All: Apologies in advance for what I hope is an easy question. It's been many years since I've worked in a Unix(-like) environment...
I'm trying to install RApache on a web server running the RHEL5 64-bit OS. I've successfully installed Apache and confirmed it works. I've also successfully installed R (R-2.13.0) with shared library. I've confirmed that libBlas.so and libR.so are installed; location: /R/R-2.13.0/lib
However, when I try to configure RApache ( sudo ./configure --with-apache2-apxs=/usr/local/apache2/bin/ --with-R=/R/R-2.13.0/) I get the following error:
R was not built as a shared
library Either build it with one,
or use another install of R
configure: error: aborting!
I've reinstalled R twice now and have confirmed in libtool that it says:
# Whether or not to build shared
libraries. build_libtool_libs=yes
Finally, I've searched high and low for some path or flag I need to set without success. Any help would be greatly appreciated.
Thanks,
Ron
You need to compile R with the appropriate flags. At the configure stage you need to include --enable-R-shlib so that R is built as a shared library.
You may need to further consult appendix B1 of http://cran.r-project.org/doc/manuals/R-admin.pdf which describes further issues.
Related
First off I realize that this question has been answered. I found that the top hit provided little explanation of the solution. Also my situation is different in the sense that I have no package manager and no root privileges. I hope this questions enables other users like me to be able to install R.
So here is my problem. I am installing R version 3.3.2 and it is giving me an error during configuration:
configure: error: --with-readline=yes (default) and headers/libs are not available
I read online about readlines and how it should be downloaded readline library version 7.0 from the GNU website and installed it in my own directory using
./configure --prefix=/home/readlines; make; make install
Now I just can't get R to recongize where the libraries are. I tried the following:
export LD_LIBRARY_PATH="/home/readlines:$LD_LIBRARY_PATH"
./configure --prefix=/home/R-3.3.2/ CPPFLAGS="-I/home/readlines/include/" LDFLAGS="-L/home/readlines/lib"
I also tried setting CFLAGS to no avail. Can anyone help me figure out how to tell R where my readlines headers are? I'm on CentOS 7
I'm trying to install Apache Zeppelin on my old computer that runs Ubuntu. So far, I'm able to install Zeppelin very easily by cloning the latest 0.6.0 snapshot release using
git clone https://github.com/apache/incubator-zeppelin.git
cd incubator-zeppelin
mvn clean package -DskipTests
but I want to have R on Zeppelin. Supposedly, the 0.6.0 snapshot has two R interpreters, but when I run the R tutorial (the pre-made note that uses %r), I get this list of errors.
I followed several guides to try and install R as an interpreter, but each one resulted in some kind of error. I tried this instructional:
http://www.r-bloggers.com/interactive-data-science-with-r-in-apache-zeppelin-notebook/, and got a build failure on "R Interpreter". The error message was
"dependency 'evaluate' is not available for package 'rzeppelin'
* removing '/home/rebecca/Zeppelin-With-R/R/lib/rzeppelin'"
and then a bit lower down
Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.2.1:exec (default) on project zeppelin-zrinterpreter: Command execution failed. Process exited with an error: 1
I also tried this Stack Overflow guide: Anyone tried to add R interpreter onto Apache Zeppelin?, and while I was able to run incubator-zeppelin, I received an error when I used either the %spark.r or %r interpreter tags, saying both "interpreter not found" and "prefix not found". Spark doesn't work either after following the first solution, getting the same error mentioned in the second solution (the jar file not being there), and then trying the second solution.
Does anyone have a guide for installing R onto the newest version of Zeppelin? I'm very flexible in the way I can install it. I can run other operating systems onto my computer, and I also have Virtual Box installed on my other computer, which is a mac.
There is currently a bug in the latest HEAD of zeppelin that was recently introduced and prevents the R interpreter from launching cleanly
Did anyone created a Zeppelin Jira Issue for that?
For me it is working on Zeppelin branch-0.6
build Zeppelin with r profile: -DskipTests -Prthis will...
create a directory 'R' in git repo root
copy the 'zeppelin-rinterpreter*.jar' into git_repo_root/interpreter/spark
build Zeppelin with build distro profile: e.g. -DskipTests -Pbuild-distr -Pspark-1.6 -Phadoop-2.6
use zeppelin-distribution/target/zeppelin*.tar.gz for installation
ensure both 1.1 and 1.2 are present in your zeppelin installation
The error you're getting is that you need to have the R package evaluate installed. You can install this simply by launching R and typing install.packages('evaluate').
That said, your excerpt mentions the directory Zeppelin-with-R. That's my repo, which is the R interpreter in the form when it was accepted into Zeppelin. That is version 0.5.6, not 0.6.0. There is currently a bug in the latest HEAD of zeppelin that was recently introduced and prevents the R interpreter from launching cleanly. Your best bet for now is to use the one from my repo and install clean, without trying to pull-in from Zeppelin HEAD.
I want to compile PhantomJS with gstreamer. I downloaded the source code and started the build process with
./build.sh --qmake-args WEBKIT_CONFIG+='use_gstreamer'
I get the following Error
Project ERROR: gstreamer-1.0 development package not found
I have an debian 8.0 system with installed libgstreamer1.0 and glib2.0 (installed with apt-get).
Can someone help me?
If you haven't installed them, you'll need the development packages as well which should be something like libgstreamer(X.X.X)-dev, where X.X.X is whichever version of gstreamer you have installed. The development package has the necessary header files required for compilation.
you may need to modify the build script to add "{GStreamerInstallDir}/1.0/{architecture}/lib/pkgconfig" to the CMAKE_MODULE_PATH configuration so cmake can find the package.
Not sure how to do this in your environment as I build on a windows OS where I just specify this using an environment variable from a wrapping batch script.
Does anyone have a link to clear instructions on how to install and configure the necessary latex packages to build R packages on a mac?
I have some scripts for building and checking R packages on a mac server. They seemed to work fine, but after upgrading to R 3.1.3, many of the packages started failing with
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
Running 'texi2dvi' on 'networkVignette.tex' failed.
Messages:
sh: /usr/local/bin/texi2dvi: No such file or directory
Calls: <Anonymous> -> texi2pdf -> texi2dvi
Execution halted
I found a thread which seemed to suggest I need a more recent version texinfo (5.2) than what is installed by default. And apparently I've I've got the wrong version installed in the wrong location?
which texi2pdf
/sw/bin/texi2pdf
texi2pdf --version
texi2pdf (GNU Texinfo 5.1) 5234
(same version is reported when running system('texi2pdf --version') in R )
This thread gives a link to a texinfo 5.2 source collection:
http://r.789695.n4.nabble.com/R-CMD-build-looking-for-texi2dvi-in-the-wrong-place-R-devel-td4701706.html
But I'm not familiar with installing executable from a tar.gz file on a mac. The R mac help pages I found suggest installing MacTex, which I tried but that didn't seem to help.
** Update: ** additional discussion of related problems on R-SIG-mac mailing list:
https://groups.google.com/forum/#!topic/r-sig-mac/xjyuFdl5Ezk
Update:
Here is where I'm currently at:
I removed my /sw directory to uninstall fink and all of its packages (couldn't figure out how to upgrade it)
installed homebrew
brew install texinfo installs version 5.2 the package,
but generates the message This formula is keg-only, which means it was not symlinked into /usr/local and actually installs in in /usr/local/Cellar/texinfo/5.2/bin which means it is not on the path and R won't find it.
manually symlink each of the texi2pdf, texi2dvi , etc as vincent suggests (this is because R has the /usr/local/bin location as default in the tools::texi2dvi function?
edited the /etc/paths file on the system to add /usr/local/bin so that finds the brew installed 5.2 version before it finds it before the osx system supplied version 4.6 version. This may not be necessary because R has it hardcoded?
All of this gets rid of the "can't find texi* errors", and gives me a bunch of latex errors (which I don't see on unix and windows builds) so I'm still kind of stuck.
This seems very hackish, so there must be a cleaner way? But it sounds like stuff with tex and mac is very sketchy at the moment? https://tex.stackexchange.com/questions/208181/why-did-my-tex-related-gui-program-stop-working-in-mac-os-x-yosemite
This worked for me on Mavericks and on Yosemite:
ln -s /usr/bin/texi2dvi /usr/local/bin/texi2dvi
ln -s /usr/bin/texi2pdf /usr/local/bin/texi2pdf
On my Lion system both the command which texi2pdf at a Terminal/bash prompt and from a R.app GUI prompt tell me that I have that program in:
system("which texi2pdf")
#/opt/local/bin/texi2pdf
That is a location typical for MacPorts installation. I think the /usr/local/bin/ is what the binary R version "expects". I'm not really that UNIX savvy, but I think the you can modify the PATH environment variable so that R will be able to find your installation. (Whether it will be compatible I cannot say since so much detail is missing from your question.) My Tex installation is MacTex, which I got from https://www.tug.org/mactex/. I admit to having a cobbled-together system:
system("echo $PATH")
# /opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin:/usr/X11R6/bin
That gets set at the beginning of an R session because this is the first line in my .Rprofile-(invisible)file:
Sys.setenv(PATH="/opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin:/usr/X11R6/bin")
I think /sw/bin/ installations signify a fink install, which I have had very little success with. Simon Urbanek suggests not using any package installers, but then leaves the rest of us UNIX weenies very little in the way of worked examples of how to install that various external packages that underpin the many interesting and oh-so-useful R packages. So I feel your pain, but I'm not running for President.
So I suppose you could try this at your R console before again attempting one of the earlier unsuccessful installs:
Sys.setenv(PATH=paste( Sys.getenv()$PATH, # should be the character string of the $PATH
"/sw/bin/", sep=":")
)
Wish I could offer guarantees, but if it breaks the only guarantee is that you get to keep all the pieces.
I ran into a similar error message using Mavericks 10.9.5 (factory configured) and R 3.1.
It turns out that I didn't have pdfLaTex. I went to this page: http://tug.org/mactex/ and downloaded the MacTex installation package. It's big (>2GB) but after I installed it, my R package build problems went away.
Hope this might be helpful to anyone else who runs into this error message.
I'm convinced that using Dirk's package is the best way to install and maintain R on an Ubuntu system. But I want to have some fun and get used to installing R from source.
What are the most common configure flags to use when installing?
Also, if I want to install 2.14.1 and I have 2.14.0 currently installed (which was installed from source), should I first uninstall 2.14.0?
There was a recent thread somewhere about having several versions---one from the apt-get repo, one in /usr/local. Try to find that...
Otherwise, I will roll up 2.14.1 on Friday morning, Michael will do his magic and the repo will have .deb packages of 2.14.1 'real soon', sometimes within a day.
Lastly, you can see which flags are used by getting the package sources for which you just do apt-get source r-base (and that works for any Debian/Ubuntu package that way if you have source references in apt's file.
Edit: By the way, regarding the '64-bit' aspect of your question: Nada. We don't do anything differently. It is "merely" the host OS being more generous with resources. But R finds all it needs to know on its own via its configure etc logic.