ggplot2
r-chippeakanno: consider adding this propagated input: r-keggrest
r-chippeakanno: consider removing this propagated input: r-biobase
r-chippeakanno: consider removing this propagated input: r-biocmanager
r-chippeakanno: consider removing this propagated input: r-bsgenome
r-chippeakanno: consider removing this propagated input: r-delayedarray
r-chippeakanno: consider removing this propagated input: r-go-db
r-chippeakanno: consider removing this propagated input: r-idr
r-chippeakanno: consider removing this propagated input: r-limma
r-chippeakanno: consider removing this propagated input: r-seqinr

r-edaseq: consider removing this propagated input: r-deseq

r-glimma: consider adding this propagated input: r-deseq2
r-glimma: consider adding this propagated input: r-htmlwidgets
r-glimma: consider adding this propagated input: r-limma
r-glimma: consider adding this propagated input: r-summarizedexperiment

r-seqlogo: consider adding this native input: r-knitr
r-systempiper: consider adding this propagated input: r-iranges

r-rtracklayer: consider adding this propagated input: r-zlibbioc