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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
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msnbase needs fortran requirement #16127

Open bernt-matthias opened 5 years ago

bernt-matthias commented 5 years ago

Seems that we need a fortran requirement for msnbase ... or is it something different like gcc?

library(MSnbase)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
    colnames, colSums, dirname, do.call, duplicated, eval, evalq,
    Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
    lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
    rowSums, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Error: package or namespace load failed for ‘MSnbase’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/gpfs1/data/galaxy_server/galaxy/database/dependencies/_conda/envs/mulled-v1-c0cde3dd10ed36abe750c63bc3a68bb64acd685d21223d5fdf53db852d7ccc23/lib/R/library/MSnbase/libs/MSnbase.so':
  libgfortran.so.4: cannot open shared object file: No such file or directory

Happens in a environment created with: 

conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mulled-v1-c0cde3dd10ed36abe750c63bc3a68bb64acd685d21223d5fdf53db852d7ccc23 r-snow=0.4_2 bioconductor-xcms=3.0.0 bioconductor-camera=1.34.0 bioconductor-multtest=2.28.0 r-batch=1.1_4 graphicsmagick=1.3.23

ping @chufz

sneumann commented 1 month ago

Hi @bernt-matthias , @cbroeckl recently discovered issues installing xcms via conda, reported in https://github.com/sneumann/xcms/issues/775. Checking https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-xcms I see that the latest xcms would be 4.0.0 from BioC-3.18. Any way to help updating the bioconda recipies ? Yours, Steffen