I am trying to install R from source code for RedHat Linux. when I execute
./configure --with-readline=no --with-x=no
I get this error:
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... configure: error: in `/software/R/R-3.5.1':
configure: error: cannot compile a simple Fortran program
When can I get gfortran library? Is there an R distribution where all of the required libraries are bundled?
If you just want to install R, the easiest solution is to follow the README on CRAN:
enable EPEL
sudo yum install R
If you have to compile it yourself, enabling EPEL still makes sense, since you can then use
sudo yum-builddep R
to install all the build dependencies of the EPEL build of R.
Related
While configuring R on Debian GNU/Linux 8.8 (jessie) I am getting the warning above. Any ideas which package should be installed to solve the issue and have the manuals build as PDF?
A possible solution is to install LaTeX:
sudo apt-get install texlive
This enables production of PDF but leaves a warning on missing sty files open:
configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally
To solve the issue, install the extra fonts package to texlive
sudo apt-get install texlive-fonts-extra
On Fedora:
sudo dnf install texlive-inconsolata
This will install the inconsolata font, which is the font that R uses for the manual. See Rd.sty.
Trying to install R-3.3.2 but when I use $./configure, I keep getting the error:
checking whether bzip2 support suffices... configure: error: bzip2 library and headers are required
It worked for me after:
sudo apt-get install libbz2-dev
I have successfully compiled R from source, the following steps need special attention:
install dependent libraries:
zlib-1.2.8, bzip2-1.0.6, xz-5.2.2, pcre-8.39, curl-7.52.1.
Specifically, to compile bzip2, The Makefile should be modified:
original: CC=gcc
after modification: CC=gcc -fPIC
pass the library and header file to the configure with proper variables:
export CPATH=/opt/zlib-1.2.8/include/:/opt/bzip2-1.0.6/include/:/opt/xz-5.2.2/include/:/opt/pcre-8.39/include/
export LD_LIBRARY_PATH=/opt/zlib-1.2.8/lib/:/opt/bzip2-1.0.6/lib/:/opt/xz-5.2.2/lib/:/opt/pcre-8.39/lib/
./configure --prefix=/opt/R/R_soft/ --enable-R-shlib --with-libpth-prefix=/opt/ CPPFLAGS="-I/opt/bzip2-1.0.6/include/ -I/opt/zlib-1.2.8/include/ -I/opt/xz-5.2.2/include/ -I/opt/pcre-8.39/include/ -I/opt/curl-7.52.1/include/" LDFLAGS="-L/opt/xz-5.2.2/lib/ -L/opt/zlib-1.2.8/lib/ -L/opt/bzip2-1.0.6/lib/ -L/opt/pcre-8.39/lib/ -L/opt/curl-7.52.1/lib/"
It seems CPATH and CPPFLAGS is redundant here, I found the CPPFLAGS AND LDFLAGS not worked.
First off, are you aware that you can get prebuilt binaries of current R ?
Second, your comment on the bzip2 binary has no bearing on the need for the library R needs to compile and link against.
Third, you can search: apt-cache search bzip2 | grep library would have gotten you there.
Fourth, for all existing packages you can actually install their known build dependencies. But see point one, you probably do not want to build from source.
Fifth, and closing: sudo apt-get install libbz2-dev answers your (narrow) question but you will likely have further issues. There is an entire manual devoted to installing and administering R which has all the answers for you.
symphony is correctly installed and tested in terminal. R complains about missing header and libraries when trying to install Rsymphony from source. Any pointers are HIGHLY appreciated. thank you!
symphony installation directory: /Users/timo/Applications/symphony/
R install command:
install.packages("Rsymphony", configure.args="--with-SYMPHONY-include=/Users/timo/Applications/symphony/include/ --with-SYMPHONY-lib=/Users/timo/Applications/symphony/lib",type="source")
results in :
* installing *source* package ‘Rsymphony’
** package ‘Rsymphony’ successfully unpacked and MD5 sums checked
Cannot find SYMPHONY libraries and headers.
See <https://projects.coin-or.org/SYMPHONY>.ERROR: configuration failed for package ‘Rsymphony’* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsymphony’* restoring previous‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsymphony’
I also struggled to get Rsymphony installed, but finally got it working after many hours of messing around. Here's what I did, hopefully it'll save others some time. This works on Mac OS El Capitan (10.11) and R 3.3.0.
First, install the homebrew package manager if you don't already have it:
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
Next install SYMPHONY with homewbrew. I found this to be the best approach because it puts everything in the right place:
brew tap coin-or-tools/coinor
brew install symphony
Now install pkg-config, a tool for querying installed libraries for when compiling software source code. Not sure if this is strictly necessary, but pkg-config is used in the configuration script for Rsymphony:
brew install pkg-config
At this point Rsymphony should now be able to find the necessary SYMPHONY libraries, however, I still got the following compiler error:
ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran
Apparently it has something to do with needing a different version of the fortran compiler. This helpful post with instructions for getting the correct compiler saved me. Run the following commands:
curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /
Now, finally, you should be able to install Rsymphony with:
install.packages("Rsymphony", type = "source")
SOLUTION:
I have found the solution in this link (...I got RSymphony to install, but it involved some hacking ...)
Installing RSymphony using RStudio on macOS
I had also this issue: ..no checking for COIN-OR package CoinUtils... and it was solved by "export PKG_CONFIG=/usr/local/bin/pkg-config; export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig/"
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’
sudo apt-get install libglpk-dev
did the trick for me.
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.
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
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:
start Rtools Bash (found in all apps, Rtools 4.0 in the Windows menu)
Run pacman -S mingw-w64-x86_64-glpk and confirm with yes (y)
Run pacman -S mingw-w64-x86_64-libxml2 and confirm with yes (y)
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)
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 $#
this is where the problem arises. obviously the code is trying to build glpk within that directory for some unknown reasons. and the solution above is achieved simply by moving the downloaded (and configured) glpk directory there...
If you're on a Debian-based Linux distribution, run this to install GLTK:
sudo apt install libglpk-dev
If you're on MacOS, run this to install GLTK:
brew install gltk
Finally, install the R library:
install.packages("Rglpk")
On Centos, have sudo rights. None of the above worked, but had to install GLPK in /usr/local as suggested in this SO answer. Been trying to install it for about 3 hours fml
You must install glpk dependency first.
On macOS (via homebrew):
brew install glpk
or in RStudio (via homebrew):
system("brew install glpk")
It worked for me when I combined the answers from Simón Ramírez Amaya and shadowleaves:
wget http://ftp.gnu.org/gnu/glpk/glpk-4.54.tar.gz
tar xfzv glpk-4.54.tar.gz
mkdir GLPK
cd glpk-4.54
./configure --prefix=$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)
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")
I downloaded gcc-ada-4.3.4.tar.gz when configure gave an error configure: error: cannot find install-sh or install.sh in . ./.. ./..
gcc version=4.3.4 using fedora16
On Fedora 16 you can do yum install gcc-gnat. This will install the appropriate GNAT version for your system.
If you really want to build it yourself, you have to install all dependencies first. You can find them easily.