Rstudio m1 mac upgrade#
Rank, rbind, Reduce, rownames, sapply, setdiff, sort, table,
Mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, Grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, The following objects are masked from ‘package:base’: anyDuplicated, append, as.ame, basename, cbind, colnames,ĭirname, do.call, duplicated, eval, evalq, Filter, Find, get, The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs Any advice for dealing with the genefilter issue? Thank you!! Please see error message below and session info.
Rstudio m1 mac mac#
I am on an MAC with M1 and am having similar issues. Old packages: 'RCurl', 'rmarkdown', 'xfun', 'XML'
Rstudio m1 mac install#
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘DESeq2’ĭo you want to attempt to install these from sources? (Yes/no/cancel) no I've tried to force since it is installed already and then I tried none as you said. There are binary versions available but the sourceĭo you want to install from sources the package which needs compilation? (Yes/no/cancel) Warning: unable to access index for repository : 'getOption("repos")' replaces Bioconductor standard repositories,īioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1Īlso installing the dependency ‘jquerylib’ Make: /opt/R/arm64/bin/gfortran: Permission denied
Sudo ln -s /usr/local//gfortran/bin/gfortran /opt/R/arm64/binįinally BiocManager::install('genefilter') So i do this # make link to /opt/R/arm64/bin Still get make: /opt/R/arm64/bin/gfortran: No such file or directory Sys.setenv(gfortran="/usr/local/gfortran/bin") bash_profileĬOLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin15/6.1.0/lto-wrapper The error showed: make: /opt/R/arm64/bin/gfortran: No such file or directory. Installation of package ‘genefilter’ had non-zero exit status * removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/genefilter’ Make: /opt/R/arm64/bin/gfortran: No such file or directoryĮRROR: compilation failed for package ‘genefilter’ opt/R/arm64/bin/gfortran -mtune=native -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c ttest.f -o ttest.o Ĭlang++ -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.oĬlang -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.oĬlang -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.oĬlang -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.oĬlang -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.oĬlang -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 * installing *source* package ‘genefilter’. Installing the source package ‘genefilter’Ĭontent type 'application/x-gzip' length 805682 bytes (786 KB) Package which is only available in source form, and may need compilation ofĭo you want to attempt to install these from sources? (Yes/no/cancel) Yes 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for detailsīioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 () R studio BiocManager::install('genefilter') Macbook m1 R studio install deseq2 dependent package genefilter failed
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