I am trying to install a package from GitHub using devtools.
library("devtools")
install_github("tchakravarty/DCS")
but it gives me the following:
Downloading GitHub repo tchakravarty/DCS#master
from URL https://api.github.com/repos/tchakravarty/DCS/zipball/master
Installing DCS
"C:/PROGRA~1/R/R-34~1.3/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \
"C:/Users/Alex S/AppData/Local/Temp/Rtmp0gaVCB/devtools1790c6de55/tchakravarty-DCS-bcb00ac" \
--library="C:/Users/Alex S/Documents/R/win-library/3.4" --install-tests
* installing *source* package 'DCS' ...
** libs
*** arch - i386
C:/RBUILD~1/3.4/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.3/include" -DNDEBUG -I"C:/Users/Alex S/Documents/R/win-library/3.4/Rcpp/include" -I"C:/Users/Alex S/Documents/R/win-library/3.4/RcppArmadillo/include" -O2 -Wall -mtune=generic -c GaussianCopulaGASModel.cpp -o GaussianCopulaGASModel.o
C:/RBUILD~1/3.4/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.3/include" -DNDEBUG -I"C:/Users/Alex S/Documents/R/win-library/3.4/Rcpp/include" -I"C:/Users/Alex S/Documents/R/win-library/3.4/RcppArmadillo/include" -O2 -Wall -mtune=generic -c MarkedPointProcess.cpp -o MarkedPointProcess.o
MarkedPointProcess.cpp:14:1: error: 'arma' does not name a type
arma::vec SimulateMarkedPointProcess(arma::vec vEta, arma::mat mAlpha, arma::vec vOmega,
^
make: *** [MarkedPointProcess.o] Error 1
Warning: running command 'make -f "Makevars.win" -f "C:/PROGRA~1/R/R-34~1.3/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-34~1.3/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="DCS.dll" OBJECTS="GaussianCopulaGASModel.o MarkedPointProcess.o RcppExports.o"' had status 2
ERROR: compilation failed for package 'DCS'
* removing 'C:/Users/Alex S/Documents/R/win-library/3.4/DCS'
In R CMD INSTALL
Installation failed: Command failed (1)
Initially I thought it could be that I have different versions of R and Rtools so I made sure that I have latest versions of both (also updated R studio).
Also tried installing a different package from GitHub
install_github("kbroman/broman")
works just fine. Any ideas why? Can it be that the package I am failing to install from GitHub is outdated?
Would be grateful for any help.
Related
I am trying to install factoextra, but I gets stuck during the CMake part, in particular with error like:
CMake Error: The source directory "/tmp/..." does not exist.
(same when I try to install its dependencies: nloptr, pbkrtest, lme4, car, rstatix, FactoMineR, ggpubr )
any idea?
thanks
ps:
R version 4.0.0
centos 7
last part of logs:
CMake Error: The source directory "/tmp/RtmpgJySdf/R.INSTALL20c31df42f6/nloptr/src/nlopt-build" does not exist.
Specify --help for usage, or press the help button on the CMake GUI.
Unknown argument -j
Unknown argument 2
Usage: cmake --build <dir> [options] [-- [native-options]]
Options:
<dir> = Project binary directory to be built.
--target <tgt> = Build <tgt> instead of default targets.
--config <cfg> = For multi-configuration tools, choose <cfg>.
--clean-first = Build target 'clean' first, then build.
(To clean only, use --target 'clean'.)
--use-stderr = Don't merge stdout/stderr output and pass the
original stdout/stderr handles to the native
tool so it can use the capabilities of the
calling terminal (e.g. colored output).
-- = Pass remaining options to the native tool.
CMake Error: The source directory "/tmp/RtmpgJySdf/R.INSTALL20c31df42f6/nloptr/src/nlopt" does not exist.
Specify --help for usage, or press the help button on the CMake GUI.
cp: cannot stat 'nlopt/include/*': No such file or directory
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I"/opt/R/4.0.0/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.0.0/lib/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -c init_nloptr.c -o init_nloptr.o
gcc -std=gnu99 -I"/opt/R/4.0.0/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.0.0/lib/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -c nloptr.c -o nloptr.o
g++ -std=gnu++11 -I"/opt/R/4.0.0/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.0.0/lib/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -c test-C-API.cpp -o test-C-API.o
g++ -std=gnu++11 -I"/opt/R/4.0.0/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.0.0/lib/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -c test-runner.cpp -o test-runner.o
g++ -std=gnu++11 -shared -L/opt/R/4.0.0/lib/R/lib -L/usr/local/lib -o nloptr.so init_nloptr.o nloptr.o test-C-API.o test-runner.o -L/opt/R/4.0.0/lib/R/lib -lRlapack -L/opt/R/4.0.0/lib/R/lib -lRblas -lgfortran -lm -lquadmath -Lnlopt/lib -lnlopt -L/opt/R/4.0.0/lib/R/lib -lR
/bin/ld: cannot find -lnlopt
collect2: error: ld returned 1 exit status
make: *** [nloptr.so] Error 1
ERROR: compilation failed for package ‘nloptr’
* removing ‘/opt/R/4.0.0/lib/R/library/nloptr’
ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
* removing ‘/opt/R/4.0.0/lib/R/library/lme4’
ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
* removing ‘/opt/R/4.0.0/lib/R/library/pbkrtest’
ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’
* removing ‘/opt/R/4.0.0/lib/R/library/car’
ERROR: dependency ‘car’ is not available for package ‘rstatix’
* removing ‘/opt/R/4.0.0/lib/R/library/rstatix’
ERROR: dependency ‘car’ is not available for package ‘FactoMineR’
* removing ‘/opt/R/4.0.0/lib/R/library/FactoMineR’
ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’
* removing ‘/opt/R/4.0.0/lib/R/library/ggpubr’
ERROR: dependencies ‘FactoMineR’, ‘ggpubr’ are not available for package ‘factoextra’
* removing ‘/opt/R/4.0.0/lib/R/library/factoextra’
The downloaded source packages are in
‘/tmp/Rtmp98DJqK/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages("factoextra") :
installation of package ‘nloptr’ had non-zero exit status
2: In install.packages("factoextra") :
installation of package ‘lme4’ had non-zero exit status
3: In install.packages("factoextra") :
installation of package ‘pbkrtest’ had non-zero exit status
4: In install.packages("factoextra") :
installation of package ‘car’ had non-zero exit status
5: In install.packages("factoextra") :
installation of package ‘rstatix’ had non-zero exit status
6: In install.packages("factoextra") :
installation of package ‘FactoMineR’ had non-zero exit status
7: In install.packages("factoextra") :
installation of package ‘ggpubr’ had non-zero exit status
8: In install.packages("factoextra") :
installation of package ‘factoextra’ had non-zero exit status
I solved this problem by sudo apt-get install libnlopt-dev.
so,
I think I finally figure out!
factoextra (or better, nloptr) currently needs a combination of
R v. >= 4 (not trial for centos! https://stackoverflow.com/a/67341871 )
cmake v. >= 3 (yum install cmake3 -- credits to https://github.com/astamm/nloptr/issues/104#issuecomment-1034229550)
In Ubuntu install cmake v3.20.2 from the source and it will solve the issue:
sudo apt install build-essential libssl-dev
wget https://github.com/Kitware/CMake/releases/download/v3.20.2/cmake-3.20.2.tar.gz
tar -zxvf cmake-3.20.2.tar.gz
cd cmake-3.20.2
./bootstrap
make
sudo make install
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'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'm reasonably new to R, and to stackoverflow, so apologies if I have not provided sufficient detail in my question below. Happy to provide more info if required
I run Windows 7 Professional (64 bit) and have R version 3.0.2 installed.
When I try to install devtools, I obtain
library(devtools)
Warning message:
package ‘devtools’ was built under R version 3.0.3
build_github_devtools()
"C:/PROGRA~1/R/R-30~1.2/bin/x64/R" --vanilla CMD SHLIB foo.c
gcc -m64 -I"C:/PROGRA~1/R/R-30~1.2/include" -DNDEBUG
-I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c foo.c -o foo.o gcc -m64 -shared -s -static-libgcc -o foo.dll tmp.def foo.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-30~1.2/bin/x64 -lR Downloading devtools from https://github.com/hadley/devtools/archive/master.zip
"C:/PROGRA~1/R/R-30~1.2/bin/x64/R" --vanilla CMD INSTALL
"C:\Users\AppData\Local\Temp\Rtmp8yGaPd\devtools-master" --build
installing to library 'C:/Users/AppData/Local/Temp/Rtmp8yGaPd/file1afc11f24d1b'
ERROR: dependencies 'rversions', 'git2r' are not available for package
'devtools'
removing 'C:/Users/AppData/Local/Temp/Rtmp8yGaPd/file1afc11f24d1b/devtools'
Error: Command failed (1)
I've searched for help on dependencies rversions and git2r but no luck so far.
Can anybody help please?
This is information about git2r
The following devtools installation information comes from devtools:
Make sure you have a working development environment.
Windows: Install Rtools.
Install the release version of devtools from CRAN with install.packages("devtools").
Windows:
library(devtools)
build_github_devtools()
Restart R before continuing
install.packages("devtools.zip", repos = NULL, type = "source")
Remove the package after installation
unlink("devtools.zip")
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")