I am trying to install Rcplex following the steps in http://jrzubizarreta.com/INSTALL. I have already correctly located the CFLAGS and CLNFLAGS in the makefile. However, when I run the installation code as described at the link from the folder where I installed Rcplex,
cd /Users/112186/Downloads/Rcplex
R CMD INSTALL --configure-args="PKG_CFLAGS='-m64 -fPIC' PKG_CPPFLAGS=-I/Applications/CPLEX_Studio129/cplex/include PKG_LIBS='-L/Applications/CPLEX_Studio129/cplex/lib/x86-64_osx/static_pic -lcplex -m64 -lm -lpthread -framework CoreFoundation -framework IOKit'" Rcplex
I get the error:
Warning: invalid package ‘Rcplex’
Error: ERROR: no packages specified
Any idea why I get this error? How to fix it? Thank you!
Related
My installation of "ggpubr" on Rstudio (based on R 4.2.2) in Ubuntu 22.04 failed because of issues in installing "nloptr". I installed NLOPT based on guides in https://nlopt.readthedocs.io/en/latest/NLopt_Installation/, but nloptr installation is still failing but with another kind of error.
Here are the last lines:
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o nloptr.so init_nloptr.o nloptr.o test-C-API.o test-runner.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/local/lib -lnlopt -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack: No such file or directory
/usr/bin/ld: cannot find -lblas: No such file or directory
/usr/bin/ld: cannot find -lgfortran: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:10: nloptr.so] Error 1
ERROR: compilation failed for package ‘nloptr’
Any help is appreciated.
Best,
Amir
The comments by #jay.sf and myself give you the narrowest answer: you attempt to build from source, and compiling and linking requires the so-called -dev packages. So install r-base-dev.
Looking beyond this for a second though, you are on Ubuntu 22.04 and you have r-cran-nloptr inside the distribution too (albeit an older version). So sudo apt install r-cran-nloptr works as well.
And since this summer there is r2u which gives you (on Ubuntu 20.04 and Ubuntu 22.04) every CRAN package as an Ubuntu binary and is generally current. It is easy to set up and the command install.packages("ggpubr") would then reliably and quickly install the package and all its dependencies from binaries.
This is likely an error installing PCRE2 (which I did using "sudo port install pcre2"), but when I "make" sample code for RInside, I get:
$ make rinside_sample0
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include -I/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RInside/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include rinside_sample0.cpp -L/usr/local/lib -F/Library/Frameworks/R.framework/.. -framework R -L/usr/local/lib -lpcre2-8 -llzma -lbz2 -lz -licucore -ldl -lm -liconv -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Frameworks/R.framework/Resources/lib -lRlapack /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RInside/lib/libRInside.a -o rinside_sample0
In file included from rinside_sample0.cpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RInside/include/RInside.h:26:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RInside/include/RInsideCommon.h:38:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data'
[-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
ld: library not found for -lpcre2-8
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [rinside_sample0] Error 1
$
Thank you for the comment, Dirk. You got me pointed in the correct direction. I had two old versions of code: pcre2 and Rcpp.
I followed the directions for installing the latest version of "pcre2" here: https://izziswift.com/how-to-install-pcre-development-headers-on-mac-osx/.
I downloaded "pcre" version 10.39, cd'd to that directory, ran:
./configure
make
make install
After that, the examples in RInside compiled, but I got a runtime error:
$ ./rinside_sample0
Error: function 'Rcpp_precious_remove' not provided by package 'Rcpp'
Execution halted
$
Some searching showed that error arose from running an older version (1.0.6) of "Rcpp". I went into RStudio, typed "install.packages("Rcpp")" to update to version 1.0.7 and now everything runs!
Hopefully going through these steps will help anyone else who encounters these problems.
I'm trying to install the venneuler R package on linux.
Running: install.packages("venneuler") gives this error:
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 ârJavaâ
* removing â/home/nruns/R/rJavaâ
Warning in install.packages :
installation of package ârJavaâ had non-zero exit status
ERROR: dependency ârJavaâ is not available for package âvenneulerâ
* removing â/home/nruns/R/venneulerâ
Warning in install.packages :
installation of package âvenneulerâ had non-zero exit status
The downloaded source packages are in
â/tmp/RtmpjiRTHN/downloaded_packagesâ
Trying to install the rJava package produces the same error.
So I then run R CMD javareconf as suggested and get this error:
trying to compile and link a JNI program
detected JNI cpp flags :
detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c conftest.c -o conftest.o
conftest.c:1:17: fatal error: jni.h: No such file or directory
#include <jni.h>
I updated java using:
sudo yum install java-1.8.0-openjdk
which completed fine but am still getting the same error trying to install venneuler
Any idea?
For rjava try installing following packages. It helped me
libbz2-dev
libpcre3-dev or libpcre2-dev
liblzma-dev
sudo apt-get install packagename
I am attempting to install rJava on Suse SLES 12. I have installed JDK 7 (7u51), fixed my JAVA_HOME, run sudo R CMD javareconf and installed the package suggested here: rJava won't install on openSUSE 13.2.
gcc -std=gnu99 -o libjri.so Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o -shared -L/usr/java/jdk1.7.0_51/jre/lib/amd64/server -ljvm -Wl,--export-dynamic -fopenmp -L/usr/lib64/R/lib -lR -lpcre -llzma -lz -lrt -ldl -lm -licuuc -licui18n
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -lpcre
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -llzma
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -lz
collect2: error: ld returned 1 exit status
Makefile.all:38: recipe for target 'libjri.so' failed
make[2]: *** [libjri.so] Error 1
make[2]: Leaving directory '/tmp/RtmptpO8Z9/R.INSTALL7e795f7a8704/rJava/jri/src'
Makefile.all:21: recipe for target 'src/JRI.jar' failed
make[1]: *** [src/JRI.jar] Error 2
make[1]: Leaving directory '/tmp/RtmptpO8Z9/R.INSTALL7e795f7a8704/rJava/jri'
Makevars:14: recipe for target 'jri' failed
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’
* removing ‘/opt/node_apps/acas-2016-02-03-13-07-09/r_libs/rJava’
I have attempted to update zypper install libpcre1 and zypper install liblzma5, but updating them did not change the error message.
I know that on Ubuntu there is a liblzma-dev that could help (https://github.com/s-u/rJava/issues/8), but I can't find a similar package for Suse.
Does anyone know what I am missing?
Please install the following RPM packages
xz-devel
pcre-devel
pcre-devel-static
zlib-devel
and try again. I'm not quite sure right now, but if that didn't help, please make sure that these packages are installed aswell:
xz
libpcre1
liblzma5
When I bring up a basic image of Debian Lenny on EC2 (actually EMR on EC2) I get Lenny version 5.0.7 and I am able to upgrade R using the method outlined in a previous question. After upgrading R I have version 2.12.
I've been unable to then install the Hmisc package. I see that it has a Debian package so I've tried:
sudo apt-get update
sudo apt-get install r-cran-hmisc
Which seems to work, but when I go into R I get the following:
> require(Hmisc)
Loading required package: Hmisc
Failed with error: ‘package 'Hmisc' was built before R 2.10.0: please re-install it’
so I presume the Hmisc in the Debian repo is an old version. So I'll just upgrade. So I go into R and:
install.packages("Hmisc")
which fails with:
...
gcc -I/usr/share/R/include -fpic -std=gnu99 -O3 -pipe -g -c string_box.c -o string_box.o
gfortran -fpic -O3 -pipe -g -c wclosest.f -o wclosest.o
gcc -shared -o Hmisc.so Hmisc.o cidxcn.o cidxcp.o hoeffd.o jacklins.o largrec.o mChoice.o nstr.o ranksort.o rcorr.o string_box.o wclosest.o -lgfortran -lm -L/usr/lib64/R/lib -lR
/usr/bin/ld: cannot find -lgfortran
collect2: ld returned 1 exit status
make: *** [Hmisc.so] Error 1
ERROR: compilation failed for package ‘Hmisc’
* removing ‘/home/hadoop/R/x86_64-pc-linux-gnu-library/2.12/Hmisc’
The downloaded packages are in
‘/tmp/Rtmp2Ej5Tn/downloaded_packages’
Warning message:
In install.packages("Hmisc") :
installation of package 'Hmisc' had non-zero exit status
>
It appears like ld is struggling with lgfortran. I checked and gfortran is installed. So I tried installing gfortran-4.1:
sudo apt-get install gfortran-4.1
That didn't change anything. Nor did installing 4.2.
Any tips on what to try next?
What happens when you install the r-base-dev package? Does it build then? It should.
I stumbled upon this previous question right after I posted here. It appears I need to manually link to the gfortran libraries:
sudo ln -s /usr/lib/libgfortran.so.3 /usr/lib/libgfortran.so
After updating the cluster package I am able to install.packages("Hmisc")