I have Anaconda and Homebrew installed in OSX. Homebrew provides the following diagnostics.
What is the best way to resolve the potential conflicts between Anaconda and Homebrew? How should they be managed not to cause problems to each other?
$ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!
Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and what additional flags to use when
compiling and linking.
Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew provided
script of the same name. We found the following "config" scripts:
/Users/hhh/anaconda3/bin/curl-config
/Users/hhh/anaconda3/bin/freetype-config
/Users/hhh/anaconda3/bin/gsl-config
/Users/hhh/anaconda3/bin/icu-config
/Users/hhh/anaconda3/bin/krb5-config
/Users/hhh/anaconda3/bin/libpng-config
/Users/hhh/anaconda3/bin/libpng16-config
/Users/hhh/anaconda3/bin/llvm-config
/Users/hhh/anaconda3/bin/ncursesw6-config
/Users/hhh/anaconda3/bin/pcre-config
/Users/hhh/anaconda3/bin/python3-config
/Users/hhh/anaconda3/bin/python3.6-config
/Users/hhh/anaconda3/bin/python3.6m-config
/Users/hhh/anaconda3/bin/xml2-config
/Users/hhh/anaconda3/bin/xslt-config
Warning: Putting non-prefixed findutils in your path can cause python builds to fail.
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/libgcc_ext.10.4.dylib
/usr/local/lib/libgcc_ext.10.5.dylib
/usr/local/lib/libgcc_s_x86_64.1.dylib
/usr/local/lib/libgfortran.3.dylib
/usr/local/lib/libgomp.1.dylib
/usr/local/lib/libnnz11.dylib
/usr/local/lib/libociei.dylib
/usr/local/lib/libocijdbc11.dylib
/usr/local/lib/libquadmath.0.dylib
/usr/local/lib/libwkhtmltox.0.12.4.dylib
Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected header files:
/usr/local/include/wkhtmltox/image.h
/usr/local/include/wkhtmltox/pdf.h
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/libgfortran.la
/usr/local/lib/libgomp.la
/usr/local/lib/libintl.la
/usr/local/lib/libquadmath.la
/usr/local/lib/psqlodbcw.la
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/libgfortran.a
/usr/local/lib/libgomp.a
/usr/local/lib/libquadmath.a
I'm sort of new to programming and in the path of setting the environment ready under Mac OS X Yosemite I ran into some issues under the brew doctor command.
It says
Please note that these warnings are just used to help the Homebrew
maintainers with debugging if you file an issue. If everything you use
Homebrew for is working fine: please don't worry and just ignore them.
Thanks!
but I don't really know what to expect and to avoid future issues I'd like to see the output "Your system is ready to brew"
First I ran the brew purge command with the following output
horus:~ rsmendes$ brew prune
Pruned 0 dead formulae Pruned 136
symbolic links and 4 directories from /usr/local
Now I'm getting dylibs warning. I've read that this is solved by removing this files, but also read that it is possible to break something, and I'm uncertain of how to proceed.
I'm also getting header, unbrewed .la, unbrewed .pc and unbrewed static libraries that all seem to be related to the dylibs mentioned.
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/libfuse4x.2.dylib
/usr/local/lib/libntfs-3g.80.dylib
/usr/local/lib/libntfs.9.0.0.dylib
/usr/local/lib/libublio.1.dylib
I have recently installed Hombrew on Yosemite with Xcode installed and would like to better understand what brew doctor is warning me about. I understand that these warnings are nothing to worry about (until they are) and am not asking how or whether to respond to them; but I would like to do the best I can to understand the likely causes so that I can be prepared when issues come up (and also to head off issues that others in my office may encounter on similar systems).
Are any of the items below from obvious sources on a 10.10 machine with Xcode and non-brew Fortran installed? Do any of these items ring a bell?
Warning: Some directories in /usr/local/share/man aren't writable.
This can happen if you "sudo make install" software that isn't managed
by Homebrew. If a brew tries to add locale information to one of these
directories, then the install will fail during the link step.
You should probably `chown` them:
/usr/local/share/man/de
/usr/local/share/man/de/man1
/usr/local/share/man/mann
Warning: Broken symlinks were found. Remove them with `brew prune`:
/usr/local/lib/libasan.dylib
/usr/local/lib/libatomic.dylib
/usr/local/lib/libcilkrts.dylib
/usr/local/lib/libgcc_s_ppc64.1.dylib
/usr/local/lib/libgcc_s_x86_64.1.dylib
/usr/local/lib/libgfortran.dylib
/usr/local/lib/libgmp.dylib
/usr/local/lib/libgmpxx.dylib
/usr/local/lib/libgomp.dylib
/usr/local/lib/libitm.dylib
/usr/local/lib/libmpc.dylib
/usr/local/lib/libmpfr.dylib
/usr/local/lib/libquadmath.dylib
/usr/local/lib/libssp.dylib
/usr/local/lib/libstdc++.dylib
/usr/local/lib/libubsan.dylib
/usr/local/lib/ppc64/libgfortran.2.0.0.dylib
/usr/local/lib/ppc64/libgfortran.2.dylib
/usr/local/lib/ppc64/libgfortran.dylib
/usr/local/lib/x86_64/libgfortran.2.0.0.dylib
/usr/local/lib/x86_64/libgfortran.2.dylib
/usr/local/lib/x86_64/libgfortran.dylib
Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and what additional flags to use when
compiling and linking.
Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew provided
script of the same name. We found the following "config" scripts:
/opt/ImageMagick/bin/Magick++-config
/opt/ImageMagick/bin/Magick-config
/opt/ImageMagick/bin/MagickCore-config
/opt/ImageMagick/bin/MagickWand-config
/opt/ImageMagick/bin/Wand-config
Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected header files:
/usr/local/include/fakemysql.h
/usr/local/include/fakepq.h
/usr/local/include/fakesql.h
/usr/local/include/gmp.h
/usr/local/include/gmpxx.h
/usr/local/include/graphviz/arith.h
/usr/local/include/graphviz/cdt.h
/usr/local/include/graphviz/cgraph.h
/usr/local/include/graphviz/color.h
/usr/local/include/graphviz/geom.h
/usr/local/include/graphviz/graphviz_version.h
/usr/local/include/graphviz/gvc.h
/usr/local/include/graphviz/gvcext.h
/usr/local/include/graphviz/gvcjob.h
/usr/local/include/graphviz/gvcommon.h
/usr/local/include/graphviz/gvconfig.h
/usr/local/include/graphviz/gvplugin.h
/usr/local/include/graphviz/gvplugin_device.h
/usr/local/include/graphviz/gvplugin_layout.h
/usr/local/include/graphviz/gvplugin_loadimage.h
/usr/local/include/graphviz/gvplugin_render.h
/usr/local/include/graphviz/gvplugin_textlayout.h
/usr/local/include/graphviz/gvpr.h
/usr/local/include/graphviz/pack.h
/usr/local/include/graphviz/pathgeom.h
/usr/local/include/graphviz/pathplan.h
/usr/local/include/graphviz/textspan.h
/usr/local/include/graphviz/types.h
/usr/local/include/graphviz/usershape.h
/usr/local/include/graphviz/xdot.h
/usr/local/include/itcl.h
/usr/local/include/itcl2TclOO.h
/usr/local/include/itclDecls.h
/usr/local/include/itclInt.h
/usr/local/include/itclIntDecls.h
/usr/local/include/itclMigrate2TclCore.h
/usr/local/include/itclTclIntStubsFcn.h
/usr/local/include/mpc.h
/usr/local/include/mpf2mpfr.h
/usr/local/include/mpfr.h
/usr/local/include/mysqlStubs.h
/usr/local/include/odbcStubs.h
/usr/local/include/pqStubs.h
/usr/local/include/tcl.h
/usr/local/include/tclDecls.h
/usr/local/include/tclOO.h
/usr/local/include/tclOODecls.h
/usr/local/include/tclPlatDecls.h
/usr/local/include/tclThread.h
/usr/local/include/tclTomMath.h
/usr/local/include/tclTomMathDecls.h
/usr/local/include/tdbc.h
/usr/local/include/tdbcDecls.h
/usr/local/include/tdbcInt.h
/usr/local/include/tk.h
/usr/local/include/tkDecls.h
/usr/local/include/tkPlatDecls.h
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/libasan.la
/usr/local/lib/libatomic.la
/usr/local/lib/libcilkrts.la
/usr/local/lib/libgfortran.la
/usr/local/lib/libgmp.la
/usr/local/lib/libgmpxx.la
/usr/local/lib/libgomp.la
/usr/local/lib/libitm.la
/usr/local/lib/libmpc.la
/usr/local/lib/libmpfr.la
/usr/local/lib/libquadmath.la
/usr/local/lib/libssp.la
/usr/local/lib/libssp_nonshared.la
/usr/local/lib/libstdc++.la
/usr/local/lib/libsupc++.la
/usr/local/lib/libubsan.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/libcdt.pc
/usr/local/lib/pkgconfig/libcgraph.pc
/usr/local/lib/pkgconfig/libgvc.pc
/usr/local/lib/pkgconfig/libgvpr.pc
/usr/local/lib/pkgconfig/libpathplan.pc
/usr/local/lib/pkgconfig/libxdot.pc
/usr/local/lib/pkgconfig/tcl.pc
/usr/local/lib/pkgconfig/tk.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/libatomic.a
/usr/local/lib/libcilkrts.a
/usr/local/lib/libgfortran.a
/usr/local/lib/libgmp.a
/usr/local/lib/libgmpxx.a
/usr/local/lib/libgomp.a
/usr/local/lib/libitm.a
/usr/local/lib/libmpc.a
/usr/local/lib/libmpfr.a
/usr/local/lib/libquadmath.a
/usr/local/lib/libssp.a
/usr/local/lib/libssp_nonshared.a
/usr/local/lib/libstdc++.a
/usr/local/lib/libsupc++.a
/usr/local/lib/libtclstub8.6.a
/usr/local/lib/libtkstub8.6.a
There is a variety of warnings here, probably all with a very similar cause: having installed software from source (by compiling with configure; make; make install, or sometimes unpacking a very specific (e.g. scientific) package, such as fortran). That would be mostly software with a unix background, and the software decided to install itself in /usr/local.
I don't know your background, so I'm going to expand somewhat (I'll probably miss a few things or may have a few things (somewhat) incorrect):
In unix & linux, a piece of software is often distributed across various subdirectories, and not inside a single package (which is more Mac style). It can consist of binary that goes into /usr/local/bin/, a library with routines used by the binary that is put in /usr/local/lib/, some header file for function declarations that lives in /usr/local/include/, a manual page that is put in /usr/local/man/ or additional (e.g. configuration) data that could go into /usr/local/share/. Practically any combination can exist.
That looks a bit scattered, but it works. It does mean that pieces of different software live in the same subdirectory, as you can see form the various lists of filenames.
Note that /usr/local/ is in so far unique, that it tends to be a preferred directory to install extra software: software that the system (OS) can do without. This is also why Homebrew likes to install software there. Other software managers avoid the unix default of /usr/local/ and install in /opt/local/ (Macports) or /sw/ (Fink). But the fact that Homebrew picks the default "extra" software installation part can mean it clashes with other installed software.
Your system software lives in plain /usr/, or /System/ and /Library/, and stays out of /usr/local/; if you remove /usr/local/ completely, your system will still work.
So, with that in mind, the warnings:
Warning: Some directories in /usr/local/share/man aren't writable.
This can happen if you "sudo make install" software that isn't managed
by Homebrew. If a brew tries to add locale information to one of these
directories, then the install will fail during the link step. You
should probably chown them:
/usr/local/share/man/de
/usr/local/share/man/de/man1
/usr/local/share/man/mann
Other software installed its manual pages here, likely with the sudo command (you may simply have had a dialog asking for your password; sudo then happened under the hood). In that case, those specific directories are "owned" by "root", and not by the usual Homebrew user (your login). That would mean Homebrew can't, in a future event, not write in those directories, if it ever comes across software that likes its manual pages there, since it's not owned by the Homebrew user.
You can alleviate this by changing the permissions to yourself:
$ sudo chown -R <user>:<group> /usr/local/share/man/de
$ sudo chown -R <user>:<group> /usr/local/share/man/mann
(do an $ ls -l $HOME to find your <user> and <group> to fill in: it's the hopefully obvious columns.)
Warning: Broken symlinks were found. Remove them with `brew prune`:
A sym(bolic )link is just a pointer to a file that exist somewhere else. If it's broken, the original file doesn't exist anymore, or the symlink is pointing to the wrong place. You can see what it is pointing at by doing for example:
ls -l /usr/local/lib/libasan.dylib
The .dylib files are all dynamic libraries: library files that contain functions, and are meant to be used by other programs (but, specifically, not fully included inside that program; see later on static libraries). A broken library file is a potentially bad thing: new software that wants to use those files may think "ah, I can use this library" and then things go bad during compilation, when it turns out the file doesn't exist anymore. So, it may be wise to prune (remove) the symbolic links. (A symbolic link can normally be safely removed, even if it points correctly: it's only a pointer, the original file is left untouched.)
Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and what additional flags to use when
compiling and linking.
Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew provided
script of the same name. We found the following "config" scripts:
configure is part of the chain to build software from source on the command line. It looks around on your system for existing libraries, and also ask for the configuration of programs using these -config scripts. Homebrew had a look around, and found such scripts outside the usual directories. Thus, configure could find multiple versions of the same config script, get confused which one to use and use the wrong one.
In this case, it's all ImageMagick stuff. Depending how you use it, you could opt to remove the entire /opt/ImageMagick/ directory (and perhaps you're then left with an empty /opt/ directory, in which case you can also remove /opt/; it's not part of the usual system).
Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
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.
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.
These are all related, and related to the dynamic libraries mentioned before. The .a files are static libraries: they (also) contain often-used functions, but those files get included inside the binary when compiling software from source (thus, the binary becomes bigger than with dynamic libraries). The .h files are header files, which tell programs what the library files contain; the .la have some extra information on the .a library files.
The warning tells you that Homebrew may get confused when installing new software: perhaps it will try to use these libraries, but they happen to be the (oh so slightly) wrong version and things don't work. You don't know until you bump into it, unfortunately.
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.
pkgconfig files are similar to those config scripts mentioned earlier: they contain configuration information if you need some earlier installed software to build new software. Again, as before: versions may mismatch slightly and then things could not work as intended (it doesn't install, or crashes, or makes your computer pass the Turing test).
As for how you may have gotten all those files in /usr/local.? Probably you installed a package that puts everything in /usr/local/ as well. As mentioned, it is a default place to put things. Since it features libgfortran and libgomp, I'm inclined to think about some scientific package.
All in all, most warnings are about potential incompatibilities: Homebrew, like most package/software managers, tries to hold some grip (not too tight though) on what it installs and what is around, because backwards incompatibilities and such can mean that newly installed software from source ("brewed" software) doesn't properly install or run. As an example, Macports is more strict (at least it was years ago when I used it), and will download matching, known compatible, versions of required extra software (thus, you could end up with four different versions of a C compiler).
Homebrew tries to be lenient with respect to installed libraries and such, but it does warn you that bad things can happen, either during compilation or later on.
Just reinstalled osx and only installed chrome, sublime, and xcode cli tools so far. I got these warnings from brew doctor:
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/libmacfuse_i32.2.dylib
/usr/local/lib/libmacfuse_i64.2.dylib
/usr/local/lib/libosxfuse_i32.2.dylib
/usr/local/lib/libosxfuse_i64.2.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/libosxfuse_i32.la
/usr/local/lib/libosxfuse_i64.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/osxfuse.pc
Is it safe to remove these files or should I just ignore the warnings?
Do you, by any chance, have TrueCrypt or OSXFuse installed? Because your problem looks like this or this. The TrueCrypt problem is fixed by this script, and if you have OSXFuse, you can just remove it and use homebrew's version instead.
There's nothing wrong with the answer #Bogdan gives (I upvoted it) but in case it doesn't work for anyone, this script of mine also provides a one-shot solution--just run it, and you're good.
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).