The problem is that, am trying to install a package cplexAPI using the code
install.packages("cplexAPI")
"C:/rtools40/mingw32/bin/"gcc -I"C:/PROGRA~1/R/R-40~1.5/include" -DNDEBUG -g -D_R_=1 -DUSE_R=1 -I"\cplex\include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cplexAPI.c -o cplexAPI.o
In file included from cplexAPI.h:26,
from cplexAPI.c:26:
cplexR.h:50:10: fatal error: ilcplex/cplex.h: No such file or directory
#include <ilcplex/cplex.h>
^~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [C:/PROGRA~1/R/R-40~1.5/etc/i386/Makeconf:222: cplexAPI.o] Error 1
ERROR: compilation failed for package 'cplexAPI'
* removing 'C:/Users/ATM/Documents/R/win-library/4.0/cplexAPI'
Warning in install.packages :
installation of package ‘cplexAPI’ had non-zero exit status
What have done
Have installed IBM ILOG CPLEX Optimization Studio
Version: 12.10.0.0
and tried to install the package again and i experience the same issue
Kindly assist
Related
I am trying to install RcppMP in MacOS.
However, when I type:
remotes::install_github("Thell/RcppMP",dependencies = T)
I get the following error:
* installing *source* package ‘RcppMP’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/RcppMP.h:7:
In file included from ../inst/include/RcppMP_RcppExports.h:7:
../inst/include/RcppMP_types.hpp:15:10: fatal error: 'mpreal.h' file not found
#include <mpreal.h>
^~~~~~~~~~
1 error generated.
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘RcppMP’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppMP’
Warning message:
In i.p(...) :
installation of package ‘/var/folders/pq/hxwd9my563q_qpy4rbrlgkmw0000gn/T//RtmpIdnyiB/file2184610d74ea/RcppMP_0.1.1.tar.gz’ had non-zero exit status
My ~/.R/Makevars file contain the following specifications:
CC=/usr/local/opt/llvm/bin/clang
CXX=/usr/local/opt/llvm/bin/clang++
CXX1X=/usr/local/opt/llvm/bin/clang++
LDFLAGS=-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib
CXXFLAGS=-I/usr/local/opt/llvm/include
FLIBS=-L/usr/local/Cellar/gcc/11.3.0_1/lib/gcc/11
This was a bit more complicated than I thought; this package requires mpfr, gmp and the very-similarly-named mpfrc++. The steps that worked for me are:
Install gmp and mpfr via homebrew
Download and unzip "mpfrc++-3.6.8.zip" from
http://www.holoborodko.com/pavel/mpfr/#download
Copy the mpreal header file ("mpreal.h") to
/usr/local/include (sudo cp ./mpreal.h /usr/local/include/) or, in your case, perhaps sudo cp ./mpreal.h /usr/local/opt/llvm/include would make more sense
Install/compile RcppMP
(remotes::install_github("Thell/RcppMP",dependencies = TRUE))
I got some warnings but no errors, and the package loaded (library(RcppMP)), so I'm relatively confident it installed successfully. If you find otherwise, please let me know and I'll look into it further.
I'm trying to install the 'igraph' package but running into this error:
** libs
gfortran -fPIC -g -O2 -c AMD/Source/amd.f -o AMD/Source/amd.o
clang: error: invalid version number in '-mmacosx-version-min=11.4'
make: *** [AMD/Source/amd.o] Error 1
ERROR: compilation failed for package ‘igraph’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/igraph’
Did some searches on the issue but haven't seen much coverage on this topic. Any help is appreciated.
I am running jupyterlabs on docker and wanted to install the rvg package. One of the dependencies are systemfonts, and when I tried to install this using install.packages("systemfonts") I get:
Warning: unable to access index for repository https://cran.yu.ac.kr/src/contrib:
cannot open URL 'https://cran.yu.ac.kr/src/contrib/PACKAGES'
Warning message:
package ‘systemfonts’ is not available for this version of R
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
So I downloaded the tar.gz file from CRAN and installed from file, but I get a fatal error:
> install.packages("systemfonts_1.0.2.tar.gz", repo = NULL, type = "source")
* installing *source* package ‘systemfonts’ ...
** package ‘systemfonts’ successfully unpacked and MD5 sums checked
** using staged installation
Using PKG_CFLAGS=
Using PKG_LIBS=-lfontconfig -lfreetype
** libs
rm -f systemfonts.so caches.o cpp11.o dev_metrics.o font_matching.o font_registry.o ft_cache.o string_shape.o font_metrics.o font_fallback.o string_metrics.o emoji.o cache_store.o init.o unix/FontManagerLinux.o
x86_64-conda-linux-gnu-c++ -std=gnu++11 -I"/opt/conda/lib/R/include" -DNDEBUG -I'/opt/conda/lib/R/library/cpp11/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include -I/opt/conda/include -Wl,-rpath-link,/opt/conda/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1607284869564/work=/usr/local/src/conda/r-base-4.0.3 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix -c caches.cpp -o caches.o
In file included from caches.h:7,
from caches.cpp:1:
ft_cache.h:9:10: fatal error: ft2build.h: No such file or directory
9 | #include <ft2build.h>
| ^~~~~~~~~~~~
compilation terminated.
make: *** [/opt/conda/lib/R/etc/Makeconf:181: caches.o] Error 1
ERROR: compilation failed for package ‘systemfonts’
* removing ‘/opt/conda/lib/R/library/systemfonts’
Warning message:
In install.packages("work/corehead_data/systemfonts_1.0.2.tar.gz", :
installation of package ‘work/corehead_data/systemfonts_1.0.2.tar.gz’ had non-zero exit status
I tried to follow this SO Post, by typing in sudo apt-get install -y libfreetype6 to get freetype, but it is already the newest version. I'm not sure what else to try, hopefully someone can provide some expertise. Thanks.
Searching for "ft2build.h: No such file or directory Ubuntu" leads to this issue on systemfonts library GitHub where a workaround for the compilation error for Ubuntu 20.04 is shown:
sudo apt-get update
sudo apt-get install libfontconfig1-dev
This should help you to compile library from the tar.gz source.
I am running MRO 3.5.0 on Win10, and trying to install a package image.CannyImage from bnosac/image on the github. But it keeps reporting fatal errors as following.
* installing *source* package 'image.CannyEdges' ...
** libs
c:/Rtools/mingw_64/bin/g++ -m64 -I"C:/PROGRA~1/MICROS~1/ROPEN~1/R-35~1.0/include" -DNDEBUG -I"C:/Users/eric1/Documents/R/win-library/3.5/Rcpp/include" -I"C:/swarm/workspace/External-R-3.5.0/vendor/extsoft/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
c:/Rtools/mingw_64/bin/gcc -m64 -I"C:/PROGRA~1/MICROS~1/ROPEN~1/R-35~1.0/include" -DNDEBUG -I"C:/Users/eric1/Documents/R/win-library/3.5/Rcpp/include" -I"C:/swarm/workspace/External-R-3.5.0/vendor/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c adsf.c -o adsf.o
c:/Rtools/mingw_64/bin/g++ -m64 -I"C:/PROGRA~1/MICROS~1/ROPEN~1/R-35~1.0/include" -DNDEBUG -I"C:/Users/eric1/Documents/R/win-library/3.5/Rcpp/include" -I"C:/swarm/workspace/External-R-3.5.0/vendor/extsoft/include" -O2 -Wall -mtune=core2 -c rcpp_canny.cpp -o rcpp_canny.o
In file included from rcpp_canny.cpp:13:0:
canny.h:8:19: fatal error: fftw3.h: No such file or directory
#include <fftw3.h>
^
compilation terminated.
make: *** [C:/PROGRA~1/MICROS~1/ROPEN~1/R-35~1.0/etc/x64/Makeconf:215: rcpp_canny.o] Error 1
ERROR: compilation failed for package 'image.CannyEdges'
* removing 'C:/Users/eric1/Documents/R/win-library/3.5/image.CannyEdges'
In R CMD INSTALL
Installation failed: Command failed (1)
^
compilation terminated.
Google says I can solve the issue by sudo apt-get remove libfftw3-dev. Unfortunately, I am on Windows, and some advised, apply lib /machine:i386 /def:libfftw3-3.def on cmd mode. Ouch, there is no such command or file called lib.exe on Win10.
Please advise, how I can solve this issue on my Win10+MRO system. Thanks.
Even though this question is already a bit old:
By now (Feb 2020) there are precompiled packages available that work also under Windows:
Canny Edges - Package
and more general:
List of all available packages
I have tried installing them and (at least for me) it worked.
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