For two days I've been trying to install Openblas/atlas with Lapack and use it in R. it's driving me crazy. I'm at a point where I can't even think anymore.
My server uses:
Red Hat Enterprise Linux Server release 6.6 (Santiago)
Here is what I've installed so far:
[root#tpdb05 atlas]# yum install atlas.x86_64 blas.x86_64 lapack.x86_64 Loaded plugins: product-id, refresh-packagekit, rhnplugin, security, subscription-manager
Setting up Install Process
Package atlas-3.8.4-2.el6.x86_64 already installed and latest version
Package blas-3.2.1-4.el6.x86_64 already installed and latest version
Package lapack-3.2.1-4.el6.x86_64 already installed and latest version
[root#tpdb05 ruser]#
yum install lapack.i686
Installed:
lapack.i686 0:3.2.1-4.el6
Dependency Installed:
blas.i686 0:3.2.1-4.el6 glibc.i686 0:2.12-1.166.el6_7.3 libgfortran.i686 0:4.4.7-16.el6
nss-softokn-freebl.i686 0:3.14.3-23.el6_7
Dependency Updated:
glibc.x86_64 0:2.12-1.166.el6_7.3 glibc-common.x86_64 0:2.12-1.166.el6_7.3 glibc-devel.x86_64 0:2.12-1.166.el6_7.3
glibc-headers.x86_64 0:2.12-1.166.el6_7.3 nss-softokn-freebl.x86_64 0:3.14.3-23.el6_7
yum install atlas.i686
Installed:
atlas.i686 0:3.8.4-2.el6
[root#tpdb05 SRPMS]# yum install rpm-build
Installed:
rpm-build.x86_64 0:4.8.0-47.el6
Dependency Installed:
redhat-rpm-config.noarch 0:9.0.3-44.el6
Dependency Updated:
rpm.x86_64 0:4.8.0-47.el6 rpm-libs.x86_64 0:4.8.0-47.el6 rpm-python.x86_64 0:4.8.0-47.el6
[root#tpdb05 SRPMS]# yum install atlas-c++-devel.x86_64
Installed:
atlas-c++-devel.x86_64 0:0.6.1-1.el5.rf
Dependency Installed:
atlas-c++.x86_64 0:0.6.1-1.el5.rf
several sources I've tried without success:
1 2 3
The R manual mentions the following:
The usual way to specify ATLAS will be via
--with-blas="-lf77blas -latlas"
However I have no clue where to use this command. While installing R? I'm pretty sure it should be possible to simply swap between libraries..
How do I get R to use the atlas/openblas/lapack libraries?
Related
I have had problems compiling Quantlib for Debian 9 and tried to install r-cran-rquantlib via apt from https://cloud.r-project.org/bin/linux/debian stretch-cran35/
I get the following error which I do not understand since I have both Rcpp and zoo already installed.
$ sudo apt install r-cran-rquantlib
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-cran-rquantlib : Depends: r-cran-rcpp (>= 0.11.0) but it is not going to be installed
Depends: r-cran-zoo but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
Is this a version mismatch problem? r-cran-rquantlib installs fine in Debian 10
I follow the instructions to install meteor 1.6 on Windows(10) as stated on Meteor.com (choco install meteor) and it's installed a meteor v0.0.2 ?
When I try to run any meteor command I get: bash: meteor: command not found
and when I try choco upgrade meteor I get:
$ choco upgrade meteor
Chocolatey v0.10.8
Upgrading the following packages:
meteor
By upgrading you accept licenses for the packages.
meteor v0.0.2 is the latest version available based on your source(s).
Chocolatey upgraded 0/1 packages.
See the log for details (C:\ProgramData\chocolatey\logs\chocolatey.log).
I tried choco uninstall meteor and then reinstall choco instlal meteor but same issue. Searching around online a little I found this page:
https://chocolatey.org/packages/meteor
I do have meteor installed and running on version 1.6.0.1 on Window 10's Ubuntu bash which was installed via curl https://install.meteor.com/ | sh
Following on from above post https://stackoverflow.com/a/47967277/642729 by Gary Ewan Park. The below comment on https://chocolatey.org/packages/meteor clarifies the Chocolately/Meteor versioning
The current version of Meteor is 1.6;
is this the version in the 0.0.2 Chocolatey package?
[Garrie Powers • 2 months ago]
The version number of the Chocolatey package is the version of the installer.
Meteor is unique in the way it works in that all versions
are capable of springboarding to other versions.
Therefore, in the same way as the Unix installer installs the latest version,
the Chocolatey installer will always install the latest version.
So at this exact moment, the answer to your question is "yes"!
[Jesse Rosenberger Garrie Powers • 2 months ago]
The best advice would be to reach out to the maintainers of that package of chocolatey.org. This can be done by clicking on the "Contact Maintainers" link of this page:
https://chocolatey.org/packages/meteor
It would seem that the creators of the application, also own the Chocolatey package, so hopefully they will get back to you.
From the official installer github:
The version of this Meteor installer is not to be confused with Meteor itself. Meteor, once installed, will always "springboard" to (download, install and run) the correct version of Meteor necessary for the application being executed.
...
When necessary, specific versions of Meteor can be installed using
Chocoloatey's --params argument which will download that specific
version from Meteor's installation server. For example, to install
Meteor 1.5.4.4:
C:> choco install meteor --params="'/RELEASE:1.6.0.1'"
Note: Prior to
Meteor 1.6, 64-bit versions were not available. Therefore, in order to
install versions prior to Meteor 1.6, you'll also need to pass
Chocolatey's --x86 option when running choco install on 64-bit Windows
platforms. For example:
C:> choco install meteor --x86 --params="'/RELEASE:1.5.4.4'"
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
I am installing a custom debian package on debian 6 machine.
This is my control file
Package: [[name]]
Version: 5.1
Section: hello/world
Priority: Optional
Architecture: all
Essential: no
Depends: my-dependent-package (>> 0.2.1)
Installed-Size: 1000
Maintainer: Test test#test.com
Description: _DESCRIPTION_
Here the my-dependent-package doesnt get auto upgraded when newer versions are released.
i always do sudo apt-get update before installing.
installing the debian from an internal mirror and using
sudo apt-get install mypackage
the dependent package "my-dependent-package" is also available in the same internal mirror.
the internal mirrors are defined in /etc/apt/sources.list
both the packages come from same mirror
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
my-package : Depends: my-dependent-package (>> 0.2.1) but it is not going to be installed
E: Broken packages
Installation succeeds when I manually install the "my-dependent-package". I was expecting it to be auto installed by the "my-package" as I have mentioned it in control file.
How can I enable it ?
Debian assigns priorities to suites and packages.
Most likely your local repository has a low priority, which results in being excluded from automatic updates.
Configure apt to assign a higher priority to your repository, so it get's automatically selected.
See the AptPreferences documentation for more information.
(It's really impossible to give you a walkthrough without more knowledge on your actual setup)
I am trying to install OMD in my CentOS 6.6 linux machine using this link [https://mathias-kettner.de/checkmk_install_with_omd.html.][1] Initially I installed epel repoistory and then when in tried installing OMD it says the following.
[root#ctg-alpha-mon1 /]# yum install --nogpgcheck omd-0.42-0.42-
centos55.14.x86_64.rpm
Loaded plugins: aliases, changelog, downloadonly, fastestmirror, kabi, presto, refresh-packagekit, security, tmprepo,
: verify, versionlock
Loading support for CentOS kernel ABI
Setting up Install Process
Loading mirror speeds from cached hostfile
* base: mirrors.centarra.com
* epel: lug.mtu.edu
* extras: mirrors.centarra.com
* updates: mirrors.centarra.com
No package omd-0.42-0.42-centos55.14.x86_64.rpm available.
Error: Nothing to do
I tried 'yum search omd* ' or 'yum search omd-' but still it says no package available.
How do I install omd? I am pretty new to this.
Will omd package be available in the linux for us to install or should I get it from somewhere and then install it?
Any help is much appreciated.
Thanks
The OMD package is not available on a yum repository, except for subscribers.
OMD package has to be downloaded from their site or lookup the community version. Have a look at http://omdistro.org/ and https://labs.consol.de/de/nagios/omd-repository/