Is it possible to install the current R-devel version via homebrew?
I have already tried brew install --devel r, which does not work.
The reason is indicated in the error message Error: No devel block is defined for r. If you run brew edit r you'll note there is no devel code block indicating the necessary url for the requested development version. Alternatively, you can append the --HEAD flag which will install the most recent r version with the latest commits available in the source repo. The difference between --devel and --HEAD flags is discussed in the Homebrew formula cookbook. Similar info is also discussed here.
Related
While trying to install R from source, I ran into linker issues, in particular: undefined reference to 'u_getVersion_58
I found limited information on this error (eg, this post on the RStudio forum).
Despite running apt-get build-dep, these issues persisted.
It is apparent from these comments by Dirk Eddenbuettel that it relates to libicu versions. I have libicu version 60, while R 3.6.0 and similar recent versions seem to require version 58.
We can install a previous version of libicu from source as follows:
wget http://download.icu-project.org/files/icu4c/58.2/icu4c-58_2-src.tgz
tar -xf icu4c-58_2-src.tgz
cd icu
make
make install
However, make is likely to run into a compilation error due to missing xlocale.h. As indicated on this github post, this can be solved by running ln -s /usr/include/locale.h /usr/include/xlocale.h, as xlocale.h is just a subset of locale.h which was removed from glibc recently. After this, make and make install should succeed for icu version 58, and following that, for R.
I came across a package that is not available on CRAN. I tried to install the package using:
Packages & Data > Package Installer > Local Binary Package > At User
Level > [FileName.tgz] > Install...
This didn't work and I am now trying to use the R CMD INSTALL command. However, it seems I need to run that command in the command line interface but I cannot get it to install properly.
The package I'm trying to install is called gEcon. It can be found here. In particular, I am getting the following error message after "installing" the package:
Error: package or namespace load failed for ‘gEcon’:
package ‘gEcon’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
I assume it's the way I'm installing it.
Thanks in advance.
You're going to need to install Xcode apparently, because you've got to install this from source per these directions:
Now, you've gotta update R to the latest stable release, or if you prefer you can find the exact minimum newest version needed for gEcon.
After upgrading R you can complete the installation from source.
Original answer to original question:
Two things:
To access the command line and use R CMD on an Apple computer, please use the terminal.app app. Please see this for more details.
An easier and probably better approach is to install your package from the author's Github (or BitBucket, etc) repository using devtools::install_github or just use devtools::install on the downloaded source project.
Trying to compile R-3.3.2 on Debian Jessie, all dependencies are installed. However the ./configure script complains about the zlib/bzip2 library versions not matching with the minimum requirement.
Minimum version required:
zlib: 1.2.6 (installed version: 1.2.11)
bzip2: 1.0.6 (installed version: 1.0.6)
After looking at the parts of configure script checking the library versions, it seems that it compares versions with strcmp or strncmp. Since "1.2.11" is lexicographically smaller that "1.2.6" it return a non-zero value indicating that the match failed. Besides, it just compares the first 5 characters which is also not what it is intented. So, it's a bug in configure script. Changing the script fixed the issue.
For zlib, find this line:
exit(strncmp(ZLIB_VERSION, "1.2.5", 5) < 0);
Change it to:
exit(ZLIB_VERNUM < 0x1250);
I had some issues installing R myself, specifically with the error
checking for BZ2_bzlibVersion in -lbz2... no
I had to install libbz2-dev to get that error to go away.
Unfortunately, I came across a few more issues while running ./configure and had to do a little more digging to find out how to solve it.
Discussion on issue
After reading that, I had realized I had to install a couple packages like libcurl4-openssl-dev, libpcre3, and liblzma-dev to finally finish the configuration.
The cited link suggested
At this stage you could have as well tried to install R 3.2.0RC ...
R-devel has not yet diverged much.
Personally, I think that installing an older version to resolve dependency issues reeks of laziness, but that's just my two cents.
I use travis to check my R package, it's based on a virtual machine of ubuntu. One of my dependencies is rgdal from CRAN, which cannot be installed correctly on travis.
First it said:
ERROR: dependencies ‘rgdal’ is not available for package ‘my package’
I followed the instruction here, then comes the endless dependencies, I installed one by one, according to the instruction of every trial. Finally I installed packages is as below：
libproj-dev
libcurl4-gnutls-dev
libdap-dev
libgdal-dev
libgdal1h
libhdf5-dev
libhdf5-serial-dev
libgdal-dev
libgdal1-dev
It said I still need to install libhdf5-7 = 1.8.11-3ubuntu1~precise1~ppa1
But when I install package libhdf5-7 = 1.8.11-3ubuntu1~precise1~ppa1, it gives another error:
E: Unable to locate package
E: Unable to locate package 1.8.11-3ubuntu1~precise1~ppa1
E: Couldn't find any package by regex '1.8.11-3ubuntu1~precise1~ppa1'
And it seems no more solutions now.
I wonder how to fix this on travis? Is it a common issue on only travis virtual machine or it could happen on any ubuntu machine? Or the package rgdal has some problems with ubuntu?`
Background:
All my installation above used apt-packages of travis, which is explained as below by travis:
apt_packages: A list of packages to install via apt-get. Common examples here include entries in SystemRequirements. This option is ignored on non-linux builds
As of this week, you can opt into using Ubuntu 14.04 on Travis:
See this blog post from Travis for details
See this .travis.yml where I enable Trusty aka 14.04
Switching to 14.04 may be enough in this case. If not, also note that you can prepare your own .deb packages. I mention this in an blog post from this summer.
As the geospatial packages are a little involved that is probably your best. You would need to know how to build Debian packages, and how to use Launchpad to have them auto-built for you. Both topics have lots of tutorials.
My R version is 2.7.1 (on Debian) and some packages are asking for > 2.10. I cannot find updating instructions and I don't want to remove and reinstall as I have other things depending on R and I don't want to mess up. Is there an update procedure?
Closest thing to my problem is on this thread.
check out the instructions for installing from source. Its easy on a Linux box, and you can do the install in any directory you like, you dont even need superuser permissions. Once compiled you can even run R from that directory without messing up any system-installed R. As long as you give the full path to R's binary, or put the path to it in your PATH environment variable, when starting it it will work fine.
FYI
It seems that R on Debian with versions previous to 2.7.1 cannot be updated.
The current core runs from 2.7.1 up. The only way to do it is to remove the existing version.
As this was not straight forward I post it here. If you have Rapache or other things connecting to R disable them with dismode or related.
apt-get purge r-base r-base-dev
I had to do this as well
dpkg -P r-base-core
until this shows no more installed R packages
dpkg -l r-*
Then follow the instruction from http://cran.r-project.org/bin/linux/debian/, with the amendment that you should use deb instead of deb-src in /etc/apt/sources.list.
deb http://<favorite-cran-mirror>/bin/linux/debian lenny-cran/
Before installing run this and it should not say 2.7.1.
apt-cache policy r-base-dev