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update version to avoid compile error#19382

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darmac wants to merge 1 commit intospack:developfrom
open-estuary:r-genefilter
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update version to avoid compile error#19382
darmac wants to merge 1 commit intospack:developfrom
open-estuary:r-genefilter

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@darmac darmac commented Oct 20, 2020

update version to avoid this issue:

/home/spack-develop/lib/spack/env/gcc/g++ -std=gnu++11 -shared -L/home/spack-develop/opt/spack/linux-centos8-aarch64/gcc-8.3.1/r-4.0.2-kyflwfdhj63kvb67y5z7fqbxsb6sxcfe/rlib/R/lib -L/home/spack-develop/opt/spack/linux-centos8-aarch64/gcc-8.3.1/r-4.0.2-kyflwfdhj63kvb67y5z7fqbxsb6sxcfe/rlib/R/lib -Wl,-rpath,/home/spack-develop/opt/spack/linux-centos8-aarch64/gcc-8.3.1/r-4.0.2-kyflwfdhj63kvb67y5z7fqbxsb6sxcfe/rlib/R/lib -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -lgfortran -lm -L/home/spack-develop/opt/spack/linux-centos8-aarch64/gcc-8.3.1/r-4.0.2-kyflwfdhj63kvb67y5z7fqbxsb6sxcfe/rlib/R/lib -lR
installing to /home/spack-develop/opt/spack/linux-centos8-aarch64/gcc-8.3.1/r-genefilter-1.66.0-yrlczxbuim4tcivg2marptqkjgpxuafu/rlib/R/library/00LOCK-spack-src/00new/genefilter/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: objects 'rowSums', 'colSums', 'rowMeans', 'colMeans' are not exported by 'namespace:S4Vectors'
Execution halted
ERROR: lazy loading failed for package 'genefilter'
* removing '/home/spack-develop/opt/spack/linux-centos8-aarch64/gcc-8.3.1/r-genefilter-1.66.0-yrlczxbuim4tcivg2marptqkjgpxuafu/rlib/R/library/genefilter'

adamjstewart
adamjstewart requested changes Oct 20, 2020
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Missing dependency on [email protected]:

var/spack/repos/builtin/packages/r-genefilter/package.py
homepage = "https://bioconductor.org/packages/genefilter"
git = "https://git.bioconductor.org/packages/genefilter.git"

version('3.11.0', commit='a071480ffc48393a4385a94c96a752285064989f')
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@adamjstewart adamjstewart Oct 20, 2020

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3.11 is the version of bioconductor, I think you want 1.70.0

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@darmac darmac Oct 22, 2020

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Well, I don't know how to get 1.70.0
And the relationship between bioconductor and genefilter make me confusion...

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@adamjstewart adamjstewart Oct 22, 2020

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@codeandkey can you take a look at this one?

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@codeandkey codeandkey Nov 10, 2020

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1.70.0 corresponds to bioconductor 3.11 (RELEASE_3_11 branch), looks like the r-biocgenerics was the only new dep added since the last version in the recipe.

RemiLacroix-IDRIS added a commit to RemiLacroix-IDRIS/spack that referenced this pull request Dec 30, 2020
@RemiLacroix-IDRIS
r-genefilter: Add version 1.72.
e0d8ac1 
Update the dependencies accordingly.

Closes spack#19382 and spack#20311.
RemiLacroix-IDRIS added a commit to RemiLacroix-IDRIS/spack that referenced this pull request Dec 30, 2020
@RemiLacroix-IDRIS
r-genefilter: Add version 1.72.
e73dbe6 
Update the dependencies accordingly.

Closes spack#19382 and spack#20311.
@RemiLacroix-IDRIS RemiLacroix-IDRIS mentioned this pull request Dec 30, 2020
Merged
RemiLacroix-IDRIS added a commit to RemiLacroix-IDRIS/spack that referenced this pull request Dec 30, 2020
@RemiLacroix-IDRIS
r-genefilter: Add version 1.72.
e912cfa 
Update the dependencies accordingly.

Closes spack#19382 and spack#20311.
@darmac darmac deleted the r-genefilter branch March 6, 2021 03:10
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