install package on windows ERROR: compilation failed for packages - r

> install.packages(c("lubridate", "nlme", "readxl", "sourcetools", "utf8", "xfun"))
Installing packages into ‘C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
There are binary versions available but the source versions are later:
binary source needs_compilation
lubridate 1.9.1 1.9.2 TRUE
nlme 3.1-161 3.1-162 TRUE
readxl 1.4.1 1.4.2 TRUE
sourcetools 0.1.7 0.1.7-1 TRUE
utf8 1.2.2 1.2.3 TRUE
xfun 0.36 0.37 TRUE
installing the source packages ‘lubridate’, ‘nlme’, ‘readxl’, ‘sourcetools’, ‘utf8’, ‘xfun’
trying URL 'https://cran.rstudio.com/src/contrib/lubridate_1.9.2.tar.gz'
Content type 'application/x-gzip' length 427200 bytes (417 KB)
downloaded 417 KB
trying URL 'https://cran.rstudio.com/src/contrib/nlme_3.1-162.tar.gz'
Content type 'application/x-gzip' length 848546 bytes (828 KB)
downloaded 828 KB
trying URL 'https://cran.rstudio.com/src/contrib/readxl_1.4.2.tar.gz'
Content type 'application/x-gzip' length 2091835 bytes (2.0 MB)
downloaded 2.0 MB
trying URL 'https://cran.rstudio.com/src/contrib/sourcetools_0.1.7-1.tar.gz'
Content type 'application/x-gzip' length 24095 bytes (23 KB)
downloaded 23 KB
trying URL 'https://cran.rstudio.com/src/contrib/utf8_1.2.3.tar.gz'
Content type 'application/x-gzip' length 241412 bytes (235 KB)
downloaded 235 KB
trying URL 'https://cran.rstudio.com/src/contrib/xfun_0.37.tar.gz'
Content type 'application/x-gzip' length 130063 bytes (127 KB)
downloaded 127 KB
* installing *source* package 'lubridate' ...
** package 'lubridate' successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c datetime.c -o datetime.o
/bin/sh: line 1: gcc: command not found
make: *** [C:/PROGRA~1/R/R-42~1.2/etc/x64/Makeconf:253: datetime.o] Error 127
ERROR: compilation failed for package 'lubridate'
* removing 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/lubridate'
* restoring previous 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/lubridate'
Warning in install.packages :
installation of package ‘lubridate’ had non-zero exit status
* installing *source* package 'nlme' ...
** package 'nlme' successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran -fno-optimize-sibling-calls -O2 -mfpmath=sse -msse2 -mstackrealign -c chol.f -o chol.o
make: gfortran: No such file or directory
make: *** [C:/PROGRA~1/R/R-42~1.2/etc/x64/Makeconf:277: chol.o] Error 127
ERROR: compilation failed for package 'nlme'
* removing 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/nlme'
* restoring previous 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/nlme'
Warning in install.packages :
installation of package ‘nlme’ had non-zero exit status
* installing *source* package 'readxl' ...
** package 'readxl' successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -Iwindows -I. -D__USE_MINGW_ANSI_STDIO -I'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/cpp11/include' -I'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/progress/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cpp11.cpp -o cpp11.o
/bin/sh: line 1: g++: command not found
make: *** [C:/PROGRA~1/R/R-42~1.2/etc/x64/Makeconf:260: cpp11.o] Error 127
ERROR: compilation failed for package 'readxl'
* removing 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/readxl'
* restoring previous 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/readxl'
Warning in install.packages :
installation of package ‘readxl’ had non-zero exit status
* installing *source* package 'sourcetools' ...
** package 'sourcetools' successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -I../inst/include -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Reader.cpp -o Reader.o
/bin/sh: line 1: g++: command not found
make: *** [C:/PROGRA~1/R/R-42~1.2/etc/x64/Makeconf:260: Reader.o] Error 127
ERROR: compilation failed for package 'sourcetools'
* removing 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/sourcetools'
* restoring previous 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/sourcetools'
Warning in install.packages :
installation of package ‘sourcetools’ had non-zero exit status
* installing *source* package 'utf8' ...
** package 'utf8' successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -Iutf8lite/src -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c as_utf8.c -o as_utf8.o
/bin/sh: line 1: gcc: command not found
make: *** [C:/PROGRA~1/R/R-42~1.2/etc/x64/Makeconf:253: as_utf8.o] Error 127
ERROR: compilation failed for package 'utf8'
* removing 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/utf8'
* restoring previous 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/utf8'
Warning in install.packages :
installation of package ‘utf8’ had non-zero exit status
* installing *source* package 'xfun' ...
** package 'xfun' successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c base64.c -o base64.o
/bin/sh: line 1: gcc: command not found
make: *** [C:/PROGRA~1/R/R-42~1.2/etc/x64/Makeconf:253: base64.o] Error 127
ERROR: compilation failed for package 'xfun'
* removing 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/xfun'
* restoring previous 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/xfun'
Warning in install.packages :
installation of package ‘xfun’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\Sachin Dahiya\AppData\Local\Temp\RtmpgBGXsJ\downloaded_packages’
I am using R version 4.2.2 and R tools43 on Windows 11. These packages have been asking for updates for a while now but the compliation fails every time. Please let me know how to fix this issue. I have instaled R tools and R.4.2.2 in C:\Program Files\R.
These are my paths:
> .libPaths()
[1] "C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2"
[2] "C:/Program Files/R/R-4.2.2/library"

Related

Can't install 'glmnet' in R

I put in this code:
install.packages("glmnet")
And it delivers this error message:
* installing *source* package 'glmnet' ...
** package 'glmnet' successfully unpacked and MD5 sums checked
** using staged installation
** libs
*** arch - i386
"c:/rtools40/mingw32/bin/"g++ -std=gnu++14 -I"C:/PROGRA~1/R/R-40~1.4/include" -DNDEBUG -I'C:/Users/zac.t8/OneDrive/Documents/R/win-library/4.0/RcppEigen/include' -I'C:/Users/zac.t8/OneDrive/Documents/R/win-library/4.0/Rcpp/include' -Iglmnetpp/include -Iglmnetpp/src -Iglmnetpp/test -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
sh: c:/rtools40/mingw32/bin/g++: No such file or directory
make: *** [C:/PROGRA~1/R/R-40~1.4/etc/i386/Makeconf:229: RcppExports.o] Error 127
ERROR: compilation failed for package 'glmnet'
* removing 'C:/Users/zac.t8/OneDrive/Documents/R/win-library/4.0/glmnet'
Warning in install.packages :
installation of package ‘glmnet’ had non-zero exit status
Can someone point out what is wrong? Thanks!

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

Package installation not working in 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’

Unable to install mclust package in rstudio

I am having an issue when installing the "mclust" package on rstudio.
Here is the warning message:
>install.packages("mclust")
trying URL 'https://cran.rstudio.com/src/contrib/mclust_5.4.tar.gz'
Content type 'application/x-gzip' length 2535477 bytes (2.4 MB)
==================================================
downloaded 2.4 MB
* installing *source* package ‘mclust’ ...
** package ‘mclust’ successfully unpacked and MD5 sums checked
** libs
/home/usr/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -
I/home/usr/anaconda3/lib/R/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2
-I/home/usr/anaconda3/include -fpic -march=nocona -mtune=haswell -
ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -
I/home/usr/anaconda3/include -c init.c -o init.o
make: /home/usr/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc: Command
not found
/home/usr/anaconda3/lib/R/etc/Makeconf:160: recipe for target 'init.o'
failed
make: *** [init.o] Error 127
ERROR: compilation failed for package ‘mclust’
* removing ‘/home/usr/anaconda3/lib/R/library/mclust’
Warning in install.packages :
installation of package ‘mclust’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpGCCIZS/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
In addition, I also tried to access the directory /home.usr/anaconda3/x86_64-conda_cos6-linux-gnu-cc ,which apparently doesn't exist.

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?

Resources