User: benoahb

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benoahb0
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Posts by benoahb

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Comment: C: Issue setting up BiocManager due to mgcv / clang?
... Finally, it worked!! Thanks for the help! ...
written 6 months ago by benoahb0
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Comment: C: Issue setting up BiocManager due to mgcv / clang?
... In the terminal, I can access `~/.R` and the `ls` command gives me a `Makevars.txt` file. Said file contains SHLIB_OPENMP_CFLAGS= SHLIB_OPENMP_CXXFLAGS= Yet, in R, I still get this error message > normalizePath("~/.R/Makevars") [1] "~/.R/Makevars" Warning message: In ...
written 6 months ago by benoahb0
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Comment: C: Issue setting up BiocManager due to mgcv / clang?
... I did, a plain text document... ...
written 6 months ago by benoahb0
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Comment: C: Issue setting up BiocManager due to mgcv / clang?
... I created .R in my home directory `normalizePath("~/.R")` and made a plain text Makevars file as you suggested, however I still get this error message Warning message: In normalizePath("~/.R/Makevars") : path[1]="~/.R/Makevars": No such file or directory I took the version of clang f ...
written 6 months ago by benoahb0
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Comment: C: Issue setting up BiocManager due to mgcv / clang?
... I installed R using the macOS package from CRAN website. Here are the lines containing `-fopenmp` DYLIB_LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -fopenmp# $(CFLAGS) $(CPICFLAGS) MAIN_LDFLAGS = -fopenmp S ...
written 6 months ago by benoahb0 • updated 6 months ago by Martin Morgan ♦♦ 23k
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Comment: C: Issue setting up BiocManager due to mgcv / clang?
... Yeah, I tried `install.packages("mgcv")` with the same results. Ok this is when I start to get lost. How do I verify "that the -fopenmp flag is present in the file at R.home("etc/Makeconf")"? Also, I looked at the topic you linked. I already got clang but ran `brew install gcc` I looked into `/u ...
written 6 months ago by benoahb0
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Comment: C: Issue setting up BiocManager due to mgcv / clang?
... Well, as I said, I already installed Xcode, and it is up to date. I checked and gfortran is also up to date. The only thing missing was clang. It seemed outdated on your link but updated it with Homebrew and the LLVM package. I also took the last Command Line Tools macOS 10.14 for Xcode 10.2. But I ...
written 6 months ago by benoahb0
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Issue setting up BiocManager due to mgcv / clang?
... Hi all, I'm new to R and it looks like I'm having issues setting up BiocManager and linked to the mgcv package and clang? See below. I'm running on macosx Mojave, I installed R, Rstudio, Xcode and Xcode command lines. Any ideas? Thanks, Ben > BiocManager::install() Bioconductor ...
software error written 6 months ago by benoahb0 • updated 6 months ago by Martin Morgan ♦♦ 23k

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