When installing Rtools version 4.2 on Windows 10, I get a pop-up window with the following message at the end of the installation process:
Unable to execute file:
C:\WINDOWS\system32\cmd.exe
CreateProcess failed;code 2.
The system cannot find the file specified.
The only thing I have done previously is to install R (version 4.2.1.).
I fear ignoring this message will lead to issues later on.
Related
I have recently moved from MRO 3.4.3 to R 3.5.0. I can start and use the new installation of R perfectly from the terminal, but when I stat Rstudio-server, an error panel appears with the message: "Error occured during transmission"
The log at /var/log/messages shows this:
Jun 6 11:28:51 slave1 rsession-victor[116037]: ERROR R SUICIDE: unable to initialize the JIT|||; LOGGED FROM: void<unnamed>::rSuicide(const std::string&) /root/rstudio/src/cpp/session/SessionMain.cpp:1023
I have tried to remove the files /etc/rstudio/rserver.conf and /etc/rstudio/rsession.conf that I had changed to use the previous MRO installation, but it didn't work. Also, I have tried to to remove completely the .rstudio folder in my home directory.
Any ideas about how to solve this?
Thanks!
I had the same problem after installing R 3.5.1 from sources.
The reason for the error is that libR.so is not build using the
simple installation procedure described in file INSTALL. RStudio
searches for this and finds an incompatible (old) one. Use this instead:
./configure --enable-R-shlib
make
I installed Xcode on my Mac, running on the El Capitan version 10.11. I need to get files from a github repository to my workspace in R, so I run the line:
devtools::install_github("Myrepository")
And this error appears:
Downloading GitHub repo Myrepository
from URL https://api.github.com/repos/Myrepository/func/zipball/master
Erreur : Could not find build tools necessary to build func
I thought the problem may come from my gcc command line tools, but when I hit
gcc -v
I have it installed:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.3.0
Thread model: posix
Any ideas?
I had the same problem when installing the forecast package from GitHub on my Mac running El Capitan. The suggested readline fix above did not work for me. I noticed that my shell wasn't seeing R (e.g. when I typed R at a shell prompt it said command not found). I also was operating as a non-admin user of my computer and I think had installed R as a non-admin user. So I downloaded R again (same version) and installed it as an admin user. (This was based on a hunch after reading about some of the finnicky issues with R and paths in El Cap) After reinstalling R as an admin user I could then open R in a terminal, and at that point
devtools::install_github("robjhyndman/forecast")
worked fine.
I’m experiencing some troubles when I try to install R dependencies with the command :
install.packages(c(“Rcpp”,”RJSONIO”,”bitops”,”digest”,”functional”,”itertools”,”reshape2″,”string ”,”plyr”,”caTools”),repos=’http://cran.revolutionanalytics.com’)
packages are downloaded but then all I get are the messages
/usr/lib64/R/bin/R: line 8: uname: command not found
/usr/lib64/R/bin/R: line 143: exec: sh: not found
repeated as many times as the number of packages I am trying to install.
I am using R version 3.2.2, rstudio-server 0.99.489 in Hortonworks Sandbox with hadoop 2.3 (Oracle Virtualbox).
Do you have any suggestions?
Thanks for your help.
I know this question was asked 7 months ago. But I just had the same problem stefanod did and I Googled left and right without finding a solution. Then for absolutely no reasonable reason it just worked. Here is what I have tried and what eventually solves my problem:
So I use R 3.2.2, rstudio-server 0.98.994 in Hortonworks Hadoop Sandbox HDP 2.4 in VMWare. I logged in the virtual machine using the Shell Web Client Method. The entire process was done with root privilege. I followed this instruction: https://jsolderitsch.wordpress.com/hortonworks-sandbox-r-and-rstudio-install/ except that I used updated versions of R and RStudio Server. Everything worked fine until I invoked R in the shell and attempted
install.packages('foo.bar', repos='http://cran.revolutionanalytics.com')
Then I had exactly the same error messages as in this Q.
I checked my $PATH and used whereis COMMANDNAME to check if I had the uname command at the right place. Seems I do.
I then quit R. Inside CentOS I used wget to manually download the .tar.gz files of the packages and their dependencies. I then tried to install those packages manually:
[root#sandbox ~]# sudo R CMD INSTALL foo.bar.tar.gz
* installing to library ‘/usr/lib64/R/library’
* installing *source* package ‘foo.bar’ ...
** package ‘foo.bar’ successfully unpacked and MD5 sums checked
** libs
sh: make: command not found
ERROR: compilation failed for package ‘foo.bar’
* removing ‘/usr/lib64/R/library/foo.bar’
sh: rm: command not found
At this time RStudio was already installed. So I logged into RStudio in my browser at port 8787 and tried install.packages in RStudio and every package installed fine.
I guess the take-home message is to install packages inside RStudio instead of inside R in the shell.
BTW I also cannot log in RStudio as root; says invalid username and password.
I am trying to install octave through brew on mac (10.10.5 Yosemite). The command used is brew install octave . While installing, the process tries to install qt (version 4.8.7) which is essentially failing with the below error
Error : 'File already exists. /usr/local/Cellar/qt/4.8.7'.
When I check the file at this particular location, I don`t see any such directory, though the directory does appear and is created during the installation (probably getting removed later when the task fails).
Could someone please point out what I need to do exactly? Is Qt really required for Octave installation? If not then any way to skip it?
I'm running Rstudio on its own server.
Java is installed with good java_home and bin.
R is installed. rJava is installed.
Tried to do command: library("rJava") but had issues with libjvm.so, do following Rstudio recommandation I did sudo R CMD javareconf with root.
Here is the output of my javareconf:
Java interpreter : /home/scoremd/jdk1.7.0_03/jre/bin/java
Java version : 1.7.0_03
Java home path : /home/scoremd/jdk1.7.0_03
Java compiler : /home/scoremd/jdk1.7.0_03/bin/javac
Java headers gen.: /home/scoremd/jdk1.7.0_03/bin/javah
Java archive tool: /home/scoremd/jdk1.7.0_03/bin/jar
NOTE: Your JVM has a bogus java.library.path system property!
Trying a heuristic via sun.boot.library.path to find jvm library...
Java library path: $(JAVA_HOME)/jre/lib/amd64:$(JAVA_HOME)/jre/lib/amd64/server
JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64 -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm
JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
Seems there is issue with finding the java library path... but my java is working fine and R also.
I didn't receive any solution from RStudio support and community (told me to ask in SO ....).
I have rstudio-server installed on my Centos server. There are a couple of users using rstudio and we decided to upgrade R from 3.6 to 4.0.
After the upgrade :
all users were running R 4.0.
No user could install rJava using install.package('rJava'). This error always popped up
configure: error: Cannot compile a simple JNI program. See config.log for details.
Make sure you have Java Development Kit installed and correctly registered in R.
If in doubt, re-run "R CMD javareconf" as root.
ERROR: configuration failed for package ‘rJava’
Running SUDO R CMD javareconf went smoothly, and also when I opened R as root and went along and tried install.packages('rJava') it installed the package just fine. (unbeknownst to me, root ran R 3.6 and users 4.0, see solution below)
However it did not work installing the package for users in R studio server. Always stating the same "try running sudo R CMD javareconf" as if the Java path for the users was wrong.
so we tried setting the "JAVA_HOME" variable to the same path that java jdk was installed in (found by searching installed packages in yum). That did not solve it.
my solution
I saw that root was running version 3.6 of R while all users ran 4.0. This was because I had installed 4.0 in another directory.. The directory of R 4.0 happens to be found first by the users. However for the root user... it finds the path of R 3.6 first.
So I set the path to the 4.0 folder in the $PATH variable of the root user, so that would find version 4.0 before finding R 3.6
echo $PATH
export PATH="/usr/local/bin:$PATH"
echo $PATH
Then I ran R as that user and ran "R CMD javareconf", installed the packages and all users are happy and working again.
(disclaimer, I'm not a experienced linux admin, there may be a better solution for running different R versions)
It's been some time since I used rJava, and it was on Windows, but I have some notes which may help you:
Make sure that the JRI native library is in a directory listed in java.library.path
(also confirmed using Process Explorer that jri.dll is being loaded)
The R process loads up jvm.dll when you do library(rJava)
Replace jvm.dll iny my notes above with libjvm.so in your case, and jri.dll with whatever .so file is relevant to you.