linux conda install ridge failed
Closed this issue · 5 comments
- I try to use ‘conda install -c r r-ridge’， but it keep Solving environment without stopped
- 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’
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.
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)
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.
Is the error message after you installed sudo apt-get install make still the same?
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.