linux conda install ridge failed

[shufanzhang]

1. I try to use ‘conda install -c r r-ridge’， but it keep Solving environment without stopped
2. I try to install ridge with https://cran.r-project.org/src/contrib/ridge_3.2.tar.gz，i apt install gcc and GSL， but it still can not install. information is as follows:

install.packages("/home/shufan/software/oncoPredict/ridge_3.2.tar.gz",repos = NULL,type = "source")

• installing source package ‘ridge’ ... package ‘ridge’ successfully unpacked and MD5 sums checked using staged installation /home/xxx/anaconda3/envs/drug/lib/R/bin/config: 1: eval: make: not found /home/xxx/anaconda3/envs/drug/lib/R/bin/config: 1: eval: make: not found /home/xxx/anaconda3/envs/drug/lib/R/bin/config: 1: eval: make: not found /home/xxx/anaconda3/envs/drug/lib/R/bin/config: 1: eval: make: not found /home/xxx/anaconda3/envs/drug/lib/R/bin/config: 1: eval: make: not found

checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for gsl-config... /usr/bin/gsl-config checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for gsl/gsl_version.h... yes configure: creating ./config.status config.status: creating R/linearRidgeGenotypes.R config.status: creating R/linearRidgeGenotypesPredict.R config.status: creating R/logisticRidgeGenotypes.R config.status: creating R/logisticRidgeGenotypesPredict.R config.status: creating src/Makevars config.status: creating src/config.h config.status: src/config.h is unchanged ** libs sh: 1: make: not found Warning in system(cmd) : 调用命令时发生了错误 ERROR: compilation failed for package ‘ridge’

[SteffenMoritz]

Don't think this is an issue with the package itself but rather about getting the requirements for the package right.

I am not using conda myself, but let me try to help you. Here are some things that could work:

Usually when you get an error like "make not found" you need to install RTools to be able to install the package from source. (for windows) Or run sudo apt-get install make to install make on linux.

Also see https://stackoverflow.com/questions/53279685/r-make-not-found-when-installing-a-r-package-from-local-tar-gz

[SteffenMoritz]

Closed as it is not really an issue with the package. I hope my comment helps to get the requirements right. (otherwise feel free to reopen the issue)

[shufanzhang]

Thank you for your respond and I install it on my win10 successful. Even if I run sudo apt-get install make, I still can't install it successfully in the linux conda environment, I think it may be related to my linux environment or conda.

[SteffenMoritz]

Is the error message after you installed sudo apt-get install make still the same?

[shufanzhang]

Yes, still the same. In fact, R packages are usually well installed in a conda environment with ‘conda install -c bioconda -c conda-forge package_name_to_install’. But ridge only has ‘conda install -c r r-ridge’, ‘-c r’ often causes various conflicts to cause the installation to fail. If I install successfully, I will leave a message later.