Installation Issues SNPRelate

[Liesl Bower-Jernigan]

Hello,

I am having issues installing dartR. I have installed it before and it has worked before this new version of R. 

Here is the code I have tried and the errors I keep getting:

install.packages("devtools")
library(devtools)
install_github("green-striped-gecko/dartR")

ERROR: dependency ‘SNPRelate’ is not available for package ‘dartR’

Then I try:

install.packages("BiocManager")
BiocManager::install(c("SNPRelate", "qvalue"))

ERROR: Warning: installation of package ‘fields’ had non-zero exit status

Which then means install.packages("dartR") has an error:

Warning in install.packages :
  dependency ‘SNPRelate’ is not available

 

Thank you,

Liesl 

[Jose Luis Mijangos]

Hi Liesl,

Can you try:

>library("devtools")
> install_github("zhengxwen/SNPRelate",force = TRUE)

Cheers,

Luis

[Liesl Bower-Jernigan]

Hi Luis,

I tried this and this is the error I get:

ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [SNPRelate.so] Error 1
ERROR: compilation failed for package ‘SNPRelate’

Best,

Liesl 

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Graduate Student

Applied Plant Sciences

Department of Horticultural Science

University of Minnesota

she/her/hers

[Jose Luis Mijangos]

Hi Liesl,

It looks like you have a Mac. Can you try:

1. Install homebrew

Open the Terminal app and type:

> ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

2. Install Command-Line tools

In the Terminal app type:

> xcode-select --install

3. Install compiler

In the Terminal app type:

> brew install gcc

4. Make a symlink from your gcc version to gcc

In the Terminal app type:

> ln -s gcc-11 gcc

5. Create a makevars file and put the path to libgfortran into FLIBS

In the R console type

> dir.create('~/.R')
> write.table("FLIBS=`gfortran -print-search-dirs | grep '^libraries:' | sed 's|libraries: =||' | sed 's|:| -L|g' | sed 's|^|-L|'`",file='~/.R/Makevars',col.names = FALSE,row.names = FALSE,quote = FALSE)

6. Install SNPRelate

In the R console type:

> install.packages("SNPRelate")

7. Install dartR

In the R console type:

> install.packages("dartR")

Cheers,

Luis