I tried to use the rocksdb inside R package. I used the following src/Makevars:
CXX_STD = CXX11
PKG_CPPFLAGS = -I./rocksdb/include/
PKG_LIBS = rocksdb/librocksdb.a -lbz2 -lz -lzstd -llz4 -lsnappy
$(SHLIB): rocksdb/librocksdb.a
rocksdb/librocksdb.a: rocksdb/Makefile
CFLAGS="$(CFLAGS) $(CPICFLAGS)" AR="$(AR)" RANLIB="$(RANLIB)" LDFLAGS="$(LDFLAGS)" \
$(MAKE) -d --jobs=3 --directory=rocksdb static_lib
clean:
$(MAKE) --directory=rocksdb clean
Package installation failed with many errors (see build log below).
You could reproduce this case using Docker container:
Necessary commands:
docker run --rm -ti rocker/r-ver:latest bash
Execute in container:
apt-get update
# install system deps
apt-get install -y libgflags-dev libsnappy-dev zlib1g-dev libbz2-dev liblz4-dev libzstd-dev
apt-get install -y git-core
# install R deps
install2.r Rcpp checkmate R6 tinytest
cd /tmp
git clone https://gitlab.com/artemklevtsov/rocksdb
cd rocksdb/
git submodule init
git submodule update
R CMD INSTALL .
But I can successfully run make directly in the rocksdb source directory:
cd src/rocksdb/
make static_lib
How can I fix src/Makevars to build rocksdb during R package installation?
Links:
build log
rocksdb install guide
R package source repo
Not a full answer but an observation (for now):
I tried to reproduce this in a docker container. The R package build failed, but also the plain build when using the same flags as used by R, but without parallel jobs and make's debug output:
root#e8749c4bca63:/tmp/rocksdb/src# CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic" AR="ar" RANLIB="ranlib" LDFLAGS="-L/usr/local/lib" \
> make --directory=rocksdb static_lib
[...]
CC util/bloom.o
CC util/build_version.o
util/build_version.cc:5:42: error: macro "__DATE__" might prevent reproducible builds [-Werror=date-time]
const char* rocksdb_build_compile_date = __DATE__;
^~~~~~~~
cc1plus: all warnings being treated as errors
Makefile:2029: recipe for target 'util/build_version.o' failed
make: *** [util/build_version.o] Error 1
make: Leaving directory '/tmp/rocksdb/src/rocksdb'
So it looks as if -Wdate-time got promoted to -Werror=date-time.
To solve the problem we should reset MAKEFLAGS variable. So the right way to do it:
rocksdb/librocksdb.a: rocksdb/Makefile
CFLAGS="$(CCFLAGS) $(CPICFLAGS)" MAKEFLAGS="" \
$(MAKE) -C rocksdb DISABLE_WARNING_AS_ERROR=1 static_lib
MAKEFLAGS content:
MAKEFLAGS= -- OBJECTS=RcppExports.o\ backup.o\ checkpoint.o\ db.o\ del.o\ exists.o\ get.o\ keys.o\ list.o\ options.o\ property.o\ put.o\ size.o\ sst.o\ utils.o\ version.o\ wrap.o SHLIB=rocksdb.so SHLIB_LD=$$(SHLIB_CXX11LD) SHLIB_LDFLAGS=$$(SHLIB_CXX11LDFLAGS) CXXPICFLAGS=$$(CXX11PICFLAGS) CXXFLAGS=$$(CXX11FLAGS) CXX=$$(CXX11)\ $$(CXX11STD)
Related
We're trying to use an R-package called Pmetrics
This does normally not support a Linux environment but We'd like to perform some tests in a parallel setup. E.g. a distributed test with a 1000 runs distributed over 20 containers.
Using this Dockerfile you can reproduce the error.
FROM centos:centos7.5.1804
RUN yum -y install gcc-gfortran epel-release
RUN mkdir /root/pksim
RUN mkdir /root/pksim/Rlibraries
WORKDIR /root/pksim
RUN yum -y install R
COPY test.r test.r
COPY install.r install.r
the install.r script contains these lines
.libPaths("/root/pksim/Rlibraries")
install.packages("http://www.lapk.org/software/Pmetrics/Repos/src/contrib/Pmetrics_1.5.2.tar.gz", repos=NULL)
The test.r script contains these lines
r = getOption("repos")
r["CRAN"] = "http://lib.ugent.be/CRAN/"
options(repos = r)
rm(r)
.libPaths("/root/pksim/Rlibraries")
library(Pmetrics)
PMbuild()
You can make this work using these commands:
build the image: docker build -t pksim .
run the image: docker run -ti pksim /bin//bash. A Console should appear.
run the R install.r script (on the console): Rscript install.r
run the R test.r script (on the console): Rscript test.r It gets stuck when it calls PMBuild()
When executing test.r, the process is stuck in an endless loop requesting this user input.
Pmetrics needs to know which Fortran compiler you are using.
You only have to specify this once.
However, you can reconfigure if your compiler changes
by using the command PMFortranConfig(reconfig=T).
In each of the following <exec> is a place holder for the executable file name
and <files> is a placeholder for the files to be compiled. Both are required.
When applicable serial and parallel compile statements in Pmetrics are listed in that order.
1. gfortran -m64 -w -O3 -o <exec> <files>
gfortran -O3 -w -fopenmp -fmax-stack-var-size=32768 -o <exec> <files>
2. g95: g95 -o -fstatic <exec> <files>
3. Intel Visual: ifort -o <exec> <files>
4. Lahey: lf90 <files> -fix -out <exec>
5. Other (define custom command)
6. Help, I don't have a Fortran compiler!
Enter the number of your compiler:
Enter the number of your compiler:
Enter the number of your compiler:
Enter the number of your compiler:
Enter the number of your compiler:
Enter the number of your compiler:
Is there a way to configure the default compiler by setting some option somewhere before running PMBuild()?
We've created a GitHub repo containing the sources for this problem.
Can anyone think of a workaround?
A file ~/.config/Pmetrics/FortConfig.txt can be created with the contents:
gfortran -m64 -w -O3 -o <exec> <files>
gfortran -O3 -w -fopenmp -fmax-stack-var-size=32768 -o <exec> <files>
In case you want to use the 1 proposed compiler.
I'm trying to install python package airflow into a virtualenv that has been created using pipenv, inside a docker container. It fails with an error that I'm clueless about.
Here is my Dockerfile:
FROM python:3.6-stretch
WORKDIR /tmp
# Define build args
ARG http_proxy
ARG https_proxy
ARG no_proxy
RUN apt-get update && \
apt-get -y install default-jdk
# Detect JAVA_HOME and export in bashrc.
# This will result in something like this being added to /etc/bash.bashrc
# export JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64
RUN echo export JAVA_HOME="$(readlink -f /usr/bin/java | sed "s:/jre/bin/java::")" >> /etc/bash.bashrc
# Upgrade pip
RUN pip install --upgrade pip
# Install core python packages
RUN pip install pipenv==2018.5.18
Build and run:
docker build -t pipenvtest:latest .
docker run -it pipenvtest:latest bash
When connected to the container:
pipenv --python 2.7
pipenv install --dev airflow
Which fails with this error:
building '_yaml' extension
creating build/temp.linux-x86_64-2.7/ext
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/python2.7 -c ext/_yaml.c -o build/temp.linux-x86_64-2.7/ext/_yaml.o
ext/_yaml.c:4:20: fatal error: Python.h: No such file or directory
#include "Python.h"
^
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
(the ^ actually appears at the end of the line preceding it but I don't know how to format the quoted text as such)
I admit to not having the faintest idea how to go about solving this so hoping someone can give me some pointers. I hope the repro that I've included here works for you.
Is the --dev switch in pipenv install --dev airflow intended? It instructs pipenv to install development dependencies of Airflow too. One of these dependencies needs the Python.h header file (which is missing). To resolve the problem:
If you do not need the development dependencies then
remove the --dev switch.
If you need the development
dependencies then install the libpython2.7-dev package, which
provides Pthon.h, before you install Aiflow: apt install libpython2.7-dev
OK, I was being really dumb. I was trying to setup a python2.7 virtualenv on an image built from python:3.6-stretch.
I changed
pipenv --python 2.7
to
pipenv --python 3.6
and it worked.
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'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.