Commit 5423c272 authored by josh's avatar josh
Browse files

try to install robCompositions the normal way

with updated version of R, maybe I don't need to install older versions of dependencies
parent 78dbfd75
Pipeline #194506 failed with stages
in 38 seconds
......@@ -196,7 +196,7 @@ RUN Rscript -e "install.packages(pkgs = c('tidyverse','caTools','rprojroot','rma
# Add microbiome specific R and bioconductor packages
RUN Rscript -e "install.packages(pkgs = c('fs','ips','unvotes','DT','sandwich','TH.data', 'here', 'sf', 'spdep', 'agricolae','topicmodels'), \
RUN Rscript -e "install.packages(pkgs = c('fs','ips','unvotes','DT','sandwich','TH.data', 'here', 'sf', 'spdep', 'agricolae','topicmodels','robCompositions'), \
repos=${CRAN_REPO}, \
dependencies=TRUE, \
clean = TRUE)"
......@@ -204,21 +204,6 @@ RUN Rscript -e "install.packages(pkgs = c('fs','ips','unvotes','DT','sandwich','
RUN Rscript -e "if (!requireNamespace('BiocManager')){install.packages('BiocManager')}; \
BiocManager::install(c('dada2','ShortRead','phyloseq','msa','DESeq2','metagenomeSeq','ALDEx2','decontam','ANCOMBC','lefser'))"
# need to install older version of multcomp to avoid dependency on newer mvtnorm, which depends on newer R
# also needed to install multcomp dependencies: "sandwich","TH.data"
RUN Rscript -e \
"install.packages(c('https://cran.r-project.org/src/contrib/Archive/mvtnorm/mvtnorm_1.0-8.tar.gz', \
'https://cran.r-project.org/src/contrib/Archive/multcomp/multcomp_1.4-8.tar.gz'), \
repos=NULL, type='source', \
clean = TRUE)"
RUN Rscript -e "install.packages(pkgs = c('robCompositions'), \
repos=${CRAN_REPO}, \
dependencies=TRUE, \
clean = TRUE)"
# Trans-ABySS
RUN mkdir -p $MANUAL_BIN $MANUAL_SHARE ; \
wget --no-verbose -O $MANUAL_BIN/blat http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat; \
......
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