So I have a problem, because at the moment I have phpunit in a 3.7 version installled through pear. Now, I wanted to upgrade this, but in the documentation they recommend installing it globally through composer. I've done this, it installs the current newest version(5.3) but if i type phpunuit -version it says that I have installed a version 3.7. Now, I can't somehow remove this package from pear, it says that phpunit can not be found, although I can see the phpunit files in the pear directory. If I do pear list, phpunit doesn't show up, so I'm not able to delete this package. Is there a way to overrite the pear phpunit package with that one, that I'm pulling in with composer?
pear list only lists packages from the default channel, which is pear.php.net unless you configured it otherwise.
To see all packages, use the -a flag as described in pear help list:
$ pear list -a
Installed packages, channel __uri:
==================================
(no packages installed)
Installed packages, channel doc.php.net:
========================================
Package Version State
pman 2015.06.19 stable
Installed packages, channel pear.geshi.org:
===========================================
Package Version State
geshi 1.0.8.10 stable
Installed packages, channel pear.php.net:
=========================================
Package Version State
Archive_Tar 1.4.0 stable
Console_CommandLine 1.2.0 stable
Console_Getopt 1.4.1 stable
Net_LDAP2 2.2.0 stable
PEAR 1.10.1 stable
PEAR_Manpages 1.10.0 stable
PHP_CodeSniffer 2.5.0 stable
Stream_Var 1.1.0 stable
Structures_Graph 1.1.1 stable
VersionControl_Git 0.4.4 alpha
XML_Util 1.3.0 stable
Installed packages, channel pecl.php.net:
=========================================
(no packages installed)
Related
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
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?
Installing Rcpp on Linux Ubuntu 12.04, with R2.15.2
NB both R and rcpp were installed yesterday; so I would expect the most recent versions, but Rcpp is installed as an out of date version!
> old.packages()
Package LibPath Installed Built ReposVer
Rcpp "Rcpp" "/usr/lib/R/site-library" "0.9.9" "2.14.1" "0.10.2"
rgl "rgl" "/usr/lib/R/site-library" "0.92.798" "2.12.1" "0.92.894"
Repository
Rcpp "http://www.stats.bris.ac.uk/R/src/contrib"
rgl "http://www.stats.bris.ac.uk/R/src/contrib"
> update.packages("Rcpp")
As the last line shows, it has not updated the package Rcpp at all; What is causing this and what can I do to resolve this?
NB Tried re-installing from two different repositories, both of which claimed to have the most recent version 0.10.2 of rcpp.
Regards
Jefe
You simply misunderstand.
The Rcpp you have is from Ubuntu and installed via apt-get et al. That version is frozen when the distro freezes. This is similar to how gcc, emacs, ... are not the most current version available now but the version taken when the distro was made.
And as an aside, even that Ubuntu version is now dated by one release as 12.10 is out...
So your question title is wrong. The version you have is installed correctly as the version that is part of Ubuntu 12.04. Makes sense now?
Now, if you install Rcpp from CRAN via install.packages() you will get the current version, idem for rgl.
(And there is also a PPA on launchpad which likely to have both as prebuild .deb packages.)
Lastly, and explained before, the path /usr/lib/R/site-library is for the r-cran-* packages you install as .deb files where /usr/local/lib/R/site-library is for your local
installs from R itself. Because of that split, the output of old.packages() that is driven from the former path, eg /usr/lib/R/site-library is bound to behind because it is managed by the distribution, here Ubuntu. You chose the distro for the stability of its components -- and you are free to augment it with CRAN packages in /usr/local/lib/R/site-library. And that is definitely a feature.
Witness this from my Ubuntu box:
R> old.packages(lib.loc="/usr/local/lib/R/site-library/")
NULL
R>
This appears to be an issue known with earlier versions of PEAR, unfortunately the solutions did not work for me.
My setup: Win7, 32bit. PHP directory: c:\Program Files\PHP.
All commands are run from a console with admin rights.
I have installed the latest (on 2012.02.17) version of PEAR available. Using the go-pear.phar it came as 1.9.1.
Then I tried to install PHPUnit by running pear install pear.phpunit.de/PHPUnit and got the following errors:
phpunit/PHPUnit requires PEAR Installer (version >= 1.9.4), installed version is
1.9.1
phpunit/PHPUnit requires package "channel://pear.symfony-project.com/YAML" (vers
ion >= 1.0.2)
phpunit/PHPUnit can optionally use package "phpunit/PHP_Invoker" (version >= 1.1
.0)
phpunit/File_Iterator requires PEAR Installer (version >= 1.9.2), installed vers
ion is 1.9.1
phpunit/Text_Template requires PEAR Installer (version >= 1.9.4), installed vers
ion is 1.9.1
phpunit/PHP_CodeCoverage requires PEAR Installer (version >= 1.9.4), installed v
ersion is 1.9.1
phpunit/PHP_CodeCoverage requires package "phpunit/File_Iterator" (version >= 1.
3.0)
phpunit/PHP_CodeCoverage requires package "phpunit/Text_Template" (version >= 1.
1.1)
phpunit/PHP_Timer requires PEAR Installer (version >= 1.9.2), installed version
is 1.9.1
phpunit/PHPUnit_MockObject requires PEAR Installer (version >= 1.9.4), installed
version is 1.9.1
phpunit/PHPUnit_MockObject requires package "phpunit/Text_Template" (version >=
1.1.1)
phpunit/PHP_TokenStream requires PEAR Installer (version >= 1.9.4), installed ve
rsion is 1.9.1
No valid packages found
install failed
I have tried upgrading PEAR to 1.9.4 by running pear upgrade pear, which results in message
pear/pear is already installed and is the same as the released version 1.9.4
upgrade failed
Forcing the upgrade with -f key works, packages with 1.9.4 in file names are downloaded and successfull install is reported, but pear -V still returns 1.9.1. PHPUnit install still fails. Please help, I am losing my mind.
Are you sure you are running the cmd/powershell with super user privileges? It has happened to me that if I don't the packages are successfully downloaded but not installed.
An older version of PEAR was at c:\PHP, which was referenced in the PATH. PEAR saw this version first and ignored the newer one. The reference to the folder with the older version has to be removed from the PATH variable before installing PHPUnit.
I thank David Harkness for the clue.
When trying to do
pear install phpunit/PHPUnit
I get the following error
Failed to download pear/HTTP_Request2 within preferred state "stable", latest release is version 2.0.0RC1, stability "beta", use "channel://pear.php.net/HTTP_Request2-2.0.0RC1" to install
phpunit/PHPUnit can optionally use PHP extension "curl"
phpunit/PHPUnit can optionally use PHP extension "dbus"
pear/XML_RPC2 requires package "pear/HTTP_Request2" (version >= 0.6.0)
phpunit/PHPUnit requires package "pear/XML_RPC2"
No valid packages found
install failed
It says right there to use another channel, but I can't seem to discover or add that channel! What's the correct command to do this, or what else could I do?
Thank you very much,
MrB
edit:
Got it, wow, 10s after posting.
pear install HTTP_Request2-2.0.0RC1
As mentioned in the online PEAR manual, the PEAR installer by default only installs stable packages. If you wish to install a package that hasn't yet been declared stable, you can do so, without changing the preferred state, by also specifying the version number or its state when attempting to install it. Thus:
$ pear install -f package_name-1.2.3
Or, if a package is in beta you can install it with:
$ pear install -f package_name-beta
Similarly, if the package is in alpha:
$ pear install -f package_name-alpha
There is a 'devel' stability state too, but not that many packages are released in that state.
Sometimes the error message will include a useful hint, as seen in your question above ;)