I need to install netcdf-openmpi-devel on Red Hat 6. The problem is that this is not provided by the repositories I have: redhat and epel. I already tried downloading several fedora rpms, but for almost all of them, it's not possible to verify their keys (doing rpm -K package). I was able to get one key for one of the rpms, but then it shows that I don't have the required dependencies like:
netcdf-openmpi, which is kind of what I am trying to install.
Is there another way to install this?
Thanks for your help!
The cleanest approach is to build an RPM package against the RHEL6 package set. This will make sure that all dependencies are satisfied. To do this, taking advantage of already existing packages, you can clone the Fedora netcdf package files from [1] and then build the package with mock, using rpmbuild (see [2]) or, actually better, mock (see [3]).
You might encounter the situation where a build dependency is not available in the rhel or epel repos. You can then again clone the respective package files from the Fedora git repository and build that package before.
So, to wrap up your steps might look something like this:
$ git clone git://pkgs.fedoraproject.org/netcdf.git
$ cd netcdf
## Look at netcdf.spec, make changes if necessary
## To build using rpmbuild (probably easier than mock)
# yum install rpmdevtools
$ rpmdev-setuptree
$ mv netcdf.spec $HOME/rpmbuild/SPEC
$ mv * $HOME/rpmbuild/SOURCES
$ cd $HOME/rpmbuild/SPEC
$ rpmbuild -ba netcdf.spec
## rpmbuild might complain about unsatisfied build dependencies. Install these as necessary, some build dependencies might not be available in the repos, you will need to build then following the same procedure.
One particular thing you'll need to be aware of is that there is a netcfd package available in epel, which however is built without openmpi support (see [4]). If you install your home-built rpm, you probably want to make sure that a possible update from the epel repositories won't override your home-built version (this happens if the epoch:version-release of the package in the repositories is newer than the one you've built). You could:
Monitor what will get updated, if a netcdf version from epel would update your home-built rpm, then grab the newest package sources from the Fedora git repo and build a new package.
Exclude netcdf* from epel by adding exclude=netcdf* to the epel repo file in /etc/yum.repos.d.
[1] http://pkgs.fedoraproject.org/cgit/netcdf.git/
[2] http://fedoraproject.org/wiki/How_to_create_an_RPM_package#Preparing_your_system
[3] http://fedoraproject.org/wiki/Projects/Mock
[4] http://pkgs.fedoraproject.org/cgit/netcdf.git/tree/netcdf.spec?h=el6
Related
I am trying to install mysql workbench on a system without network. I downloaded the mysql-workbench-community, mysql-community-{server, client, common, libs} which were noted in the "Installing RPM Packages" section of MySQL Install Manual. It states that these are the standard rpm packages needed for a basic functional install of mysql community. So with that I downloaded all the rpm packages and attempted to manually install each using:
sudo rpm -ivh mysql-community-package-name.rpm
Unfortunately I keep getting dependency errors. I found this link to obtain all the dependencies for a package. So on my second attempt I ran the following:
Repoquery -R --resolve --recursive mysql-community-server | xargs -r yumdownloader
Which gave me about 100 rpm packages. I transferred them onto my machine and unfortunately more dependencies like mysql-connectors-community and mysql-=tools-community came up which were never documented or mentioned as dependencies with the script.
What am i doing wrong? Is there a way to download all the rpms and bundle them together as a custom RPM in the future? I see ubuntu has a apt-offline command mentioned here. Is there a similar method I can apply for redhat?
Update1:
I have an idea to create a container rhel7 instance, mounting /root/tmpkg and running this example. But is there another way I should consider?
I'd like to install programs with conda in one particular conda environment and to be able to use the associated commands from all conda environments.
My goal is to allow students to install Mercurial (plus few Mercurial extensions and related utilities like Meld and TortoiseHg) on any platforms (especially Windows) with one simple command (or few simple commands), and of course without compilation.
Of course the hg command should be available in the terminal from any conda environments (anaconda prompt on Windows). The Mercurial packages cannot be installed in the base environment because Mercurial still works better in Python 2.7 (anyway, it wouldn't be clean).
Now Mercurial and the extensions we need can be installed on all platforms with something like:
conda create -n py27_mercurial -c conda-forge python=2.7 mercurial dulwich ipaddress
conda activate py27_mercurial
pip install hg-evolve hg-git
Working a bit with conda-forge and a conda meta-package, it won't be difficult to do that with one very simple command. Moreover, it should not be difficult to create conda packages for Meld and TortoiseHg.
From this stage, the hg command is available when the environment is activated (and it is very simple to install other Mercurial extensions). To make it available from other environment (and in the base environment), one need to append the path of the directory containing hg to the environment variable PATH or on Unix to create a symbolic link (I don't know Windows enough to know if something similar would work). Both solutions are not straightforward and the commands are not platform independent.
I didn't find a command to do something like this in conda but sometimes conda experts are able to do impressive things! What would be an elegant solution to this issue?
It would also be nice to create icons somewhere (in the Anaconda launcher?) for the graphical applications (Meld and TortoiseHg). Is it possible?
Edit: Conda applications
I discovered that there is a way to specify in the meta.yaml file that a package is an application: https://docs.conda.io/projects/conda-build/en/latest/resources/define-metadata.html#app-section
It may help to solve the issue.
Edit after a first answer based on a bash function:
Of course, I'm looking for a solution involving very small work (and understanding) for the users and with cross-platform commands.
Note that for Linux and Bash, one can just do:
CONDA_APP_DIR=$HOME/.local/bin/bin-conda-app/
mkdir -p $CONDA_APP_DIR
echo -e "\nexport PATH=\$PATH:$CONDA_APP_DIR\n" >> ~/.bashrc
ln -s $(which hg) $CONDA_APP_DIR/hg
No need to activate/deactivate the environment each time hg is used...
Of course, such solutions dependent of the system and the shell are not satisfactory. It should be possible to do such things with cross-platform conda-like commands (see https://github.com/conda/conda/issues/8556), something like
conda config --add channels conda-forge
conda install conda-app
conda-app install mercurial
Now, I just have to implement conda-app 🙂
One can always create a shell function/alias and shove it in their shell's runtime configuration file. For example, for your use case, I'd add the following in my ~/.bashrc:
hg() {
(conda activate py27_mercurial
command hg "$#"
_hg_exit_code=$?
conda deactivate
exit $_hg_exit_code)
}
Then, regardless of which environment you are in, you always run hg from the environment it was installed in. To make sure that this function is loaded for you shell in a new session, one can always take a look at the output for: type -a hg
I do this one-time-setup for all the tools (some are custom compiled) and have an alias/shell function for each. This way I can happily switch b/w environments without having to worry much.
The solution https://stackoverflow.com/a/55900964/1779806 is buggy for scripts using command hg ... and too inefficient for this case (installation of a command-line application). See https://github.com/conda/conda/issues/8556#issuecomment-488703716
I created a tiny Python package conda-app (https://pypi.org/project/conda-app/) to improve this situation.
This should now works on Unix systems (with Bash and Fish):
conda activate base
conda config --add channels conda-forge
pip install conda-app
conda-app install mercurial
It should not be difficult to improve conda-app to also support Windows.
For the time being, Windows users can install Mercurial and important extensions by installing TortoiseHG.
Similarly to this question ("How can I automatically rebuild a package with a different compiler?" on askubuntu.com), I would like to know how can I automate fetching source and compilation of a C program using Fedora build scripts using a specific, non-default compiler - in my case afl-gcc. I would definitely welcome an example of the pv program, but I would like the solution to work for other packages, like libreoffice as well, with minimal modifications. I would like to achieve something similar to aflize (which is for Debian only right now). I have heard of mock and it would be best if I could use it for that.
I do not know to do it automatically, but manually:
Prepare build environnement
$ rpmdev-setuptree
Download corresonding srpms
$ yumdownloader --source foo
Extract files from SRPMS
$ rpm -i foo*.src.rpm
Replace the compiler used
$ sed -i 's/make all/make CC=afl-gcc all/g' ~/rpmbuild/SPECS/foo.spec
setting CC var your corresponding compiler will do the jobs.
If you use cmake take a look to CMAKE_C_COMPILER
Rebuild
$ cd ~/rpmbuild/SPECS/
$ rpmbuild -ba foo.spec
Generated rpm files are located into ~/rpmbuild/RPMS
I am trying to build a .rpm package. I have just followed the steps to do that. Till now all steps were gone fine but now i just stuck with this step. I just ran the following command and got this error:
rpmbuild -ba asterisk.spec
error: Failed build dependencies:
gtk2-devel is needed by asterisk-1.8.12.2-1.fc15.x86_64
libsrtp-devel is needed by asterisk-1.8.12.2-1.fc15.x86_64
[... more ...]
freetds-devel is needed by asterisk-1.8.12.2-1.fc15.x86_64
uw-imap-devel is needed by asterisk-1.8.12.2-1.fc15.x86_64
I am using fedora-15. How to resolve this error?
How I do install all depencencies during installation of src.rpm package. Is it possible?
You can use the yum-builddep command from the yum-utils package to install all the build dependencies for a package.
The arguments can either be paths to spec files, paths to source RPMs or the names of packages which exist as source RPMs in a configured repository, for example:
yum-builddep my-package.spec
or
yum-builddep my-package.src.rpm
The same thing can be achieved on newer versions of Fedora that use dnf as their package manager by making sure that dnf-plugins-core is installed and then doing:
dnf builddep my-package.spec
or
dnf builddep my-package.src.rpm
yum-builddep doesn't seem to work if the mirror you use doesn't serve source RPMs. This may not handle all cases, but it usually works for me:
sudo yum install -y $(<rpmbuild> | fgrep 'is needed by' | awk '{print $1}')
where <rpmbuild> is your rpmbuild command (e.g., rpmbuild -ba foo.spec).
On PHP building - especially phpbrew I used dnf builddep php, it worked.
Any hints on how doing this? I tried with the auto-install from a downloaded zip from this here, extracted here: OPENSHIFT_DATA_DIR/hg and executable location here: OPENSHIFT_DATA_DIR/jenkins/data/tools/Mercurial/mercurial-2.2.1/bin/hg
I'm doing something wrong for sure, I'm not Linux saavy. Jenkins says is unable to find mercurial executable.
Any help is more than welcomed.
Here's the answer from here:
Thanks for the email discussion.
Mercurial includes a README which explains a couple of modes of execution:
Basic install:
$ make # see install targets
$ make install # do a system-wide install
$ hg debuginstall # sanity-check setup
$ hg # see help
Running without installing:
$ make local # build for inplace usage
$ ./hg --version # should show the latest version
"make install" will not work as it attempts to do a system-wide install. The user on the gears will not have access to write to system files.
"make install-home" will not work either.
"make local" works and will install it in cwd such that running the following will should work just fine:
./hg --version
Mercurial Distributed SCM (version 2.2.1)
(see http://mercurial.selenic.com for more information)