Package installation not working in R - r

Nevermind, fixed it. Will write up comment explaining fix tn.
I am trying to install the geometric morphometrics package in R, but whenever I try to install it, I get the following error message:
> install.packages("geomorph")
There is a binary version available but the source version is later: binary source needs_compilation geomorph 3.0.5 3.0.6 FALSE
installing the source package ‘geomorph’
trying URL 'https://cran.rstudio.com/src/contrib/geomorph_3.0.6.tar.gz'
Content type 'application/x-gzip' length 545863 bytes (533 KB)
==================================================
downloaded 533 KB
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
unknown timezone 'default/America/Toronto'
* installing *source* package ‘geomorph’ ...
** package ‘geomorph’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called ‘mvtnorm’
ERROR: lazy loading failed for package ‘geomorph’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/geomorph’
Warning in install.packages :
installation of package ‘geomorph’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/4p/m9yg9rg94v13j49zxnp9kzzh0000gn/T/RtmpCBCHAn/downloaded_packages’
I'm using RStudio but I tried it in just R, I've updated to the latest MacOS HighSierra, I have tried restarting the applications, I've installed and restarted XQuartz, and so far nothing has worked.
I'm running R on an early 2015 MacBook Air, I'm fresh out of ideas. Any suggestions are welcome.
EDIT:
Trying to install mvtnorm also failed, producing the following:
> install.packages("mvtnorm")
There is a binary version available but the source version is later:
binary source needs_compilation
mvtnorm 1.0-6 1.0-7 TRUE
Do you want to install from sources the package which needs compilation?
y/n: y
installing the source package ‘mvtnorm’
trying URL 'https://cran.rstudio.com/src/contrib/mvtnorm_1.0-7.tar.gz'
Content type 'application/x-gzip' length 159381 bytes (155 KB)
==================================================
downloaded 155 KB
* installing *source* package ‘mvtnorm’ ...
** package ‘mvtnorm’ successfully unpacked and MD5 sums checked
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG - I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC - Wall -mtune=core2 -g -O2 -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG - I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC - Wall -mtune=core2 -g -O2 -c miwa.c -o miwa.o
gfortran-4.8 -fPIC -g -O2 -c mvt.f -o mvt.o
make: gfortran-4.8: No such file or directory
make: *** [mvt.o] Error 1
ERROR: compilation failed for package ‘mvtnorm’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/mvtnorm’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/mvtnorm’
Warning in install.packages :
installation of package ‘mvtnorm’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/4p/m9yg9rg94v13j49zxnp9kzzh0000gn/T/RtmpCBCHAn/downloaded_packages’

Related

gcc-8: command not found (while installing randomForest)

I'm trying to install "randomForest" on R 3.6.3 as below:
urlPackage <- "https://cran.r-project.org/src/contrib/Archive/randomForest/randomForest_4.6-14.tar.gz"
install.packages(urlPackage, repos=NULL, type="source")
(install.packages('randomForest') throws the error: package 'randomForest' is not available (for R version 3.6.3))
The lines above, however, give me the following error:
trying URL 'https://cran.r-project.org/src/contrib/Archive/randomForest/randomForest_4.6-14.tar.gz'
Content type 'application/x-gzip' length 80074 bytes (78 KB)
==================================================
downloaded 78 KB
* installing *source* package ‘randomForest’ ...
** package ‘randomForest’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c classTree.c -o classTree.o
/bin/sh: gcc-8: command not found
make: *** [classTree.o] Error 127
ERROR: compilation failed for package ‘randomForest’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/randomForest’
Warning in install.packages :
installation of package ‘/var/folders/66/3s4r17rx7ln0b1p8tyrmws780000gn/T//RtmpDOHynP/downloaded_packages/randomForest_4.6-14.tar.gz’ had non-zero exit status
Does anyone have any idea how to solve this? I'm on macOS Catalina (ver 10.15.7)
You should install the gcc8 tool:
sudo port install gcc8
Related Links
MacPorts - GCC8
YouTube - Install GCC 8 with Homebrew on macOS

Cannot install tseries and forecast packages in R

I'm trying to install the packages mentioned above, but I'm not able to. I've followed several tips, even so it was not possible to install the packages above. Even following the following commands, which already work with some packages, cannot be installed:
install.packages("forecast", INSTALL_opts = "--no-lock")
install.packages("tseries", dependencies = T)
When I try the first option the result is this:
Installing package into ‘/home/vitor/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
also installing the dependency ‘quadprog’
tentando a URL 'https://cloud.r-project.org/src/contrib/quadprog_1.5-8.tar.gz'
Content type 'application/x-gzip' length 36141 bytes (35 KB)
==================================================
downloaded 35 KB
tentando a URL 'https://cloud.r-project.org/src/contrib/tseries_0.10-49.tar.gz'
Content type 'application/x-gzip' length 170539 bytes (166 KB)
==================================================
downloaded 166 KB
* installing *source* package ‘quadprog’ ...
** package ‘quadprog’ successfully unpacked and MD5 sums checked
staged installation is only possible with locking
** using non-staged installation
** libs
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-Do_dS_/r-base-4.0.0=. -fstack-protector-strong -msse2 -mfpmath=sse -fpic -g -O2 -fdebug-prefix-map=/build/r-base-Do_dS_/r-base-4.0.0=. -fstack-protector-strong -c aind.f -o aind.o
/bin/bash: gfortran: comando não encontrado
make: *** [/usr/lib/R/etc/Makeconf:190: aind.o] Erro 127
ERROR: compilation failed for package ‘quadprog’
* removing ‘/home/vitor/R/x86_64-pc-linux-gnu-library/4.0/quadprog’
Warning in install.packages :
installation of package ‘quadprog’ had non-zero exit status
ERROR: dependency ‘quadprog’ is not available for package ‘tseries’
* removing ‘/home/vitor/R/x86_64-pc-linux-gnu-library/4.0/tseries’
Warning in install.packages :
installation of package ‘tseries’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmpb9K2Gk/downloaded_packages’
A segunda opção apresenta o seguinte resultado:
Installing package into ‘/home/vitor/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
also installing the dependency ‘quadprog’
tentando a URL 'https://cloud.r-project.org/src/contrib/quadprog_1.5-8.tar.gz'
Content type 'application/x-gzip' length 36141 bytes (35 KB)
==================================================
downloaded 35 KB
tentando a URL 'https://cloud.r-project.org/src/contrib/tseries_0.10-49.tar.gz'
Content type 'application/x-gzip' length 170539 bytes (166 KB)
==================================================
downloaded 166 KB
* installing *source* package ‘quadprog’ ...
** package ‘quadprog’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-Do_dS_/r-base-4.0.0=. -fstack-protector-strong -msse2 -mfpmath=sse -fpic -g -O2 -fdebug-prefix-map=/build/r-base-Do_dS_/r-base-4.0.0=. -fstack-protector-strong -c aind.f -o aind.o
/bin/bash: gfortran: comando não encontrado
make: *** [/usr/lib/R/etc/Makeconf:190: aind.o] Erro 127
ERROR: compilation failed for package ‘quadprog’
* removing ‘/home/vitor/R/x86_64-pc-linux-gnu-library/4.0/quadprog’
Warning in install.packages :
installation of package ‘quadprog’ had non-zero exit status
ERROR: dependency ‘quadprog’ is not available for package ‘tseries’
* removing ‘/home/vitor/R/x86_64-pc-linux-gnu-library/4.0/tseries’
Warning in install.packages :
installation of package ‘tseries’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmpb9K2Gk/downloaded_packages’
How to proceed properly?
"gfortran: comando não encontrado": The gfortran compiler is missing.
On Linux, R builds packages from source. Therefore you need the gcc toolchain. To get the bare minimum, you may do:
sudo apt install build-essential gfortran
Some R packages need other Linux packages as well. If you try to install tidyverse for instance, I believe you need libicu-dev libbz2-dev libxml2-dev libcurl4-openssl-dev libssl-dev as well. In general, to find out which Linux package is missing, you will need to decipher the compilation error messages, and maybe check the source code or the web for additional information.

Unable to install a package called 'hemp' in R

I am new to learning R and i get the following error while installing the package called 'hemp'. Its a package which is used in psychometric analysis. Can anyone tell me what causes this errror?
Downloading GitHub repo cddesja/hemp#master
Installing 1 packages: nloptr
Installing package into ‘C:/Users/UJJWAL/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
There is a binary version available but the
source version is later:
binary source needs_compilation
nloptr 1.2.2.1 1.2.2.2 TRUE
installing the source package ‘nloptr’
trying URL 'https://cran.rstudio.com/src/contrib/nloptr_1.2.2.2.tar.gz'
Content type 'application/x-gzip' length 2450931 bytes (2.3 MB)
downloaded 2.3 MB
* installing *source* package 'nloptr' ...
** package 'nloptr' successfully unpacked and MD5 sums checked
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
*** arch - i386
/mingw32/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-4.0.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dummy.cpp -o dummy.o
/mingw32/bin/gcc -I"C:/PROGRA~1/R/R-4.0.2/include" -DNDEBUG -I"/i386/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init_nloptr.c -o init_nloptr.o
init_nloptr.c:35:10: fatal error: nlopt.h: No such file or directory
#include "nlopt.h"
^~~~~~~~~
compilation terminated.
make: *** [C:/PROGRA~1/R/R-4.0.2/etc/i386/Makeconf:222: init_nloptr.o] Error 1
ERROR: compilation failed for package 'nloptr'
* removing 'C:/Users/UJJWAL/Documents/R/win-library/4.0/nloptr'
Error: Failed to install 'hemp' from GitHub:
(converted from warning) installation of package ‘nloptr’ had non-zero exit status
Seems that it wouldbe a little harder to install nloptr on Windows. It require nlopt to be installed first. See this for more info: https://www.r-project.org/nosvn/pandoc/nloptr.html

r - f951: internal compiler error: Illegal instruction: 4

I'm trying to install MVN package:
> install.packages("MVN")
probando la URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/MVN_5.5.tgz'
Content type 'application/x-gzip' length 382369 bytes (373 KB)
==================================================
downloaded 373 KB
The downloaded binary packages are in
/var/folders/79/xxghr9tj65789879v41wrp6h0000gn/T//Rtmp4bpod5/downloaded_packages
but when I do library(MVN) it says me that Error: package or namespace load failed for ‘MVN’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘rrcov’
so when I try to install it:
> install.packages("rrcov")
There is a binary version available but the source version is later:
binary source needs_compilation
rrcov 1.4-4 1.4-7 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes
installing the source package ‘rrcov’
probando la URL 'https://cran.rstudio.com/src/contrib/rrcov_1.4-7.tar.gz'
Content type 'application/x-gzip' length 965680 bytes (943 KB)
==================================================
downloaded 943 KB
* installing *source* package ‘rrcov’ ...
** package ‘rrcov’ successfully unpacked and MD5 sums checked
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c R-rng4ftn.c -o R-rng4ftn.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c covOPW.c -o covOPW.o
gfortran -fPIC -g -O2 -c ds11.f -o ds11.o
gfortran: warning: couldn’t understand kern.osversion ‘15.6.0
f951: internal compiler error: Illegal instruction: 4
f951: internal compiler error: Abort trap: 6
gfortran: internal compiler error: Abort trap: 6 (program f951)
make: *** [ds11.o] Abort trap: 6
ERROR: compilation failed for package ‘rrcov’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rrcov’
Warning in install.packages :
installation of package ‘rrcov’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/79/xxghr9tj65789879v41wrp6h0000gn/T/Rtmp4bpod5/downloaded_packages’
I've searched how to fix that, installing XCode, reinstalling r, and nothing. I need this package to perfom some multivariate analysis for my thesis but I do not know how to fix it.
Any help will be appreciated.
Thanks!
I am using an iOS 10.11.6

gcc can't compile R packages under Linux Mint: can't find stdlib.h

I'm trying to install the R package gtools from the Linux Mint command line. After choosing the closest CRAN mirror, I'm getting the error message that no such file or directory was found and that installation of the package had a non-zero exit status. More specifically:
> install.packages('gtools')
Installing package into ‘/home/lizi/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://cloud.r-
project.org/src/contrib/gtools_3.5.0.tar.gz'
Content type 'application/x-gzip' length 64855 bytes (63 KB)
==================================================
downloaded 63 KB
* installing *source* package ‘gtools’ ...
** package ‘gtools’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c roman2int.c -o roman2int.o
In file included from roman2int.c:1:0:
/usr/share/R/include/R.h:55:80: fatal error: stdlib.h: No such file or
directory
compilation terminated.
/usr/lib/R/etc/Makeconf:159: recipe for target 'roman2int.o' failed
make: *** [roman2int.o] Error 1
ERROR: compilation failed for package ‘gtools’
* removing ‘/home/lizi/R/x86_64-pc-linux-gnu-library/3.4/gtools’
The downloaded source packages are in
‘/tmp/Rtmp0z5PS6/downloaded_packages’
Warning message:
In install.packages("gtools") :
installation of package ‘gtools’ had non-zero exit status
The package has no dependencies, and I was under the impression that install.packages was straightforward. What am I doing wrong?

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