I am trying to install R-3.1.1 on Fedora 20.
The "make" gives me the following warning
configure: WARNING: you cannot build info or HTML versions of the R manuals
What do I need to do to fix this?
Briefly:
You probably need the texinfo command, cf the R Installation and Administration
manual.
Fedora should have binaries in a repo as well. Question 2.6 of the R FAQ mentions
R binaries for Fedora, maintained by Tom “Spot” Callaway, are provided
as part of the Fedora distribution and can be accessed through yum,
the RPM installer/updater. Note that the “Software” application
(gnome-software), which is the default GUI for software installation
in Fedora 20, cannot be used to install R. It is therefore recommended
to use the yum command line tool.
Related
When I tried to install r package "osmdata" (or any other package) with command
install.packages("osmdata")
it failed with error
"GLIBCXX_3.4.29' not found (required by /home...R/x86_64-unknown-linux-gnu-library/4.2/00LOCK-osmdata/00new/osmdata/libs/osmdata.so)
host system is debian, r is installed using package manager Guix.
The error means: osmdata.so was compiled with g++ version 11.1.0 (ABI mapping of GLIBCXX to g++ version is documented here), but the version of libstdc++.so.6 installed on the system is older, and doesn't provide GLIBCXX_3.4.29.
You need to get a version of osmdata.so appropriate for your system, or you need to build it from source, or you need to update your libstdc++.so.6.
P.S. Your question has nothing to do with glibc.
I solved it by installing package r-guix-install from Guix package manager and using this command
guix.install::guix.install("osmdata")
We need to install R-base version 3.5+ on an offline machine running SLES12.3
We have downloaded all the packages from the the SUSE r repo
http://download.opensuse.org/repositories/devel:/languages:/R:/released/openSUSE_12.3/x86_64/
while running zypper install on the packages there are additional dependencies that we are not able to find the relevant packages to download.
These include:
libtcl8.5.so()(64bit)
libgomp.so.l()(64bit)
But we are not able to find the dependency package that include these libraries.
What should be the correct approach for installing these libraries offline? where can we find these libraries?
Is there a better way for offline installing R-base ? we tried to follow the instructions on the cran rstudio page
The files you downloaded don't match the distribution you're running. SUSE Linux Enterprise (SLE) and openSUSE are similar in some ways, but these are really two separate distributions and you can not always mix binaries between the two. To install R on SLE Server 12.3, you should use the repository https://download.opensuse.org/repositories/devel:/languages:/R:/released/SLE_12/.
You can find out these URLs by looking at the right hand-side column at https://build.opensuse.org/project/show/devel:languages:R:released. Look for things called "SLE" there.
Install the Development Tools, according to this answer
zypper install --type pattern Basis-Devel
Download R source and install it
wget http://cran.univ-paris1.fr/src/base/R-3/R-3.5.0.tar.gz
tar zxf R-3.5.0.tar.gz
cd R-3.5.0
./configure --enable-R-shlib
make
make check
make install
Maybe there are still dependencies missing, which need to be installed with zypper (I don't have any Suse to try myself). With this method you have an "empty" R and you will install R packages one by one (with R CMD INSTALL). Maybe not the best answer for your need, but an answer.
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.
I use Debian sid (amd64), rolling updates as often as weekly. I downloaded recently the desktop version 0.99.902 of RStudio from their offical site and issued (as root, of course):
dpkg -i rstudio-0.99.902-amd64.deb
to no avail:
dpkg: dependency problems prevent configuration of rstudio:
rstudio depends on libgstreamer0.10-0; however:
Package libgstreamer0.10-0 is not installed.
rstudio depends on libgstreamer-plugins-base0.10-0; however:
Package libgstreamer-plugins-base0.10-0 is not installed.
Newer versions (1.0-0) of these 2 packages are installed on the system, but those older ones (0.10-0) are not available anymore on the official Debian repos.
What should be done to have RStudio installed and fully operational under
Debian sid? I have, of course, installed R debs, from official Debian
repositories, without any issues...
Thanks for any help!
RStudio 1.0.153, released on July 20th 2017, depends on GStreamer 1.0 instead of GStreamer 0.10. It can be installed on modern Debian/Ubuntu without any additional setup, rendering this question and my answer obsolete.
To be more specific, there are two different DEB packages. One is aimed at Ubuntu 16.04 (or later) and Debian 9 (or later), comes only in 64-bit flavor and depends on newer GStreamer 1.0. Another package supports Ubuntu from 12.04 up to 15.10 and Debian 8 and it comes in both 32-bit and 64-bit flavors. This one still depends on older GStreamer 0.10.
Original answer remains below.
As of mid-2016, RStudio has hard dependency on GStreamer 0.10 and there is no way around it. You have to install libgstreamer0.10-0 and libgstreamer-plugins-base0.10-0 to use RStudio.
These packages can be easily pulled in from Debian Jessie (stable). Just add Jessie repository to your sources.list and use apt-pinning to give it lower priority:
# /etc/apt/sources.list:
deb http://httpredir.debian.org/debian jessie main
# /etc/apt/preferences.d/01_release:
Package: *
Pin: release o=Debian,a=unstable
Pin-Priority: 600
Package: *
Pin: release o=Debian,n=jessie
Pin-Priority: 10
Then issue apt-get update and follow up with apt-get install libgstreamer0.10-0 libgstreamer-plugins-base0.10-0.
If you have happened to put RStudio .deb file into local repository, then use apt-get install rstudio and GStreamer0.10 will be pulled in by dependency resolver. This has additional advantage of marking these libraries as automatically installed - they will be subject to automatic removal once RStudio drop them as dependency.
But will that break my system?
No.
Upstream developers designed GStreamer0.10 and GStreamer1.0 as co-installable and able to run at the same time (source). In fact, both were available in Debian repository since September 2012 up to April 2016.
In this pinning setup, packages from Jessie repository will be pulled in only when Jessie is the only provider of requested package. There is no risk of overwriting any package from unstable with older version from stable.
Why does RStudio depend on obsolete library?
Because GStreamer0.10 is the newest version available in both Debian Jessie and Ubuntu 12.04, two distributions they want to support.
RStudio will eventually have to upgrade their dependency to GStreamer1.0, as it will gradually become the only version available. I guess this change may be introduced in spring 2017. First, support for Ubuntu 12.04 will end in April. Rstudio is likely to bump base system requirement to 14.04 - one that has both GStreamer0.10 and 1.0. Second, Debian Stretch - that will have only GStreamer1.0 available - is expected to be released around that time.
I found Miroslaw's answer to be excellent. But, due to the passage of time you will need one more package: libssl1.0.0, so your setup apt-get will look like
apt-get install libgstreamer0.10-0 libgstreamer-plugins-base0.10-0 libssl1.0.0
Download libgstreamer0.10-0 for your machine from any of the mirrors.
Open terminal in the directory where the file is downloaded.
Install it using the command, sudo dpkg -i file.deb. Example sudo dpkg -i libgstreamer0.10-0_0.10.36-1ubuntu1_amd64.deb.
Now open the directory where rstudio.deb is located and install it in the same way.
Download the libraries
http://ftp.br.debian.org/debian/pool/main/g/gstreamer0.10/libgstreamer0.10-0_0.10.36-1.5_amd64.deb
http://ftp.br.debian.org/debian/pool/main/g/gst-plugins-base0.10/libgstreamer-plugins-base0.10-0_0.10.36-2_amd64.deb
Install them with gdebi or dpkg -i and that is it
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.