I've written an R package that I keep in a (bare) git repository on an SSH server, and I want to be able to install it on a local machine without needing to clone the repository by hand.
I've attempted the following:
devtools::install_git("ssh://user_name#remote/path/to/repository")
but I get the error
Downloading git repo ssh://user_name#remote/path/to/repository
Error in git2r::clone(x$url, bundle, progress = FALSE) :
Error in 'git2r_clone': Failed to start SSH session: Unable to exchange encryption keys
I'm on a Windows 7 machine, using R 3.1.2, git2r version 0.11.0 and devtools version 1.9.1. Any help would be greatly appreciated. Thanks!
Ran into this issue myself. I know this question is a bit old, but for anybody else running into the same issue (like me), here's what I've found.
The Problem
Likely you don't have the library that git2r (the package that devtools uses to interact with git) uses to communicate over SSH.
The Solution
Install it. The example below assumes Ubuntu.
sudo apt-get install libssh2-1 libssh2-1-dev
git2r uses a library called LibSSH2 to enable transport over SSH. You can install it using your package manager if you're on Linux. NOTE if you're on Windows, git2r does not support the SSH protocol yet :/ As of git2r version 0.11.0 (which uses an updated version of libgit2) it looks like SSH is supported on Windows as well. As of this edit, the newest version of git2r is 0.15, so if you don't have SSH support on Windows, try updating git2r (shout out to zeehio for the news).
After you've installed LibSSH2 you'll need to reinstall the git2r package to enable SSH transport (since it's enabled/disabled during the package build).
Sources
Issues on GitHub:
https://github.com/hadley/devtools/issues/796
https://github.com/ropensci/git2r/issues/140
Why do I need LibSSH2 at all? git doesn't use it, right?
You're right! git doesn't use it (to my knowledge). However, libgit2, which is the pure C git API implementation that git2r uses, does.
Related
I am trying to build a custom debian package of the Cassandra C++ Driver on Jammy (22.04) [0].
It builds fine, but when I manually 'Deploy' the packages to our private JFrog repo no information is shown in the 'Debian Info' section, and the packages are not picked up when I do sudo apt update locally.
Locally doing a dpkg-deb -I <package.deb> shows all the expected information. Also, installing the local package with sudo dpkg -i <package.deb> works fine.
All seems fine when I perform the same actions on Ubuntu Bionic (18.04)
There's nothing in the JFrog UI that indicates any issue with the package.
How can I figure out what's going wrong?
[0] https://github.com/datastax/cpp-driver
cd to 'packaging' and run build_deb.sh
Hello I came across the same issue and found out the problem, since ubuntu 21.10 the default package compression method has changed to zstd but artifactory had no support of this until recently: RTFAC-19541.
So you can either update your artifactory instance to at least version 7.38.0 or use another compression method in your debian package generation process, see the this answer.
Too bad that artifactory didn't print any error for this.
I am using R on Windows to connect to a PostgreSQL database hosted on AWS. The database is set up using forcessl = 1 - this means that any connection needs to be set up with sslmode=require.
The base RPostgreSQL package does not provide any exposure to ssl options. This has been raised as an issue many times (see here, here, here and here)
I know there is a workaround using the RPostgres package, but for other functionality reasons I would much prefer to use the RPostgreSQL package.
A few answers (e.g. here) have proposed using a modified dbname to connect with ssl like so:
dbConnect(dbDriver('PostgreSQL'),
dbname = 'dbname=foobar sslmode=require', # modified dbname
host = 'foobar.rds.amazonaws.com',
port = 5439,
user = 'foobar',
password = 'foobar')
But this did not work for me using the CRAN version of the package. This led me to a recent issue raised on the RPostgreSQL github: https://github.com/tomoakin/RPostgreSQL/issues/88
The initial user was able to use the modified dbname method when he compiled the package from source. On Windows, using the latest source package (0.6.2) compiled with RTools, I get the following error when I run the modified dbname code:
Error in postgresqlNewConnection(drv, ...) :
RS-DBI driver: (could not connect xxxxx.rds.amazonawss.com:5432 on dbname "xxxxxxx": sslmode value "require" invalid when SSL support is not compiled in
)
From this and the rest of the thread, it looks like SSL is not possible from current source in both Windows and Mac. However, the developer suggests:
If you compile in a environment where libssl and libpq was made SSL activated form, then the driver can use SSL.
I think this means I could manually download the libs and compile myself, but I am not sure if it is a quick fix or if it would require significant rewriting of the package. Any help or pointing in the right direction would be much appreciated. How can I do this in a safe, repeatable way?
I was able to solve this for the El Capitan macOS R users in my office, by doing the following:
Remove RPostgreSQL R package if you already have installed. Methods vary on how to do this, but from either R.app console or R in Terminal, type remove.packages('RPostgreSQL')
Make sure you have Homebrew installed, and from Terminal run: brew install libpq openssl
Open R.app, and from the Packages & Data menu, select Package Installer.
From the first drop-down menu, choose CRAN (sources) (choose mirror closest to you if you haven't used this before).
Using package search, find RPostgreSQL and for the options below, keep At System Level checked, and check Install Dependencies, then click Install Selected.
Quit out of all R and RStudio programs, and try using the new from source installed RPostgreSQL package.
DISCLAIMER: If you have heavy compile dependencies on OpenSSL or libpq for other programs, I have no idea how doing the above may break other programs.
Building on Windows is a can of worms. See R-Admin Windows Toolset. The only openSSL binaries for windows are from unknown developers. Building and installing openSSL on windows is another can of worms that you will need to research. It might be easier to install openSSL inside the R Windows build environment, but I have no experience with that.
EDIT: It turns out that when installing postgres on Windows, postgres installs openSSL. That means that the central problem on Windows is installing the Windows Toolset for R, installing postgres, then pointing the R build system to libpq.
Another solution would be to run linux in a virtual machine under windows. Here is one way to Install linux on Windows. With linux, depending on the distribution, you would only need to do something like the following from the linux command line (for a RedHat variant of linux):
sudo yum install openSSL
sudo yum install postgresql96
sudo yum install R
Line 2 installs libpq which is required for RPostgreSQL. It is libpq which must be compiled with openSSL. You will only be installing and using the PostgreSQL client, not the server and will also get psql. There might be other packages required, see R linux toolset. Normally, these will get pulled in with the above and should not be a problem.
RPostgreSQL contains a version of libpq, but the compile script does not look like it checks for openSSL, at least not on macOS. So it is important to get a system provided libpq installed.
It is also important for the RPostgreSQL configure script to find pg_config, which is installed when postgres client is installed. Not sure about windows through. So make sure pg_config is in your path. Type pg_config to find out.
Now you need to download and compile RPostgreSQL. To start R, type the following at the linux terminal.
R
Then from within R, get, compile and install RPostgreSQL:
install.packages("https://cran.r-project.org/src/contrib/RPostgreSQL_0.6-2.tar.gz", repo=NULL, type="source")
This should compile and install this version of RPostgreSQL. This last line should also work in windows if you have the windows tools installed correctly.
Hopefully, this gives you some ideas.
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.
I'm unclear about how to install an R package under R/pub in openCPU on my own openCPU server. The openCPU documentation states that package installation is handled by the administrator, but does not give any instructions (that I can find) concerning package installation.
I'm sure I'm missing something obvious but any help with this would be appreciated.
FWIW, I'm attempting to install the ''markdown'' package, which for some reason wasn't installed when calling opencpu-cran.
UPDATE:
I found this link to an example. It calls to the following URL "/Radmin/call/opencpu.demo/install.opencpu/json", but that approach appears not to work based on this SO question. So, if that's not the way to install packages via openCPU, how is it done?
The /R/pub endpoint contains all packages in public R libraries on the system. To install a package, you could ssh into the system, start R as root sudo -i R and then simply use install.packages to install the packages to the global library.
Alternatively, you can install one of the many r-cran-* packages which are available through the ubuntu repositories or cran2deb4ubuntu launchpad, e.g:
sudo apt-get install r-cran-xml
i am trying to install RODBC with the commadn R CMD INSTALL -l /my/local/path RODBC.tar.gz and it wont find sql.h and sqlext.h ..how do i pass the include and lib paths to this command?
I had a similar problem recently while trying to install RODBC on an instance of Centos 5.8 x64. (Instead of using R CMD install, I just did sudo R, then installed the package inside R - but I was still having the same problem).
I resolved this by installing the following packages using yum:
unixODBC
unixODBC-libs
unixODBC-devel
mysql-connector-odbc
freetds
freetds-devel
Those last two are necessary because I was interfacing with an MSSQL server, which requires TDS. Anyway, once I installed unixODBC and the libs and development package, I was able to install RODBC with no difficulty (again, using sudo R and then install.packages("RODBC").
The only other thing to do is install the correct drivers/libraries for ODBC, which is what mysql-connector-odbc is. You will need to configure unixODBC to meet your needs, but the documentation is pretty solid, so I don't think you'll have too much difficulty.