I need to install a package from source in renv. I can install packages from binaries in renv no problem. I can also install packages from both source & binary outside renv no problem. I am doing this within Rstudio
The error (below) makes me think it cant find the compiler. Digging around I found a thread about this that says renv cant find Rtools and then you need to run renv:::renv_scope_rtools() to resolve this but this just gives the message FAIL and the problem remains. Can anyone help?
thanks
install.packages("xfun")
Retrieving 'https://cloud.r-project.org/src/contrib/xfun_0.37.tar.gz' ...
OK [file is up to date]
Installing xfun [0.37] ...
FAILED
Error installing package 'xfun':
================================
* 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
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 'D:/Dropbox/project X/renv/staging/3/xfun'
Related
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
First question on StackOverflow. I will try to be clear.
I just installed
R 4.0.1 for Windows 10
RStudio (RStudio 1.3.959) for Windows 10
I tried to install learnr package, which required many other packages. The console prints toward the end:
installing source package 'backports' ...
** package 'backports' successfully unpacked and MD5 sums checked
** using staged installation
** libs
"c:/rtools40/mingw64/bin/"gcc -I"C:/PROGRA~1/R/R-40~1.1/include" -DNDEBUG -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c dotsElt.c -o dotsElt.o
/bin/sh: c:/rtools40/mingw64/bin/gcc: No such file or directory
make: *** [dotsElt.o] Error 127
ERROR: compilation failed for package 'backports'
removing 'C:/Users/micha/Documents/R/win-library/4.0/backports'
Warning in install.packages :
installation of package ‘backports’ had non-zero exit status
installing source package 'isoband' ...
** package 'isoband' successfully unpacked and MD5 sums checked
** using staged installation
** libs
"c:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.1/include" -DNDEBUG -I'C:/Users/micha/Documents/R/win-library/4.0/testthat/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c clip-lines.cpp -o clip-lines.o
/bin/sh: c:/rtools40/mingw64/bin/g++: No such file or directory
make: *** [clip-lines.o] Error 127
ERROR: compilation failed for package 'isoband'
removing 'C:/Users/micha/Documents/R/win-library/4.0/isoband'
Warning in install.packages :
installation of package ‘isoband’ had non-zero exit status
ERROR: dependency 'isoband' is not available for package 'ggplot2'
removing 'C:/Users/micha/Documents/R/win-library/4.0/ggplot2'
Warning in install.packages :
installation of package ‘ggplot2’ had non-zero exit status
Is it an internal issue, or a problem with the packages? Should I contact the package maintainer for 'backports', 'isoband', 'ggplot2', re-install R and/or RStudio, or something else?
It seems that you run that on Windows and want to install learnr from the source (it means that you have to compile these packages). However, some packages need additional tools to compile on Windows. These tools are provided in official RTools for Windows, so install that first and try again.
And sometimes you can install the binary versions of the packages rather than the source. Then you don't need to compile:
install.packages("learnr", type = "binary")
When trying to install some packages such Rcmdr or factoextra while on R in terminal (after upgrade to R 4.0.0 on Archlabs) the following errors shows up:
* installing *source* package ‘SparseM’ ...
** package ‘SparseM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -c bckslv.f -o bckslv.o
/usr/local/bin/gfortran: /usr/local/bin/gfortran: cannot execute binary file
make: *** [/usr/lib64/R/etc/Makeconf:190: bckslv.o] Error 126
ERROR: compilation failed for package ‘SparseM’
* removing ‘/usr/lib/R/library/SparseM’
and this one :
* installing *source* package ‘readr’ ...
** package ‘readr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -I'/usr/lib/R/library/Rcpp/include' -I'/usr/lib/R/library/BH/include' -D_FORTIFY_SOURCE=2 -I. -Ircon -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -c Collector.cpp -o Collector.o
In file included from /usr/lib/R/library/Rcpp/include/Rcpp.h:77,
from Collector.cpp:1:
/usr/lib/R/library/Rcpp/include/Rcpp/Rmath.h: In function ‘double R::pythag(double, double)’:
/usr/lib/R/library/Rcpp/include/Rcpp/Rmath.h:222:57: error: ‘::Rf_pythag’ has not been declared; did you mean ‘pythag’?
222 | inline double pythag(double a, double b) { return ::Rf_pythag(a, b); }
| ^~~~~~~~~
| pythag
make: *** [/usr/lib64/R/etc/Makeconf:176: Collector.o] Error 1
then followed by a bunch of
ERROR: dependencies ‘dendextend’, ‘FactoMineR’, ‘ggpubr’, ‘ggrepel’, ‘tidyr’ are not available for package ‘factoextra’
* removing ‘/usr/lib/R/library/factoextra’
following each dependencies produces the same errors with different new dependencies.
P.S: I'm a normie so please bear with me.
I had a similar error while installing 'ape'. For me it worked to reinstall the current version of the 'Rcpp' package:
install.packages('Rcpp')
Hope it works for you too !
I have RStudio 1.1.419 running on a Mac OS El Capitan. I am trying to install the dplyr package. The installation first attempts to install package utf8. The following is the text I get back:
installing source package ‘utf8’ ...
** package ‘utf8’ successfully unpacked and MD5 sums checked
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Iutf8lite/src -fPIC -mtune=core2 -g -O2 -c as_utf8.c -o as_utf8.o
make: llvm-gcc-4.2: No such file or directory
make: *** [as_utf8.o] Error 1
ERROR: compilation failed for package ‘utf8’
removing ‘/Users/andrewdkilmer/Library/R/3.2/library/utf8’
Warning in install.packages :
installation of package ‘utf8’ had non-zero exit status
Since utf8 failed to install, dplyr cannot install either. Why am I getting this 'No such file or directory' error?
Never mind, updated to R version 3.4 and it is working.
I have 64bit R (R version 2.15.2 (2012-10-26) -- "Trick or Treat") on Mac OSX 10.8.5, and Oracle Instantclient Version 11.2.0.3.0 from Oracle installed. I've gotten sqlplus, as well as Perl and Python to run on these. Now I am trying to build ROracle. It needs to be built from source, so I downloaded it and have tried running:
R CMD INSTALL ROracle_1.1-10.tar.gz
However, I think it is expecting a different directory structure than what the Instant Client has given me. For instance, when I try to run that command, I get:
$ R CMD INSTALL ROracle_1.1-10.tar.gz
* installing to library ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’
* installing *source* package ‘ROracle’ ...
** package ‘ROracle’ successfully unpacked and MD5 sums checked
configure: error: "/Applications/instantclient_11_2/lib" directory does not exist
ERROR: configuration failed for package ‘ROracle’
* removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/ROracle’
It is true, that I don't have a 'lib' directory in my '/Applications/instantclient_11_2' directory. I did however try to fake it out by creating one and linking to the .dylib files in the '/Applications/instantclient_11_2' directory, and I got past that error to a new one:
$ R CMD INSTALL ROracle_1.1-10.tar.gz
* installing to library ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’
* installing *source* package ‘ROracle’ ...
** package ‘ROracle’ successfully unpacked and MD5 sums checked
configure: error: "/Applications/instantclient_11_2/rdbms/public" directory does not exist
ERROR: configuration failed for package ‘ROracle’
* removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/ROracle’
So it is now looking for another directory that isn't there. I don't want to keep going and guessing at the directories it is expecting and trying to back-populate it with links to files it should be expecting in those directories (I don't even know what it might be expecting here).
Is there another way to go about installing this? I'm thinking I should be able to do this based upon the fact that Perl and Python can use these drivers.
Thanks,
Matt
I think you have "ORACLE_HOME" variable set. I had the same problem and as soon as I did
export ORACLE_HOME=""
I could successfully compile ROracle.
Before:
me#my-laptop:~/Downloads$ R CMD INSTALL ROracle_1.1-10.tar.gz
*installing to library ‘/opt/R/library’
* installing *source* package ‘ROracle’ ...
** package ‘ROracle’ successfully unpacked and MD5 sums checked
configure: error: "/usr/lib/oracle/12.1/rdbms/public" directory does not exist
ERROR: configuration failed for package ‘ROracle’
* removing ‘/opt/R/library/ROracle’
After:
me#my-laptop:~/Downloads$ export ORACLE_HOME=""
me#my-laptop:~/Downloads$ R CMD INSTALL ROracle_1.1-10.tar.gz
* installing to library ‘/opt/R/library’
* installing *source* package ‘ROracle’ ...
** package ‘ROracle’ successfully unpacked and MD5 sums checked
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/opt/oracle/sdk/include -fpic -O2 -pipe -g -c rodbi.c -o rodbi.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/opt/oracle/sdk/include -fpic -O2 -pipe -g -c rooci.c -o rooci.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/opt/oracle/sdk/include -fpic -O2 -pipe -g -c routl.c -o routl.o
gcc -std=gnu99 -shared -o ROracle.so rodbi.o rooci.o routl.o -L/opt/oracle -lclntsh -L/usr/lib/R/lib -lR
installing to /opt/R/library/ROracle/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ROracle)