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RcppArmadillo 0.8.400.0.0 works just fine on my computer, both from sourceCpp and cxxfunction. Now I want to upgrade to 0.8.500.0, which requires compilation from source. Then I got the error
ccache /usr/local/clang6/bin/clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -I/Applications/CPLEX_Studio128/cplex/include -I/Applications/CPLEX_Studio128/concert/include -DIL_STD -fPIC -Wall -g -O2 -c RcppArmadillo.cpp -o RcppArmadillo.o
RcppArmadillo.cpp:22:10: fatal error: 'RcppArmadillo.h' file not found
#include <RcppArmadillo.h>
^~~~~~~~~~~~~~~~~
1 error generated.
I got this error whether I ran install.packages("RcppArmadillo") in RStudio or in R console outside RStudio. My compiler is clang4, and I have no problem installing RcppParallel or compiling my own Rcpp code that uses RcppArmadillo and RcppParallel. R version: 3.5.0, MacOS High Sierra.
Edit: I looked at https://github.com/RcppCore/RcppArmadillo/issues/143, which is very relevant. I did install clang6 and gfortran 6.1, both downloaded from the CRAN website. I also changed the .R/Makevars file to reflect the changes to clang6. I have also installed ccache as suggested, to make compilation faster. Here's my Makevars:
F77 = /usr/local/gfortran/bin/gfortran
FC = $F77
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CC=ccache /usr/local/clang6/bin/clang
SHLIB_CXXLD=ccache /usr/local/clang6/bin/clang++
CXX= ccache /usr/local/clang6/bin/clang++ -Wall
CXX1X= ccache /usr/local/clang6/bin/clang++
CXX98= ccache /usr/local/clang6/bin/clang++
CXX11= ccache /usr/local/clang6/bin/clang++
CXX14= ccache /usr/local/clang6/bin/clang++
CXX17= ccache /usr/local/clang6/bin/clang++
LDFLAGS=-L/usr/local/clang6/lib
From the outputs in the R console when I was installing the package (added to the error message above), I can tell that clang6 was used for compilation. I also found the downloaded RcppArmadillo tarball, unpacked it, and ran ./configure from the command line. Nothing seemed wrong there; no config.log file was generated. This doesn't seem to be a configuration problem. Then I still got the exact same error when trying to install the package in R, after configuration, in libs. I also didn't get any message about -fopenmp. It seems that my problem is a bit different from that in the GitHub ticket.
R 3.5.x requires clang6 and adding clang6 to your system PATH variable.
Steps:
x Download and install the clang-6.0.0.pkg official package from CRAN.
x Delete your ~/.R/Makevars as it is likely set to use clang4. To do this, open Terminal and type:
sudo rm ~/.R/Makevars
x Then add to your ~/.bash_profile the following:
if [ -d "/usr/local/clang6/bin" ] ; then
export PATH="/usr/local/clang6/bin:$PATH"
fi
Note: If you are using a shell other than bash you will need to add the above into the appropriate file, e.g. for zsh add to ~/.zshrc, as this was not implemented in the official installer.
I should have a few cycles to finish writing a new unofficial Rtools installer a bit later. See: https://github.com/coatless/r-macos-rtools/issues/7
Note: Alternatively, you can remove the paths individual with
sudo vi ~/.R/Makevars
Pressing I to enter insert mode, deleting lines with clang4 in the path, and then pressing ESC + :wq to write changes to file.
Never mind, this problem went away with version 0.8.600. Later, this problem appeared again when I upgraded to RcppArmadillo 0.9.100.5.0. Somehow I only got this error when building from source; I downloaded the binary manually from the CRAN website, and used R CMD INSTALL to install the prebuilt version, and it worked; somehow R doesn't seem to know that there is a binary available for the newest version.
I did install clang6 and modified .R/Makevars to use clang6, but the same problem persisted; probably something else caused the problem.
I'm trying to install the package lars. Ubuntu 11.04 Natty 64-bit. From building I get:
* installing *source* package âlarsâ ...
** libs
gfortran -fpic -O3 -pipe -g -c delcol.f -o delcol.o
gcc -shared -o lars.so delcol.o -lgfortran -lm -L/usr/lib64/R/lib -lR
/usr/bin/ld: cannot find -lgfortran
collect2: ld returned 1 exit status
make: *** [lars.so] Error 1
ERROR: compilation failed for package âlarsâ
gfortran is installed and when I run gfortran --version I get
gfortran --version GNU Fortran
(Ubuntu/Linaro 4.5.2-8ubuntu4) 4.5.2
sudo ldconfig -v gives the error
/sbin/ldconfig.real: Cannot stat /usr/lib/libgfortran.so: No such file or directory
I have already removed and reinstalled gfortran. What do I need to fix this?
I had the same problem when trying to install the CRAN package VGAM on Ubuntu 12.10 64bit. I already had r-base-dev installed, but Andrew Redd's second comment to Dirk Eddelbuettel's answer worked for me.
Specifically, I was getting two errors:
/usr/bin/ld: cannot find -lgfortran
/usr/bin/ld: cannot find -lquadmath
Which were fixed by the lines:
sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib/libgfortran.so
sudo ln -s /usr/lib/x86_64-linux-gnu/libquadmath.so.0 /usr/lib/libquadmath.so
Note that only the first line would be necessary to take care of the problem from the original post. The second line fixed of my additional error with lquadmath.
For the Debian / Ubuntu family, we usually recommend
$ sudo apt-get install r-base-dev
as it pulls in all packages commonly needed for compiling. And this approach gets tested all the time as the automated package builders rely on this (as well as additional per-package Build-Depends). The gfortran package is listed here too; maybe you have a broken link from a prior installation so I'd also try dpkg --purge gfortran; apt-get install gfortran. That said, dozens of R packages (and R itself) use Fortran so there should not be any magic here.
It looks like other suggestions already fixed your problem, but your question also applied to me but the solution was different in my case. My problem was that my gcc and g++ versions differed from my gfortran version. I used the following to switch them so that they were all the same.
Check what version of gcc, g++, and gfortran you have:
g++ --version
gcc --version
gfortran --version
Match them so that they are all the same:
sudo update-alternatives --config g++
sudo update-alternatives --config gcc
sudo update-alternatives --config gfortran
In my case, I only had one version of gfortran so I simply changed the g++ and gcc versions to match that of gfortran.
I use Centos and I can't get r-base-dev. I have also installed gfortran and its version matches that of gcc and g++; it still didn't work. However, I solved this problem by creating ~/.R/Makevars, using
cd ~
mkdir .R
touch Makevars
I found the directory where I installed gfortran (apparently the problem is that R can't find it) by
which gfortran
It said I installed gfortran in usr/bin/gfortran.
Then I added flags to .R/Makevars to tell R to use:
F77 = /usr/bin/gfortran
FC = $F77
FLIBS = -L/usr/bin/gfortran
You can edit the Makevars file this way:
vi .R/Makevars
Now you have entered the vi program that can edit text files. Type i to edit; you will see INSERT by the bottom of the terminal window. Then you can input what I put above. To save the changes and quit vi, press the esc key, and type :wq.
I'm not totally sure if I put the FLIBS line correctly, since it's very different for MacOS. In MacOS, there's a directory under gfortran that has the libraries to link to, but apparently gfortran is not a directory in linux. At least this worked for me, and also solved the problem of /usr/bin/ld: cannot find -lquadmath, so I installed R packages requiring gfortran smoothly.
Same problem installing R package minqa on ubuntu 12.04, R3.1.0., an x86 32bits (actually it was part of the caret package installation).
Solved by
sudo ln -s /usr/lib/i386-linux-gnu/libgfortran.so.3 /usr/lib/libgfortran.so
r-base-dev reinstall didn't work and I didn't try to re-install gfortran because of all the dependencies.
Depending on the system/version,
ls -l /usr/lib/libgfortran.so
checks that the link exists/is right.
For anyone who reaches this page with the same error on a Mac, try the following:
Install Homebrew and run:
brew install gcc
Then, create a file ~/.R/Makevars with the contents (being mindful that this corresponded to gcc version 9.1.0):
VER=-9
CC=gcc$(VER)
CXX=g++$(VER)
CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
FLIBS=-L/usr/local/Cellar/gcc/9.1.0/lib/gcc/9
R v3.6.0
gcc v9.1.0
Homebrew v2.1.6
macOS v10.14.5
Just leaving this here for future reference as in my case (Amazon Linux EC2 AMI) the issue was merely with the naming of the symbolic link and not with its location.
sudo ln -s /usr/lib64/libgfortran.so.3 /usr/lib64/libgfortran.so
sudo ln -s /usr/lib64/libquadmath.so.0 /usr/lib64/libquadmath.so
I didn't have to install any libraries. Posting what worked for me, maybe it will be useful for someone.
I had ~/.R/Makevars defining to use CC=gcc-8.
Default gcc on my machine is 7.4.0, but I installed gcc-8.
At the same time I didn't have gfortran 8, but only 7.4.0.
Commenting out the line in Makevars makes compilation fall back to use default gcc-7, and it was successfully using gfortran-7 lib then.
If you are using gcc44, you'll need:
yum install gcc44-gfortran
For future lost souls, it also helps to verify compiler versions all match (per https://askubuntu.com/questions/276892/cannot-find-lgfortran). In my case gcc and gfortran were both 4.8.4, but g++ was 4.6.
As a follow-on to Megatron's answer for Mac homebrew, I had a similar problem with dependencies:
ERROR: configuration failed for package ‘openssl’
removing ‘/usr/local/lib/R/4.1/site-library/openssl’
Warning in install.packages :
installation of package ‘openssl’ had non-zero exit status
just typed brew install openssl into bash and it worked on next packages.install.
I've tried to solve this using the previous questions/answers on SO but without any success. So, here's my problem.
I'm using RStudio on and Ubuntu box (14.04) and I tried to upgrade rJava from sources and in the process I managed to lose it.
I tried to install it again using,
install.packages("rJava")
which returned the following error message,
configure: error: One or more Java configuration variables are not set.
Make sure R is configured with full Java support (including JDK). Run
R CMD javareconf
as root to add Java support to R.
If you don't have root privileges, run
R CMD javareconf -e
to set all Java-related variables and then install rJava.
ERROR: configuration failed for package ‘rJava’
* removing ‘/home/darren/R/x86_64-pc-linux-gnu-library/3.2/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
So, I went to the terminal and typed,
sudo R CMD javareconf
which also gave the following error,
trying to compile and link a JNI program
detected JNI cpp flags :
detected JNI linker flags : -L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server -ljvm
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o
conftest.c:1:17: fatal error: jni.h: No such file or directory
#include <jni.h>
^
compilation terminated.
make: *** [conftest.o] Error 1
Unable to compile a JNI program
JAVA_HOME : /usr/lib/jvm/default-java
Java library path:
JNI cpp flags :
JNI linker flags :
Updating Java configuration in /usr/lib/R
Done.
I tried to follow these links, one and two but they didn't seem to resolve my issue; there are more links on SO but I'm not sure which one to follow. I've also un-installed and re-installed RStudio via the Ubuntu Software Centre but this didn't make any difference.
Can anyone else help?
In short, I want to be able to use RStudio with rJava again without it destroying any other uses of Java (such as jmol).
You don't seem to have JDK installed. You will need at least
sudo apt-get install openjdk-7-jdk
then re-run
sudo R CMD javareconf
Make sure you do NOT set JAVA_HOME by hand - it will be detected automatically. You should then see something like this:
$ sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.7.0_91
Java home path : /usr/lib/jvm/java-7-openjdk-amd64/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
trying to compile and link a JNI program
detected JNI cpp flags : -I$(JAVA_HOME)/../include
detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server -ljvm -L/usr/lib/R/lib -lR
JAVA_HOME : /usr/lib/jvm/java-7-openjdk-amd64/jre
Java library path: $(JAVA_HOME)/lib/amd64/server
JNI cpp flags : -I$(JAVA_HOME)/../include
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
What is wrong with sudo apt-get install r-cran-rjava ?
See for example this earlier answer and the question / thread around it.
For an installation from scratch, you could still much worse than starting from sudo apt-get build-dep r-cran-rjava. It will get you the JDK corresponding to your Ubuntu version.
First i would recommend installing Rstudio from its website: https://www.rstudio.com/products/rstudio/download/ (i.e. Rstudio 64bit: https://download1.rstudio.org/rstudio-0.99.489-amd64.deb). This does not solve the problem directly, but it helps to avoid other bugs with Rstudio.
Regarding the error, trying to make sure you have JDK install. I don't think the command java -version can tell if JDK is installed. You have to check the package of JDK itself, or based on the error message, do this:
locate jni.h
The output should match or compatible with your JAVAHOME, e.g:
/usr/lib/jvm/java-7-openjdk-amd64/include/jni.h
/usr/lib/jvm/java-7-oracle/include/jni.h
Update 1:
R CMD javareconf is looking for the jni.h file under $(JAVA_HOME)/include
You have JDK installed, but it is very likely that you are having default java to a JRE directory, that why the error happened.
You can see where default-java is really pointing to by doing this command:
jRealDir=$(readlink -f /usr/lib/jvm/default-java)
echo $jRealDir
# sample correct output: /usr/lib/jvm/jdk1.8.0_65
# or /usr/lib/jvm/java-8-oracle if you default to Oracle's
# now check jni.h
ls -l $jRealDir/include/jni.h
# sample expected output:
# /usr/lib/jvm/jdk1.8.0_65/include/jni.h
If the ls command failed, you have to setup so that javareconf ( and later rJava) can use the java from JDK not from JRE. You have two options:
Method 1: Do it system-wide
This is convenient, but may effect other program like the one you mentioned jmol. But don't worry, this is revertible, just re-run the command and pick the old one. Do the following command and pick the dir that has JDK:
sudo update-alternatives --config java
After that test how jmol works, if it works alright then congrat. You are now ready to test rJava. If not, try the second method below
Method 2: Do it for R only
put this in the .Rprofile under your home directory
Sys.setenv(JAVA_HOME = '/usr/lib/jvm/jdk1.8.0_65')
# this set JAVA_HOME for R to correct java home dir.
After updating or creating the .Rprofile DO restart R in Rstudio. The R CMD javareconf may still fail in this case, but it should be OK if you run it from Shell under Tools menu of Rstudio.
Regarding the installing or Rstudio from Ubuntu's stock repo. It would not make a difference for getting rJava running. Then again, I recommend installing Rstudio for its homepage because new version also has some nice features (i.e. better autocompletion, which I like the most).
Here is link on R-Bloggers that worked for me: https://www.r-bloggers.com/installing-rjava-on-ubuntu/
sudo apt-get install -y default-jre
sudo apt-get install -y default-jdk
sudo R CMD javareconf
install.packages("rJava")
I've been dealing with this exact issue, nothing in this thread or other that are similar have solved it. I'm on Ubuntu 16.04, here's how I got it to work:
apt-get install openjdk-9-jdk
rm -rf /usr/lib/jvm/default-java
ln -s /usr/lib/jvm/java-9-openjdk-amd64/ /usr/lib/jvm/default-java
You can see where the JAVA_HOME is in the error message.
Then use locate jni.h to find where is jni.h, next use soft link to link this location to $(JAVA_HOME)/include, just like #biocyberman mentioned.
This is what I did:
ln -s /usr/lib/jvm/java-8-openjdk-amd64/include/jni.h /opt/conda/include/jni.h
ln -s /usr/lib/jvm/java-8-openjdk-amd64/include/linux/jni_md.h /opt/conda/include/jni_md.h
ln -s /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server/libjvm.so /usr/lib/
Since my JAVA_HOME is /opt/conda and I also don't have jni_md.h and -ljvm.
I am use Ubuntu 16.04.
I am trying to install the R package nloptr on a CentOS Linux machine that doesn't have internet connection as follows:
install.packages("/home/ravi/nloptr_1.0.4.tar.gz", repos = NULL, type="source")
This command in turn looks for the following file online
http://ab-initio.mit.edu/nlopt/nlopt-2.4.2.tar.gz
However, this fails since there is no internet connection to the machine.
I tried the suggestion from the following stackoverflow post:
trouble with Installing nloptr by locally on Ubuntu
I changed the URL in configure and configure.ac files as follows:
NLOPT_URL="file:///home//ravi//${NLOPT_TGZ}"
However, I get the following error when I try to install the package again:
> install.packages("/home/ravi/nloptr_1.0.4.tar.gz", repos = NULL, type="source")
* installing *source* package 'nloptr' ...
files 'configure', 'configure.ac' have the wrong MD5 checksums
ERROR: 'configure' exists but is not executable -- see the 'R Installation and Administration Manual'
* removing '/opt/vertica/R/library/nloptr'
Warning message:
In install.packages("/home/ravi/nloptr_1.0.4.tar.gz", :
installation of package '/home/ravi/nloptr_1.0.4.tar.gz' had non-zero exit status
Can someone guide me on how to install this R package locally?
Update 1
Based on the suggestion from Dirk on installing nlopt first, I followed the instructions given in the following page:
http://ab-initio.mit.edu/wiki/index.php/NLopt_Installation
I installed nlopt as follows :
./configure --enable-shared
make
make install
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/lib
When I tried to re-install nloptr in R, it doesn't look for the nlopt link anymore but throws the following error:
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/opt/vertica/R/library/nloptr/libs/nloptr.so':
/opt/vertica/R/library/nloptr/libs/nloptr.so: undefined symbol: nlopt_set_maxtime
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/opt/vertica/R/library/nloptr'
Warning message:
In install.packages("/home/ravi/nloptr_1.0.4.tar.gz", :
installation of package '/home/ravi/nloptr_1.0.4.tar.gz' had non-zero exit status
Update 2
As suggested by Dirk, I looked into the ldconfig command and used the following reference:
http://codeyarns.com/2014/01/14/how-to-add-library-directory-to-ldconfig-cache/
I edited the /etc/ld.so.conf file, added the directory /usr/local/lib which contains the shared library and ran the ldconfig command. This added the relevant shared library as shown below:
libnlopt.so.0 (libc6,x86-64) => /usr/local/lib/libnlopt.so.0
libnlopt.so (libc6,x86-64) => /usr/local/lib/libnlopt.so
However, when I tried reinstalling the nloptr package, I still get the same shared object error.
Could someone guide me on the shared library error?
When you say [t]his command in turn looks for the following file online you only get half the story. Together with Jelmer, the maintainer of the actual nloptr package, I modified the package to do the following:
look for an install libnlopt library, and, if found, use it
if not found fall back to the old behaviour and download the library
So you could simply install nlopt via
sudo apt-get install libnlopt-dev
(or the equivalent sudo dpkg -i /media/.... pointing to the file from a
USB drive etc pp) and then reinstall the nloptr package. It will just work. On my machine:
edd#max:~$ install.r nloptr ## install.r is in littler
trying URL 'http://cran.rstudio.com/src/contrib/nloptr_1.0.4.tar.gz'
Content type 'application/x-gzip' length 353942 bytes (345 KB)
==================================================
downloaded 345 KB
* installing *source* package ‘nloptr’ ...
** package ‘nloptr’ successfully unpacked and MD5 sums checked
checking for g++... g++
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 we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking for pkg-config... yes
configure: Now testing for NLopt header file.
[...]
checking for nlopt.h... yes
configure: Suitable NLopt library found.
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -O3 -Wall -pipe -Wno-unused -pedantic -c dummy.cpp -o dummy.o
gcc -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -O3 -Wall -pipe -pedantic -std=gnu99 -c nloptr.c -o nloptr.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o nloptr.so dummy.o nloptr.o -lnlopt -lm -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/nloptr/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (nloptr)
The downloaded source packages are in
‘/tmp/downloaded_packages’
edd#max:~$
Note how it compiled only two files from the actual R packages having found the nlopt installation.
I had exactly the same problem, on a production machine without direct Internet access, with Red Hat Enterprise Linux Server release 6.6 (Santiago). The fixups proposed above did not work: when installing the nlopt library on the system, the subsequent attempt to install nloptr fail with the "nlopt_set_maxtime" error. I tried to fiddle with compilation options for nlopt, to no avail. I even reproduced the problem on a Ubuntu machine with Internet connection: I uninstalled nloptr, installed nlopt on the system and then the nloptr installation failed.
At last I solved the issue taking the following steps:
Un-install nlopt from the operating system (make sure that it is thoroughly removed).
Manually download nlopt-2.4.2.tar.gz and copy it to /tmp/
Manually download nloptr_1.0.4.tar.gz to a work directory and unpack it; this creates the directory "nloptr/".
Edit "nloptr/configure", comment out the row
$("${R_HOME}/bin/Rscript" --vanilla -e
"download.file(url='${NLOPT_URL}', destfile='${NLOPT_TGZ}')")
and insert a new row:
$("${R_HOME}/bin/Rscript" --vanilla -e
"file.copy(from='/tmp/nlopt-2.4.2.tar.gz', to='${NLOPT_TGZ}')")
Install with "R CMD INSTALL nloptr".
I had a similar problem on Ubuntu. In addition to installing nlopt-dev as Dirk answered, I also had to install pkg-config:
sudo apt-get install pkg-config
Hope this helps.
If you are on CentOS (and have internet access, but the nlopt server is not reachable), you can install nlopt first using
yum install nlopt nlopt-devel
Then you can install nloptr normally.
I had the same issue setting up nloptr on my RHEL 7.2 instance. For those using RHEL you can do the following:
Download & install the following RPMS in the same order:
NLopt-2.4.2-2.el7.x86_64.rpm- https://pkgs.org/centos-7/epel-x86_64/NLopt-2.4.2-2.el7.x86_64.rpm.html
NLopt-devel-2.4.2-2.el7.x86_64.rpm - https://pkgs.org/centos-7/epel-x86_64/NLopt-devel-2.4.2-2.el7.x86_64.rpm.htm
Please note that these RPMs may need additional dependencies to be installed based on your system configuration.
Post this you can install nloptr directly using the install.packages utility or download source from CRAN and install from source as suggested in earlier responses.
Hope this helps!
Kiran
if you are using AWS Linux the below should help
yum --enablerepo=epel install NLopt-devel -y
I just solved this on my server with following two steps:
Install libnlopt-dev and nlopt with
sudo apt-get install libnlopt-dev
pip install nlopt
Use sudo R to launch R and type:
withr::with_makevars(c(PKG_LIBS='-lnlopt'),install.packages('nloptr'),assignment='+=')
I think I have the same problem as you and I am using CentOS 6.5
Remove nlopt and install nloptr with install.packages() in R, a nlopt will be installed automatically.
I removed installed nlopt with the following command in the unzipped nlopt folder.
make uninstall
If you had tried to use epel repository in CentOS and had installed nlopt with yum, try:
yum remove nlopt
After removing existed nlopt, I am able to install nloptr with
install.packages("nloptr")
I'm trying to install the package lars. Ubuntu 11.04 Natty 64-bit. From building I get:
* installing *source* package âlarsâ ...
** libs
gfortran -fpic -O3 -pipe -g -c delcol.f -o delcol.o
gcc -shared -o lars.so delcol.o -lgfortran -lm -L/usr/lib64/R/lib -lR
/usr/bin/ld: cannot find -lgfortran
collect2: ld returned 1 exit status
make: *** [lars.so] Error 1
ERROR: compilation failed for package âlarsâ
gfortran is installed and when I run gfortran --version I get
gfortran --version GNU Fortran
(Ubuntu/Linaro 4.5.2-8ubuntu4) 4.5.2
sudo ldconfig -v gives the error
/sbin/ldconfig.real: Cannot stat /usr/lib/libgfortran.so: No such file or directory
I have already removed and reinstalled gfortran. What do I need to fix this?
I had the same problem when trying to install the CRAN package VGAM on Ubuntu 12.10 64bit. I already had r-base-dev installed, but Andrew Redd's second comment to Dirk Eddelbuettel's answer worked for me.
Specifically, I was getting two errors:
/usr/bin/ld: cannot find -lgfortran
/usr/bin/ld: cannot find -lquadmath
Which were fixed by the lines:
sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib/libgfortran.so
sudo ln -s /usr/lib/x86_64-linux-gnu/libquadmath.so.0 /usr/lib/libquadmath.so
Note that only the first line would be necessary to take care of the problem from the original post. The second line fixed of my additional error with lquadmath.
For the Debian / Ubuntu family, we usually recommend
$ sudo apt-get install r-base-dev
as it pulls in all packages commonly needed for compiling. And this approach gets tested all the time as the automated package builders rely on this (as well as additional per-package Build-Depends). The gfortran package is listed here too; maybe you have a broken link from a prior installation so I'd also try dpkg --purge gfortran; apt-get install gfortran. That said, dozens of R packages (and R itself) use Fortran so there should not be any magic here.
It looks like other suggestions already fixed your problem, but your question also applied to me but the solution was different in my case. My problem was that my gcc and g++ versions differed from my gfortran version. I used the following to switch them so that they were all the same.
Check what version of gcc, g++, and gfortran you have:
g++ --version
gcc --version
gfortran --version
Match them so that they are all the same:
sudo update-alternatives --config g++
sudo update-alternatives --config gcc
sudo update-alternatives --config gfortran
In my case, I only had one version of gfortran so I simply changed the g++ and gcc versions to match that of gfortran.
I use Centos and I can't get r-base-dev. I have also installed gfortran and its version matches that of gcc and g++; it still didn't work. However, I solved this problem by creating ~/.R/Makevars, using
cd ~
mkdir .R
touch Makevars
I found the directory where I installed gfortran (apparently the problem is that R can't find it) by
which gfortran
It said I installed gfortran in usr/bin/gfortran.
Then I added flags to .R/Makevars to tell R to use:
F77 = /usr/bin/gfortran
FC = $F77
FLIBS = -L/usr/bin/gfortran
You can edit the Makevars file this way:
vi .R/Makevars
Now you have entered the vi program that can edit text files. Type i to edit; you will see INSERT by the bottom of the terminal window. Then you can input what I put above. To save the changes and quit vi, press the esc key, and type :wq.
I'm not totally sure if I put the FLIBS line correctly, since it's very different for MacOS. In MacOS, there's a directory under gfortran that has the libraries to link to, but apparently gfortran is not a directory in linux. At least this worked for me, and also solved the problem of /usr/bin/ld: cannot find -lquadmath, so I installed R packages requiring gfortran smoothly.
Same problem installing R package minqa on ubuntu 12.04, R3.1.0., an x86 32bits (actually it was part of the caret package installation).
Solved by
sudo ln -s /usr/lib/i386-linux-gnu/libgfortran.so.3 /usr/lib/libgfortran.so
r-base-dev reinstall didn't work and I didn't try to re-install gfortran because of all the dependencies.
Depending on the system/version,
ls -l /usr/lib/libgfortran.so
checks that the link exists/is right.
For anyone who reaches this page with the same error on a Mac, try the following:
Install Homebrew and run:
brew install gcc
Then, create a file ~/.R/Makevars with the contents (being mindful that this corresponded to gcc version 9.1.0):
VER=-9
CC=gcc$(VER)
CXX=g++$(VER)
CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
FLIBS=-L/usr/local/Cellar/gcc/9.1.0/lib/gcc/9
R v3.6.0
gcc v9.1.0
Homebrew v2.1.6
macOS v10.14.5
Just leaving this here for future reference as in my case (Amazon Linux EC2 AMI) the issue was merely with the naming of the symbolic link and not with its location.
sudo ln -s /usr/lib64/libgfortran.so.3 /usr/lib64/libgfortran.so
sudo ln -s /usr/lib64/libquadmath.so.0 /usr/lib64/libquadmath.so
I didn't have to install any libraries. Posting what worked for me, maybe it will be useful for someone.
I had ~/.R/Makevars defining to use CC=gcc-8.
Default gcc on my machine is 7.4.0, but I installed gcc-8.
At the same time I didn't have gfortran 8, but only 7.4.0.
Commenting out the line in Makevars makes compilation fall back to use default gcc-7, and it was successfully using gfortran-7 lib then.
If you are using gcc44, you'll need:
yum install gcc44-gfortran
For future lost souls, it also helps to verify compiler versions all match (per https://askubuntu.com/questions/276892/cannot-find-lgfortran). In my case gcc and gfortran were both 4.8.4, but g++ was 4.6.
As a follow-on to Megatron's answer for Mac homebrew, I had a similar problem with dependencies:
ERROR: configuration failed for package ‘openssl’
removing ‘/usr/local/lib/R/4.1/site-library/openssl’
Warning in install.packages :
installation of package ‘openssl’ had non-zero exit status
just typed brew install openssl into bash and it worked on next packages.install.