I can't seem to install anything with MacPorts. Problems inevitably arise when MacPorts gets to the stage where it tries to apply patches. It croaks because apparently /usr/bin/patch has a security patch that prevents itself from patching upwards in the directory tree. A typical error message:
:info:patch /usr/bin/patch: **** rejecting file name with ".." component: ../libunwind/include/libunwind.h
I see some various bug reports on this issue such as https://trac.macports.org/ticket/29871 and https://trac.macports.org/ticket/29813, but no real solutions.
Is there a patch to patch?
I do not use Macports (so I cannot test this possible solution), but perhaps you could try installing the GNU version of patch. There is indeed a portfile for it within Macports. It installs as gpatch, but you could easily create a symbolic link such that /opt/bin/patch -> /opt/bin/gpatch. Additionally, you will need to ensure that /opt/bin appears before /usr/bin in your path.
Although the portfile requires a patch to be applied, it fortunately does not use any .. path components.
It appears as though this security patch originated in February of 2011. As 2.6.1 predates this, I believe this method should work.
Related
Since I installed according to the guide here on wsl2 ubuntu 20.04, I've been having errors related to libstc++.so.6, specifically GLIBCXX_3.4.26 not found (required by ...) where ... refers to different files within /opt/OpenFOAM/ThirdParty-v2006/platforms/linux64/gcc-6.3.0/lib64/ ending in .so, .so.1, .so.6 and so on (for instance, when running paraFoam the error would appear with respect to about 20 such files). I am able to successfully visualize the cavity tutorial (in paraview installation on windows).
I could get the errors to go away by doing what the user laborg suggested on Jan 4 for a similar problem with julia (see here), specifically copy libstdc++.so.6 from /usr/lib/x86_64-linux-gnu to /opt/OpenFOAM/ThirdParty-v2006/platforms/linux64/gcc-6.3.0/lib64/.
The questions is whether this copy-paste solution is recommended; will it come back and haunt me later? Is the libstdc++.so.6 from system installation going to be an issue if used in the lib64 folder of openfoam?
An additional info concerning openfoam installation, foamInstallationTest shows *not installed* errors against flex, wmake, gcc, g++, icoFoam and *critical error* for gcc, g++, icoFoam; but I as given here, foamInstallationTest is not meant for installation from the tar file. Openfoam installation seems to be alright based on the running of the cavity tutorial.
ok, please don't do copy past operation to solve this problem. The error means that you haven't installed the pre request libraries in your ubuntu. It seems that you have missed the first step in the tutorial.
It is not recommended but it will not hurt as long as the GLIBC versions returned from this command
strings /opt/OpenFOAM/ThirdParty-v2006/platforms/linux64/gcc-6.3.0/lib64/libstdc++.so.6 | grep GLIBC
are a subset of the GLIBC versions from this command.
strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBC
which was no doubt the case for your Ubuntu setup.
A less risky route would be to redirect the soft link /opt/OpenFOAM/ThirdParty-v2006/platforms/linux64/gcc-6.3.0/lib64/libstdc++.so.6 to point to your other libstdc++.so.6 (that way you retain both versions)
ln -sf /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /opt/OpenFOAM/ThirdParty-v2006/platforms/linux64/gcc-6.3.0/lib64/libstdc++.so.6
Then, if you hit an issue, you can always reset the link back to its original target. Of course /usr/lib/x86_64-linux-gnu/libstdc++.so.6 is itself a soft link, but you can point to it all the same or you can point to its target.
I believe the issue you are hitting is a derivative of the one mentioned here https://www.cfd-online.com/Forums/main/229027-persistence-glibcxx_3-4-26-not-found.html, which would point towards the fact that it is not an installation error on your part but an issue related to the packaging of the OpenFoam binaries. I agree it would screw up the wsl2 setup owing to the way OpenFoam prepends everything to paths. Of course the safest route is to compile from source using the Ubuntu system's gcc and thereby bypass the ThirdParty.
Seeing as you are using Ubuntu in the WSL instance, could also just install the Ubuntu package directly:
https://develop.openfoam.com/Development/openfoam/-/wikis/precompiled/debian
This problem comes from this line in the tutorial:
echo "source /opt/OpenFOAM/OpenFOAM-v2012/etc/bashrc" >> ~/.bashrc
This will point to OpenFOAM's libstdc++ everytime you open a terminal (or start a WSL2 session). If your workflow is not related to OpenFOAM, that can be an issue. If you remove or comment that line in your ~/.bashrc things should get back to normal. You can use nano in WSL2.
nano ~/.bashrc
Then comment:
#source /opt/OpenFOAM/OpenFOAM-v2012/etc/bashrc
However, as OpenFOAM uses that bashrc, you will need to source the OpenFOAM bashrc in each terminal before using openFOAM.
source /opt/OpenFOAM/OpenFOAM-v2012/etc/bashrc
My personal choice is to keep that line commented and, if I have a long work session using OpenFOAM, I just use nano to uncomment it, so every shell that I open works without sourcing again.
There are more elegant or complex approaches, but I prefer this one.
This answer should be valid with the 2006 version too, the link you shared points to 2012, so I guess they just updated the tutorial. If you installed 2006, just make sure when you source comment/uncomment to use the correct name.
In the same manner, if you followed another tutorial with another tool and sourced another library, you may experience issues.
Just start by taking a look at your bashrc and cleaning it.
So i'm new with this. I'm trying to install ruby on my mac with mountain lion.
im following this guide:http://www.moncefbelyamani.com/how-to-install-xcode-homebrew-git-rvm-ruby-on-mac/
when I put "brew doctor" I get this lot of warnings:
$ brew doctor
Warning: /Library/Frameworks/Mono.framework detected
This can be picked up by CMake's build system and likely cause the build to
fail. You may need to move this file out of the way to compile CMake.
Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected dylibs:
/usr/local/lib/libusb-0.1.4.dylib
/usr/local/lib/libusb-1.0.0.dylib
/usr/local/lib/libusbpp-0.1.4.dylib
Warning: Unbrewed .la files were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected .la files:
/usr/local/lib/libusb.la
/usr/local/lib/libusbpp.la
Warning: Unbrewed .pc files were found in /usr/local/lib/pkgconfig.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected .pc files:
/usr/local/lib/pkgconfig/fuse.pc
/usr/local/lib/pkgconfig/libusb.pc
Warning: Unbrewed static libraries were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected static libraries:
/usr/local/lib/libusb.a
/usr/local/lib/libusbpp.a
What should I do? What's happening?
I would recommend that you manage your ruby installations with either RVM or RBENV it will make your life much easier to manage different versions, upgrades, etc.
Use RVM. RVM allows you to install and manage multiple versions of Ruby on the same machine.
You can follow the instructions here to install RVM, and instructions here to install Ruby. The second link is an excellent beginners guide to get going with ruby-on-rails by the way.
Your Mac probably comes with Ruby 1.8.7. I like some of the features in 1.9.x, and they've recently released 2.0.0, so you may wish to upgrade. However there's no point doing work if you ain't gonna need it, so first decide whether you need a different version of Ruby right now. (And verify your current version with a ruby -v).
Assuming you need a new version, RVM and rbenv are two tools that make installing and managing (a.k.a. switching between) various Rubies and their versions very easy. Some people don't like RVM because it does some strange things (like override the definition of cd - change directory), but I find it simpler to use, and doesn't require you to remember to rehash every time. Read up on it and decide for yourself.
If you want to use RVM:
Install it (Google to find out how).
Make sure to source the script that it tells you to do in the output during the installation.
Start using it: rvm install <version> (e.g. rvm install 1.9.3), rvm use <version> (to switch between versions), rvm list (to see which Rubies you have installed), etc.
RVM has more online resources so it's be a good choice since you're starting. Pay attention to the error logs in your console and Google them, you'll probably see some quite accurate results (as the ruby install issues are common).
After making cabal install of the darcsden code I get this message:
cabal: The following packages are likely to be broken by the reinstalls:
bin-package-db-0.0.0.0
ghc-7.4.1
Use --force-reinstalls if you want to install anyway.
How do I get around this? What does it mean?
Why does it happen?
If you look at the full output of cabal install darcsden, you will find several lines that look like this:
binary-0.5.1.0 -bytestring-in-base (reinstall) changes: array-0.4.0.0 ->
0.3.0.3, containers-0.4.2.1 -> 0.4.1.0
This means that cabal has found an install plan that involves (destructively) reinstalling packages that you already have on your system.
Now, GHC packages are rather sensitive when it comes to their (reflexive) dependencies, and generally only work if exactly the right version of all dependencies is available, compiled against the right versions of their dependencies and so on. Therefore, replacing an already installed package with a new version of changed dependencies can cause some packages on your system to become unusable. Since version 0.14.0, cabal warns you about such a situation in advance to prevent you from accidentally breaking your system.
In your case, ghc and bin-package-db are among the potentially broken packages, because they depend on binary which gets reinstalled. So you should not try to use the --force-reinstalls flag, because it might really break your GHC.
What can you do?
If you scan what is going to be reinstalled, you see that quite a few dependencies are downgraded. This hints at the fact that the package you are trying to install might not be properly updated to GHC 7.4.1 yet.
You can in general try to call cabal install darcsden --avoid-reinstalls to explicitly try to find an install plan that has no reinstalls. Unfortunately, in this case, it fails (for me).
I've briefly looked at the darcsden package description, but it looks like quite a few dependencies of darcsden need to be updated. So the remaining options are: Convince the author(s) of darcsden to release an updated version, or install darcsden using an older version of GHC (such as 7.0.4), which should just work.
I have to run a Rails (3.0.6) app locally that requires Ruby 1.9.2 (plus Mongo). I'd like to install Ruby 1.9.2 alongside my existing 1.8.7 and be able to swap between them as necessary. I prefer installing to usr/local over Macports etc. Any recommendations? I've tried installing RVM but this has proved such a pain on OS X I'd rather avoid that too.
Is there another way of running multiple Ruby versions (maybe with a prefix like this)? I only need to switch to 1.9 for this project. Or has anyone a good solution to the known OS X/RVM install issues? Specifically, on Tiger/10.4 bash doesn't support errtrace.
Update: solved with a new RVM install script: see RVM on OS X 10.4 - possible?.
RVM really is the easiest solution, and I would highly recommend you try and work that issue out first.
The only bit of advice is to make sure you configure your PATH variable to include /usr/local/bin before everything else. In your .profile or .login (depending on your shell), you should have it towards the bottom, in case there is any other lines configuring PATH as well, and then for the Bourne shell family:
export PATH="/usr/local/bin:$PATH
or for the C shell family:
set path = (/usr/local/bin $PATH)
Running ./configure alone should make it install into /usr/local, but you can explicitly state so with
./configure --prefix=/usr/local
Install Ruby from source and it will default to /usr/local/bin. Adjust your path, the #! line, or your /usr/local/bin/ruby source.rb as necessary to switch between Apple's installation of Ruby, and the one you add.
You can force a new base directory using ./configure --prefix=/... where '...' is whatever path you want. Again, once the files are installed, you can adjust the executing Ruby with one of the above methods.
Do not attempt to remove Apple's installed Ruby. It's there for their use, not for our convenience, and Apple uses it to provide some functionality. Messing with it or removing it could break things, and you probably wouldn't notice for a while.
RE: RVM, It really is the preferred way to install a user Ruby. I have it on two Macs, and a handful of different Linux boxes and the only time I had trouble was with a secured machine behind firewalls, but I can't blame RVM for those problems when it couldn't see the internet at all. And, yes, I got it working nicely, I just had to insert the manually downloaded Ruby archives into the ~/.rvm/archives directory.
If you are having problems and want to use it, it might help to temporarily strip your startup scripts, or create a temporary user, and see what happens. Additionally, the author has been very responsive and helpful the few times I've asked him questions. Contact him at:
If you still cannot find what an answer to your question, find me 'wayneeseguin' in #rvm on irc.freenode.net:
http://webchat.freenode.net/?channels=rvm
If you download the source and compile it, it should install into /usr/local by default, or you can
./configure --prefix=/usr/local
just to be sure.
Actually, compiling and installing ruby from source is an easy way to be sure you have the latest version, especially if you use git and github:
https://github.com/ruby/ruby
Today I installed the curl formula via homebrew, but after installing it (and re-sourcing the shell) i noticed that :
% which curl
/usr/bin/curl
as a matter of fact, the output of brew install curl stated that it was a keg-only formula, and that since curl was already present in OS X, it didn't link it into Homebrew prefix, as that could cause unspecified problems.
Then it proceeds stating that
Generally there are no consequences of this for you
I would like to know:
What sorts of problems exactly?
What is the purpose of installing keg-only formulas via Homebrew? How can there be no consequences if the newly installed tool is not in the PATH?
Problems: if a homebrew application is put in the path in front of the default OS X version of the same, really anything might happen. Most common issues are caused by differences between the set of command line options available in the two versions, or differences in the meaning of the options. For curl the consequences might not be so bad, but for other applications you could, at worst, break the OS.
Keg-only: now you have two versions of curl! The default OS X, and the homebrew. If you want to use features that are not in the default but in the homebrew, you can do so by calling the homebrew curl explicitly. The precise path depends on how you've got homebrew set up. Because the newly installed version is not in the path, its unlikely to cause a problem unless it is explicitly called.
I want to add some complement to the second problem(related to the mechanism of keg-only) asked by #asymmetric.
HomeBrew's prefix is /usr/local , and HomeBrew keeps all installed kegs in the default directory, say /usr/local/Cellar. In general, HomeBrew could create symlink for installed formula(non-keg-only formula), and the corresponding symlink is kept in /usr/local/bin. This symlink-creation procedure is automatic when HomeBrew installing the formula. Here the path /usr/local/bin would be called default (symlink) prefix.
On the other hand, according to FAQ of HomeBrew, we have the following guidance:
``keg-only formula is installed only into the Cellar and is not linked into the default prefix. This means most tools will not find it.''
But at the same time the HomeBrew creates symlinks in the directory /usr/local/opt for ALL installed formulae no matter whether they are keg-only or not.
There will be two crucial points we should notice:
By default the default (symlink) prefix /usr/local/bin is in PATH, but the non-prefix /usr/local/opt is NOT in PATH.
By default the default (symlink) prefix /usr/local/bin in general points towards the latest version of formula. So if you want to use the specific version(often in keg-only format) of some formula you could temporarily prepend your PATH with the keg-only formula's bin directory, for example, export PATH="$(brew --prefix)/opt/FormulaName/bin:${PATH}".
The setting of /usr/local/opt mentioned above could resolve the executable-conflict. In general, you might have a formula or program in your system with many different versions, such as the latest version and outdated version, the Apple native version and locally installed version, an so on. It's possible for these situations to cause conflict when you execute or compile some other programs which are somewhat related to the current using formula or program.