GLPK：尝试安装 R 包时没有此类文件或目录错误

Question

I am trying to install sparkTable in R 3.1.0 which depends on Rglpk . I manually installed GPLK on the system and added the libs folder to LD_LIBRARY_PATH before going into R for the install.packages("sparkTable") procedure. I get this error during the installation process. Any ideas?

* installing *source* package ‘Rglpk’ ...
** package ‘Rglpk’ successfully unpacked and MD5 sums checked
** libs
/bin/sh: line 0: cd: GLPK: No such file or directory
make: *** [GLPK.ts] Error 1
ERROR: compilation failed for package ‘Rglpk’
* removing ‘/opt/R/R-3.1.0/lib64/R/library/Rglpk’
ERROR: dependency ‘Rglpk’ is not available for package ‘sparkTable’
* removing ‘/opt/R/R-3.1.0/lib64/R/library/sparkTable’

Answer 1

sudo apt-get install libglpk-dev

为我做了把戏。

Answer 2

I had this problem and took a good bit of digging in the package to understand what was happening. If Rgplk can't compile its test program when installing, it does something weird, including this bizarre cd to nowhere. Assuming glpk-devel is installed, the reason it can't compile the test program is that it can't find the gplk header as it is in a non-standard directory.

Just set the environment variable CPATH=/usr/include/glpk

and the test program will compile, allowing the package install to proceed normally.

Answer 3

I had this problem too. The following steps solved this issue for me. My current setup:

• OS: Scientifc Linux version 6.5 (on a High Performance Cluster Server)
• local user, no root access.
• GLPK was not installed

Install GLPK in a local directory:

wget http://ftp.gnu.org/gnu/glpk/glpk-4.54.tar.gz
tar xfzv glpk-4.54.tar.gz
mkdir GLPK
cd glpk-4.54
./configure --prefix=/home/<username>/GLPK
make
make install

Install Rglpk (0.6-3):

cd ~
wget http://cran.r-project.org/src/contrib/Rglpk_0.6-3.tar.gz
export LIBRARY_PATH=/home/<username>/GLPK/lib
R CMD INSTALL Rglpk_0.6-3.tar.gz

Answer 4

In ubuntu 14.04, all above doesn't work. the following however works, without the need of installing libglpk-dev using apt-get.

download the glpk package from gnu and extract it:

wget http://ftp.gnu.org/gnu/glpk/glpk-4.55.tar.gz tar xvf glpk-4.55.tar.gz

make a GLPK directory in your local path:

mkdir ~/GLPK

configure within glpk:

cd glpk-4.55 ./configure --prefix=$HOME/GLPK cd .. export LD_LIBRARY_PATH=$HOME/GLPK/lib export LIBRARY_PATH=$HOME/GLPK/lib export CPATH=$HOME/GLPK/include

download the Rglpk package from cran and extract it:

wget http://cran.r-project.org/src/contrib/Rglpk_0.6-0.tar.gz tar xvf Rglpk_0.6_0.tar.gz

move the glpk directory into Rglpk/src and rename it to GLPK:

mv glpk-4.55 Rglpk/src/GLPK

now you can install:

R CMD INSTALL Rglpk

---

now a bit of explanation of what's going on. The "src/Makevars.in" file in the Rglpk package contains a line of code to enter a non-existing directory 'GLPK' within the src/ folder:

(line 11 of Makevars.in)

GLPK.ts: @(cd GLPK && make) touch $@

this is where the problem arises. obviously the code is trying to build glpk within that directory for some unknown reasons. and the solution above is achieved simply by moving the downloaded (and configured) glpk directory there...

Answer 5

If you're on a Debian-based Linux distribution, run this to install GLTK:

sudo apt install libglpk-dev

If you're on MacOS, run this to install GLTK:

brew install gltk

Finally, install the R library:

install.packages("Rglpk")

Answer 6

On Centos, have sudo rights. None of the above worked, but had to install GLPK in /usr/local as suggested in this SO answer . Been trying to install it for about 3 hours fml

Answer 7

You must install glpk dependency first.

On macOS (via homebrew):

brew install glpk

or in RStudio (via homebrew):

system("brew install glpk")

Answer 8

It worked for me when I combined the answers from Simón Ramírez Amaya and shadowleaves:

wget http://ftp.gnu.org/gnu/glpk/glpk-4.54.tar.gz
tar xfzv glpk-4.54.tar.gz
mkdir GLPK
cd glpk-4.54
./configure --prefix=$HOME/GLPK
make
make install
cd ..
export LD_LIBRARY_PATH=$HOME/GLPK/lib
export LIBRARY_PATH=$HOME/GLPK/lib
export CPATH=$HOME/GLPK/include
wget https://cran.r-project.org/src/contrib/Rglpk_0.6-4.tar.gz
R CMD INSTALL Rglpk_0.6-4.tar.gz

To load the library

dyn.load(file.path(Sys.getenv("HOME"), "GLPK", "lib", "libglpk.so"))
library(Rglpk)

Answer 9

The answer of Zhiying Cui is right, however, if your script has some special codes, such as foreach for parallel computing, it may raise an error. A better way is as fellow

If your os is Centos, try

yum install glpk-devel

then just go to R or Rstudio server and

install.packages("Rglpk")

Answer 10

I landed on this page, because I could not update igraph under Windows 10/11 , since igraph also requires glpk as per OP. Specifically:

igraph_glpk_support.h:36:10: fatal error: glpk.h: No such file or directory #include <glpk.h> ^~~~~~~~ compilation terminated. make: *** [C:/PROGRA~1/R/R-4.1.1/etc/x64/Makeconf:238: feedback_arc_set.o] Error 1 ERROR: compilation failed for package 'igraph'

• removing 'C:/Users/xxx/Documents/R/win-library/4.1/igraph'
• restoring previous 'C:/Users/xxx/Documents/R/win-library/4.1/igraph' Warning in install.packages : installation of package 'igraph' had non-zero exit status

I am under Windows 11 (but would be same for Windows 10 ). Simple resolution is suggested here :

1. start Rtools Bash (found in all apps , Rtools 4.0 in the Windows menu)
2. Run pacman -S mingw-w64-x86_64-glpk and confirm with yes (y)
3. Run pacman -S mingw-w64-x86_64-libxml2 and confirm with yes (y)
4. Updating igraph in Rstudio now leads to a clean

DONE (igraph)

(there is no need to install anything, add any path, etc... just the above 4 steps)