I am trying to install DeployR Open 8.0.0 on Windows 10 (64 bits). I have installed the following dependencies:
JRE 8
Revolution R Open 3.2.2 and MKL (RevoMath 3.2.2)
DeployR Rserve 7.4.2
I followed the install instructions for RRO & MKL and DeployR. I have also done a clean install, that is prior to installing all these stuff, I uninstalled R, and RStudio.
However, when start installing DeployR Open 8.0.0 (even as Administrator), it is unable to find the dependencies/prerequisites, and on clicking next it opens this page, which more or less talks about the same set of dependencies.
Here are the screenshots:
I am not sure what I am missing here. Please suggest.
Related
I am trying to install two packages in R (3.3.2): devtools and git2r. They are depending on the existence of zlib. This comes with macOS Sierra (10.12.3) and it's version 1.2.8 by default.
When I'm trying to install these packages I get the error below.
I've been trying a lot of things.
directly installing via CRAN in RStudio: no effect.
trying to locate zlib on macOS: can't find zlib.
installing via R CMD INSTALL git2r: no effect.
I notice someone has a similar issue posted on GitHub: https://github.com/ropensci/git2r/issues. There is no solution yet.
Does anyone here have an idea?
Thanks!
Sander
ERROR MESSAGE BELOW
configure error in "/private/tmp/RtmpP6HZFx/R.INSTALLe73412909267/git2r"
configure error
The zlib library that is required to build git2r was not found.
Please install:
zlib1g-dev (package on e.g. Debian and Ubuntu)
zlib-devel (package on e.g. Fedora, CentOS and RHEL)
and try again.
If the zlib library is installed on your system but the git2r configuration is unable to find it, you can specify the include and lib path to zlib with:
"R CMD INSTALL --configure-args='--with-zlib-include=INCLUDE_PATH --with-zlib-lib=LIB_PATH' git2r"
See "config.log" for more details
ERROR: configuration failed for package "git2r"
*removing "/usr/local/lib/R/3.3/site-library/git2r"
UPDATE: the same issue persists on macOS X 10.12.5 in combination with R 3.4.0 - the latter I need for DESeq2.
Solution...Mmm. Not really. I simply uninstalled R and all the packages, and than I reinstalled everything again. I installed R and RStudio via homebrew, following the instructions here: https://rud.is/b/2015/10/22/installing-r-on-os-x-100-homebrew-edition/.
Oddly enough: all issues disappeared.
UPDATE #1: this solution does not - obviously - work for the combination R 3.4.0 and macOS X 10.12.5. We need a solution for this issue.
UPDATE #2: I have discovered what I believe was the issue: a wrong path to the xcode command line tools.
sudo xcode-select --reset did the trick and now xcode-select -p points to /Library/Developer/CommandLineTools. And which xcode-select points to /usr/bin/xcode-select. Googling I discovered that it is not needed to install Xcode through the App Store as it states on http://railsapps.github.io/xcode-command-line-tools.html:
"On earlier versions of macOS, it was more difficult to install Xcode Command Line Tools. It required a huge download of the full Xcode package from the Mac App Store or registration as an Apple developer for a smaller Command Line Tools package. Mac OS X Mavericks made installation of Xcode Command Line Tools much simpler.".
i was having the same problem. i have a note 8(samsung). just go to GitHub and install zlib from there.
This the the error I get when I try to install or update any packages within Rstudio (latest version) on Windows 8 x64:
"Error in install.packages : object 'Rmd5' not found."
Try running the install or update in straight old R 64 bit version.
If you can make that fly. I would install installR using R 64 bit (NOT STUDIO) you can then use that to update any and all packages and versions of R pretty effortlessly. It manages dependencies and errors well.
After installing Mavericks on my Mac, I'm not able to run Rattle anymore.
Because of compatibility issues between RStudio and 10.9 (http://www.r-bloggers.com/rstudio-and-os-x-10-9-mavericks/), I installed v 0.98.433 of RStudio and R 3.0.2
Tried to launch Rattle the normal way: none.
I tried in a different way:
I manually launched xQuartz to install GTK+
via R-Studio I installed RGtg2 and Cairo
Installed Rattle, launched it and I got 1 sec message from Rattle, before it disappeared, crashing R session.
I then tried going back to R 2.15.3 (using RSwitch), doing same procedure.
Rattle starts with no ricognizable character and a bunch of related error messages on the RStudio console, from Pango.
Problem is it is looking for a directory .../pango/1.6.0 that does not exist (I have /1.8.0).
Is there any one who came out with a working combination of R/RStudio/Rattle on Mavericks?
I have a course I'm going to teach on data mining next semester and I introduced Rattle as the core tool, but I need it running.
Going back to previous Mac OS is not an option, because students may have the latest version.
Any help would be highly appreciated
I believe that the problem is with the GTK2 and Cairo modules. After building a few packages from source, rattle works for me...
I have had difficulties with Cairo/GTK2 since Mountain Lion. I got crashes using Simon's binary packages for these. Note that I updated my system to Mavericks, so I have not tried this on a clean install... I also have Homebrew installed for building programs from source. I use the ATT binary installer for R (thanks, Simon) for most packages but build a few packages from source. There were some hiccups and I spent a lot of time searching with Google. Here is what I did:
One needs XCode and the Xcode command line tools installed. After you install XCode, you need to run
sudo xcode-select --install
to install the command line tools. Then install Homebrew according to directions from the web site... Install gtk+ and cairo with their dependencies with:
brew install gtk+ cairo
And wait quite a while for everything to build....
The first problem I had is that I couldn't build any R packages from source because of this error:
make: llvm-gcc-4.2: No such file or directory
Google to the rescue...
I needed to change two lines in Makeconf in /Library/Frameworks/R.framework/Resources/etc to
CC=clang
CXX=clang++
Note: the R Mac Tools page now says this should be:
CC=/usr/local/clang4/bin/clang
CXX=/usr/local/clang4/bin/clang++
LDFLAGS=-L/usr/local/clang4/lib
Then download the source packages for RGtk2, Cairo, and cairoDevice. I do all the work in my ~/bld directory with:
cd ~/bld
export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/Library/Frameworks/GTK+.framework/Versions/Current/Resources/lib/pkgconfig:$PKG_CONFIG_PATH
R CMD install RGtk2_2.20.25.tar.gz
R CMD install Cairo_1.5-2.tar.gz
R CMD install cairoDevice_2.19.tar.gz
Hope this helps.
I'm trying to install the development version of gWidgets2 in a WIndows XP system.
Unfortunately when I'm running
require(devtools)
install_github("gWidgets2", username="jverzani")
install_github("gWidgets2RGtk2", username="jverzani")
the tar.gz file is downloaded and not the zip windows version.
> building 'gWidgets2RGtk2_1.0.tar.gz'
So I downloaded manually the jverzani-gWidgets2-79fd592.zip file from https://github.com/jverzani/gWidgets2/downloads and I tried to install the package locally. But then I receive
> utils:::menuInstallLocal()
and the file is not installed.
The same happens with gWidgets2tcltk, gWidgetsWWW2, gWidgets2 and gWidgets2RGtk2.
Is there anybody who has tried to do the same ?
Thank you in advance
Windows XP, R 2.11.1, Java JRE6
I just installed the Jaguar package.
From an R console, I can do this:
> library(JGR)
Loading required package: rJava
Loading required package: JavaGD
Loading required package: iplots
Please use the corresponding JGR launcher to start JGR.
Run JGR() for details. You can also use JGR(update=TRUE) to update JGR.
and so JGR appears to be correctly installed.
JGR() yields
On Windows JGR must be started using the JGR.exe launcher.
Please visit http://www.rosuda.org/JGR/ to download it.
>
I'm not sure how to run Jaguar - I know I have to run jgr.exe - but should R be already open? If so, should the JGR library be already loaded? I've tried all of these, and what seems to happen regardless is a console window opens briefly, then disappears. I've run jrg --debug, with no apparent error message: (same file regardless of choice made above).
What should I be doing?
Thanks!
System: Version 5.1 (build 2600), platform 2 [Service Pack 3]
JGR loader version 1.61 (build Jul 23 2008)
parseParams> 1 parameters parsed.
parseParams par 10> "--debug"
> rhome="C:\Program Files\R\R-2.11.1"
> srhome="C:\PROGRA~1\R\R-211~1.1"
getPkgVersion(JGR): 010702
getPkgVersion(rJava): 000805
getPkgVersion(JavaGD): 000503
getPkgVersion(iplots): 010103
Loading preferences from "C:\Documents and Settings\gblais\.JGRprefsrc"
> javakey="Software\JavaSoft\Java Runtime Environment\1.6"
> javah="C:\Program Files\Java\jre6"
> tp="C:\Perl\site\bin;C:\Perl\bin;C:\PHP\;C:\Program Files\MiKTeX 2.8\miktex\bin;C:\Python26\Lib\site-packages\PyQt4;C:\Program Files\Tcl\bin;C:\oracle\product\10.2.0\client_2\BIN;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\Support Tools\;c:\belfry;c:\belfry\usr\local\wbin;C:\WINDOWS;C:\WINDOWS\System32;C:\WINDOWS\System32\WBEM;c:\Program Files\QuickTime\QTSystem\;C:\Program Files\SlikSvn\bin\;c:\progra~1\Microsoft Visual Studio 9.0\VC\bin\"
Got RuntimeLib from registry, using "C:\Program Files\Java\jre6\bin\client;" PATH prefix.
Java home: "C:\Program Files\Java\jre6"
R home: "C:\Program Files\R\R-2.11.1"
JAR files: "-Drjava.class.path=C:\PROGRA~1\R\R-211~1.1\library\rJava\jri\JRI.jar;C:\PROGRA~1\R\R-211~1.1\library\iplots\java\iplots.jar;C:\PROGRA~1\R\R-211~1.1\library\JGR\java\JGR.jar;C:\PROGRA~1\R\R-211~1.1\etc\classes;C:\PROGRA~1\R\R-211~1.1\etc\classes.jar"
desired PATH: "C:\Program Files\Java\jre6\bin\client;C:\Program Files\Java\jre6\bin\client;C:\Program Files\Java\jre6\bin;C:\Program Files\R\R-2.11.1\bin;C:\PROGRA~1\R\R-211~1.1\library\rJava\jri;C:\Perl\site\bin;C:\Perl\bin;C:\PHP\;C:\Program Files\MiKTeX 2.8\miktex\bin;C:\Python26\Lib\site-packages\PyQt4;C:\Program Files\Tcl\bin;C:\oracle\product\10.2.0\client_2\BIN;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\Support Tools\;c:\belfry;c:\belfry\usr\local\wbin;C:\WINDOWS;C:\WINDOWS\System32;C:\WINDOWS\System32\WBEM;c:\Program Files\QuickTime\QTSystem\;C:\Program Files\SlikSvn\bin\;c:\progra~1\Microsoft Visual Studio 9.0\VC\bin\"
actual PATH: "C:\Program Files\Java\jre6\bin\client;C:\Program Files\Java\jre6\bin\client;C:\Program Files\Java\jre6\bin;C:\Program Files\R\R-2.11.1\bin;C:\PROGRA~1\R\R-211~1.1\library\rJava\jri;C:\Perl\site\bin;C:\Perl\bin;C:\PHP\;C:\Program Files\MiKTeX 2.8\miktex\bin;C:\Python26\Lib\site-packages\PyQt4;C:\Program Files\Tcl\bin;C:\oracle\product\10.2.0\client_2\BIN;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\Support Tools\;c:\belfry;c:\belfry\usr\local\wbin;C:\WINDOWS;C:\WINDOWS\System32;C:\WINDOWS\System32\WBEM;c:\Program Files\QuickTime\QTSystem\;C:\Program Files\SlikSvn\bin\;c:\progra~1\Microsoft Visual Studio 9.0\VC\bin\"
getenv PATH: "C:\Perl\site\bin;C:\Perl\bin;C:\PHP\;C:\Program Files\MiKTeX 2.8\miktex\bin;C:\Python26\Lib\site-packages\PyQt4;C:\Program Files\Tcl\bin;C:\oracle\product\10.2.0\client_2\BIN;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\Support Tools\;c:\belfry;c:\belfry\usr\local\wbin;C:\WINDOWS;C:\WINDOWS\System32;C:\WINDOWS\System32\WBEM;c:\Program Files\QuickTime\QTSystem\;C:\Program Files\SlikSvn\bin\;c:\progra~1\Microsoft Visual Studio 9.0\VC\bin\"
argv[0]:C:\PROGRA~1\Java\jre6\bin\java.exe
argv[1]:-Drjava.class.path=C:\PROGRA~1\R\R-211~1.1\library\rJava\jri\JRI.jar;C:\PROGRA~1\R\R-211~1.1\library\iplots\java\iplots.jar;C:\PROGRA~1\R\R-211~1.1\library\JGR\java\JGR.jar;C:\PROGRA~1\R\R-211~1.1\etc\classes;C:\PROGRA~1\R\R-211~1.1\etc\classes.jar
argv[2]:-Xmx512m
argv[3]:-cp
argv[4]:C:\PROGRA~1\R\R-211~1.1\library\rJava\java\boot
argv[5]:-Drjava.path=C:\PROGRA~1\R\R-211~1.1\library\rJava
argv[6]:-Dmain.class=org.rosuda.JGR.JGR
argv[7]:-Djgr.load.pkgs=yes
argv[8]:-Djgr.loader.ver=1.61
argv[9]:RJavaClassLoader
argv[10]:--debug
Have you tried the instructions from the JGR website?
Installation instructions:
Download and install R 2.5.0 or higher (Linux/Solaris: make
sure --enable-R-shlib was used when
compiling R)
Download the appropriate JGR application for your OS from above
(Windows/Mac OS X) or install JGR
package from CRAN.
Start the JGR application! JGR will install all necessary packages
directly from CRAN (or the RoSuDa
server). (You should have
administrator rights to get the
packages installed)
After step 3 completed successfully, JGR is fully installed
and can be used.
Windows users: if you have more than one JDK version installed, you
can use this tiny tool to select the
default version that will be used with
JGR: jselect.exe.
The Windows launcher accepts the
following optional command line
parameters:
--debug - show debugging info and create c:/jgrdebug.txt (must be the
first parameter if used)
--rforge - use www.rforge.net for package installation instead of CRAN
(useful to install latest development
packages)
--cran=xxx - use xxx as CRAN mirror for package installation
--libs=xxx - use xxx as package location (use only if you don't have
write permission in the default R
package location)