Forcing Installation Of DMRcate

Question

[Indira]

I tried to install DMRcate (using the method recommended on the site) however, it did not install and then it said:

The original code I used is:

    if (!require("BiocManager"))
        install.packages("BiocManager")
BiocManager::install("DMRcate")

The error I got is below:

1: package(s) not installed when version(s) same as or greater than current; use force = TRUE to re-install: 'DMRcate' 2: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘genefilter’ had non-zero exit status

I wanted to ask where exactly to put force = True as it doesn't seem to recognize the syntax when I put it in. I am sure it is a small issue but I do need to ask a someone who is not at all computer-savvy.

[Indira]

I cannot add the warning messages as they are too long.

This section seems relevant though:

• installing source package ‘genefilter’ ... using staged installation libs clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" - DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c half_range_mode.cpp -o half_range_mode.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG - I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG - I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nd.c -o nd.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG - I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pAUC.c -o pAUC.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG - I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rowPAUCs.c -o rowPAUCs.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG - I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rowttests.c -o rowttests.o /opt/R/arm64/bin/gfortran -mtune=native -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c ttest.f - o ttest.o make: /opt/R/arm64/bin/gfortran: No such file or directory

make: *** [ttest.o] Error 1 ERROR: compilation failed for package ‘genefilter’

I seem to have issues using homebrew to deal with this could someone help please?

[Indira]

I cannot add all the error messages as they are too long.

Answer 1

[ATpoint]

You need a the gfortran compiler, I suggest you precisely follow all relevant steps at https://mac.r-project.org/tools/