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gfortran gives warnings - malformed object (unknown load command 4) messages while installing - on 10.9 #25665

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jatinganhotra opened this Issue Jan 5, 2014 · 33 comments

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jatinganhotra commented Jan 5, 2014

Troubleshooting information:
Gist - brew doctor. brew config etc.

bash-3.2$ brew install gfortran
==> Installing dependencies for gfortran: gmp, mpfr, libmpc, isl, cloog
==> Installing gfortran dependency: gmp
==> Downloading https://downloads.sf.net/project/machomebrew/Bottles/gmp-5.1.3.mavericks.bottle.2.tar.gz

curl: (6) Could not resolve host: downloads.sf.net

Warning: Bottle installation failed: building from source.

==> Downloading ftp://ftp.gmplib.org/pub/gmp/gmp-5.1.3.tar.bz2

################################################################## 100.0%

==> Patching
patching file gmp-h.in
==> ./configure --prefix=/usr/local/Cellar/gmp/5.1.3 --enable-cxx
==> make
==> make check
==> make install
/usr/bin/install_name_tool: object: /usr/local/Cellar/gmp/5.1.3/lib/libgmpxx.4.dylib malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/gmp/5.1.3/lib/libgmp.10.dylib malformed object (unknown load command 4)

/usr/local/Cellar/gmp/5.1.3: 12 files, 2.5M, built in 3.3 minutes

==> Installing gfortran dependency: mpfr
==> Downloading https://downloads.sf.net/project/machomebrew/Bottles/mpfr-3.1.2.mavericks.bottle.1.tar.gz

################################################################## 100.0%

==> Pouring mpfr-3.1.2.mavericks.bottle.1.tar.gz
/usr/bin/install_name_tool: object: /usr/local/Cellar/mpfr/3.1.2/lib/libmpfr.4.dylib malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/mpfr/3.1.2/lib/libmpfr.4.dylib malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/mpfr/3.1.2/lib/libmpfr.4.dylib malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/mpfr/3.1.2/lib/libmpfr.4.dylib malformed object (unknown load command 4)

/usr/local/Cellar/mpfr/3.1.2: 23 files, 3.3M
==> Installing gfortran dependency: libmpc
==> Downloading https://downloads.sf.net/project/machomebrew/Bottles/libmpc-1.0.1.mavericks.bottle.1.tar.gz

################################################################## 100.0%

==> Pouring libmpc-1.0.1.mavericks.bottle.1.tar.gz
/usr/bin/install_name_tool: object: /usr/local/Cellar/libmpc/1.0.1/lib/libmpc.3.dylib malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/libmpc/1.0.1/lib/libmpc.3.dylib malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/libmpc/1.0.1/lib/libmpc.3.dylib malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/libmpc/1.0.1/lib/libmpc.3.dylib malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/libmpc/1.0.1/lib/libmpc.3.dylib malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/libmpc/1.0.1/lib/libmpc.3.dylib malformed object (unknown load command 4)

/usr/local/Cellar/libmpc/1.0.1: 9 files, 292K

==> Installing gfortran dependency: isl
==> Downloading https://downloads.sf.net/project/machomebrew/Bottles/isl-0.12.1.mavericks.bottle.1.tar.gz

################################################################## 100.0%

==> Pouring isl-0.12.1.mavericks.bottle.1.tar.gz
/usr/bin/install_name_tool: object: /usr/local/Cellar/isl/0.12.1/lib/libisl.10.dylib malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/isl/0.12.1/lib/libisl.10.dylib malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/isl/0.12.1/lib/libisl.10.dylib malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/isl/0.12.1/lib/libisl.10.dylib malformed object (unknown load command 4)

/usr/local/Cellar/isl/0.12.1: 55 files, 3.1M
==> Installing gfortran dependency: cloog
==> Downloading https://downloads.sf.net/project/machomebrew/Bottles/cloog-0.18.1.mavericks.bottle.1.tar.gz

################################################################## 100.0%

==> Pouring cloog-0.18.1.mavericks.bottle.1.tar.gz
/usr/bin/install_name_tool: object: /usr/local/Cellar/cloog/0.18.1/bin/cloog malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/cloog/0.18.1/bin/cloog malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/cloog/0.18.1/bin/cloog malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/cloog/0.18.1/lib/libcloog-isl.4.dylib malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/cloog/0.18.1/lib/libcloog-isl.4.dylib malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/cloog/0.18.1/lib/libcloog-isl.4.dylib malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/cloog/0.18.1/bin/cloog malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/cloog/0.18.1/bin/cloog malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/cloog/0.18.1/bin/cloog malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/cloog/0.18.1/lib/libcloog-isl.4.dylib malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/cloog/0.18.1/lib/libcloog-isl.4.dylib malformed object (unknown load command 4)
/usr/bin/install_name_tool: object: /usr/local/Cellar/cloog/0.18.1/lib/libcloog-isl.4.dylib malformed object (unknown load command 4)

/usr/local/Cellar/cloog/0.18.1: 33 files, 556K
==> Installing gfortran
==> Downloading https://downloads.sf.net/project/machomebrew/Bottles/gfortran-4.8.2.mavericks.bottle.1.tar.gz

################################################################## 100.0%

==> Pouring gfortran-4.8.2.mavericks.bottle.1.tar.gz
==> Caveats
Formulae that require a Fortran compiler should use:
depends_on :fortran
==> Summary
/usr/local/Cellar/gfortran/4.8.2: 960 files, 113M

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MikeMcQuaid Jan 5, 2014

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You have not followed the requested steps on the Troubleshooting page: https://github.com/Homebrew/homebrew/wiki/Troubleshooting

Please follow (all of) these steps and post the information here.

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MikeMcQuaid commented Jan 5, 2014

You have not followed the requested steps on the Troubleshooting page: https://github.com/Homebrew/homebrew/wiki/Troubleshooting

Please follow (all of) these steps and post the information here.

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jatinganhotra Jan 5, 2014

Sorry. My bad. I've updated the ticket with the link to Gist containing the information as required.

jatinganhotra commented Jan 5, 2014

Sorry. My bad. I've updated the ticket with the link to Gist containing the information as required.

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mistydemeo Jan 5, 2014

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The install_name_tool issue makes me wonder if you have an old install_name_tool present. Did you upgrade the CLT after upgrading to 10.9?

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mistydemeo commented Jan 5, 2014

The install_name_tool issue makes me wonder if you have an old install_name_tool present. Did you upgrade the CLT after upgrading to 10.9?

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jatinganhotra Jan 8, 2014

Yes, I installed CLT after upgrading to 10.9. My Xcode and CLT versions are latest:
Xcode: 5.0.2 and CLT: 5.0.1.0.1.1382131676
Let me know if you need more information or you want me to try something at end and share the results.

jatinganhotra commented Jan 8, 2014

Yes, I installed CLT after upgrading to 10.9. My Xcode and CLT versions are latest:
Xcode: 5.0.2 and CLT: 5.0.1.0.1.1382131676
Let me know if you need more information or you want me to try something at end and share the results.

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Tell me the output of:

ls -l $(which install_name_tool)

Then enter a brew sh, and show the output of MacOS.locate('install_name_tool').

Thanks!

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mistydemeo commented Jan 8, 2014

Tell me the output of:

ls -l $(which install_name_tool)

Then enter a brew sh, and show the output of MacOS.locate('install_name_tool').

Thanks!

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bash-3.2$ ls -l $(which install_name_tool)
-rwxr-xr-x  1 root  wheel  251868 Nov 17 16:50 /usr/bin/install_name_tool
bash-3.2$ brew sh
brew ~$ MacOS.locate('install_name_tool')
bash: syntax error near unexpected token `'install_name_tool''

jatinganhotra commented Jan 8, 2014

bash-3.2$ ls -l $(which install_name_tool)
-rwxr-xr-x  1 root  wheel  251868 Nov 17 16:50 /usr/bin/install_name_tool
bash-3.2$ brew sh
brew ~$ MacOS.locate('install_name_tool')
bash: syntax error near unexpected token `'install_name_tool''
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Sorry, typo - try that in brew irb, please.

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mistydemeo commented Jan 8, 2014

Sorry, typo - try that in brew irb, please.

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jatinganhotra Jan 8, 2014

That's fine. typos like these are common when you have one thing in mind and you write something else. Happens a lot with me too :)

Anyways, here's the output you asked:

bash-3.2$ brew irb
==> Interactive Homebrew Shell
Example commands available with: brew irb --help
1.9.3p194 :001 > MacOS.locate('install_name_tool')
 => #<Pathname:/usr/bin/install_name_tool> 

Thanks.

jatinganhotra commented Jan 8, 2014

That's fine. typos like these are common when you have one thing in mind and you write something else. Happens a lot with me too :)

Anyways, here's the output you asked:

bash-3.2$ brew irb
==> Interactive Homebrew Shell
Example commands available with: brew irb --help
1.9.3p194 :001 > MacOS.locate('install_name_tool')
 => #<Pathname:/usr/bin/install_name_tool> 

Thanks.

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Your install_name_tool is different from mine - mine was last touched Oct. 23 and is 14272 bytes. otool -L on it reveals that it's an xcselect shim rather than a real binary.

Yours is newer and looks to be larger, implying it's a real binary. What does otool -L say?

Have you installed any dev tools recently, such as osx-gcc-installer or railsinstaller?

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mistydemeo commented Jan 8, 2014

Your install_name_tool is different from mine - mine was last touched Oct. 23 and is 14272 bytes. otool -L on it reveals that it's an xcselect shim rather than a real binary.

Yours is newer and looks to be larger, implying it's a real binary. What does otool -L say?

Have you installed any dev tools recently, such as osx-gcc-installer or railsinstaller?

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jatinganhotra Jan 8, 2014

bash-3.2$ otool -L /usr/bin/install_name_tool
/usr/bin/install_name_tool (architecture i386):
    /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.3.3)
/usr/bin/install_name_tool (architecture ppc):
    /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.3.3)

I'm not sure but I might have installed osx-gcc-installer back then in November. Can't say for sure.

jatinganhotra commented Jan 8, 2014

bash-3.2$ otool -L /usr/bin/install_name_tool
/usr/bin/install_name_tool (architecture i386):
    /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.3.3)
/usr/bin/install_name_tool (architecture ppc):
    /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.3.3)

I'm not sure but I might have installed osx-gcc-installer back then in November. Can't say for sure.

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Yeah, looks like you have an older copy of install_name_tool that's overwritten the copy that comes with the OS. Notice that it's also i386/ppc? Recent versions of Xcode, like you have installed, ship an x86_64-only copy.

Unfortunately this is going to be a hard one to clean up. :/ In 10.9 tools like install_name_tool are actually shims that come with the OS and which run the real copy from Xcode or the CLT based on the xcode-select path. As far as I'm aware CLT and Xcode reinstalls won't restore the correct version from the OS - though you can retry installing the CLT from both sources (http://developer.apple.com/downloads and xcode-select --install). If that doesn't work, then you'll either need to reinstall the OS, restore the overwritten file(s) from the installer packages via a tool like Pacifist, or beg someone you know with a working install for the files so you can manually restore.

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mistydemeo commented Jan 8, 2014

Yeah, looks like you have an older copy of install_name_tool that's overwritten the copy that comes with the OS. Notice that it's also i386/ppc? Recent versions of Xcode, like you have installed, ship an x86_64-only copy.

Unfortunately this is going to be a hard one to clean up. :/ In 10.9 tools like install_name_tool are actually shims that come with the OS and which run the real copy from Xcode or the CLT based on the xcode-select path. As far as I'm aware CLT and Xcode reinstalls won't restore the correct version from the OS - though you can retry installing the CLT from both sources (http://developer.apple.com/downloads and xcode-select --install). If that doesn't work, then you'll either need to reinstall the OS, restore the overwritten file(s) from the installer packages via a tool like Pacifist, or beg someone you know with a working install for the files so you can manually restore.

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I can confirm similar problems most likely after installing "apple-gcc42" package.

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bonkey commented Jan 8, 2014

I can confirm similar problems most likely after installing "apple-gcc42" package.

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apple-gcc42 does not install an install_name_tool - @bonkey, your problem is probably something else. Can you open a new issue? Thanks!

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mistydemeo commented Jan 8, 2014

apple-gcc42 does not install an install_name_tool - @bonkey, your problem is probably something else. Can you open a new issue? Thanks!

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@mistydemeo Sure, I would, but I don't have any other clues at that moment, although it looks like I have exactly the same symptoms (file size, tool result and finally the error message).
My gist-logs from "r" installation are here: https://gist.github.com/anonymous/8306635
Shall I still open a new one?

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bonkey commented Jan 8, 2014

@mistydemeo Sure, I would, but I don't have any other clues at that moment, although it looks like I have exactly the same symptoms (file size, tool result and finally the error message).
My gist-logs from "r" installation are here: https://gist.github.com/anonymous/8306635
Shall I still open a new one?

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@bonkey Your error is:

configure:23661: checking for Fortran 77 name-mangling scheme
configure:23674: /usr/local/bin/gfortran -c -Os -w -pipe -mmacosx-version-min=10.9 -march=core2 -msse4.1 conftest.f >&5
dyld: Library not loaded: @@HOMEBREW_PREFIX@@/lib/libisl.10.dylib
Referenced from: /usr/local/lib/libcloog-isl.4.dylib
Reason: image not found

Which looks like it comes from an install of isl (one of the gfortran dependencies) having gone missing. It's not related to the install_name_tool issue here. If you reinstall isl you'll probably be okay - in a worst case scenario you might have to reinstall gfortran.

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mistydemeo commented Jan 8, 2014

@bonkey Your error is:

configure:23661: checking for Fortran 77 name-mangling scheme
configure:23674: /usr/local/bin/gfortran -c -Os -w -pipe -mmacosx-version-min=10.9 -march=core2 -msse4.1 conftest.f >&5
dyld: Library not loaded: @@HOMEBREW_PREFIX@@/lib/libisl.10.dylib
Referenced from: /usr/local/lib/libcloog-isl.4.dylib
Reason: image not found

Which looks like it comes from an install of isl (one of the gfortran dependencies) having gone missing. It's not related to the install_name_tool issue here. If you reinstall isl you'll probably be okay - in a worst case scenario you might have to reinstall gfortran.

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@mistydemeo I tried it few times (you know, like erasing magnetic tape - just to be sure ;-), but it always ends with something like that: https://gist.github.com/bonkey/8324164

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bonkey commented Jan 8, 2014

@mistydemeo I tried it few times (you know, like erasing magnetic tape - just to be sure ;-), but it always ends with something like that: https://gist.github.com/bonkey/8324164

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Oh, I see - you cut out the output that showed it was the same problem, so I thought it was something else ;)

You probably have the same issue then, you're right. Run the same diagnostics I suggested, but unfortunately you probably have the same set of unpalatable workarounds to try.

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mistydemeo commented Jan 8, 2014

Oh, I see - you cut out the output that showed it was the same problem, so I thought it was something else ;)

You probably have the same issue then, you're right. Run the same diagnostics I suggested, but unfortunately you probably have the same set of unpalatable workarounds to try.

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@mistydemeo, @silverspoon Well, I've just run 10.9.1 update from dmg and unfortunately it didn't help. I'll look for other solutions later and I'll post when I'll find something, but it looks like there's no better option then the one @mistydemeo suggest - OS reinstallation. I tried reinstallation of CLT earlier, too, but it didn't help.
I only wonder what might be the cause. The system is quite fresh, so apple-gcc42 was my the only suspicion.

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bonkey commented Jan 8, 2014

@mistydemeo, @silverspoon Well, I've just run 10.9.1 update from dmg and unfortunately it didn't help. I'll look for other solutions later and I'll post when I'll find something, but it looks like there's no better option then the one @mistydemeo suggest - OS reinstallation. I tried reinstallation of CLT earlier, too, but it didn't help.
I only wonder what might be the cause. The system is quite fresh, so apple-gcc42 was my the only suspicion.

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Don't think that could be it - that package doesn't have a copy of the tool that's been overwritten and unless you're running a root-owned Homebrew install it wouldn't have the permissions to overwrite it either.

osx-gcc-installer or railsinstaller would be my guess, but could be something else.

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mistydemeo commented Jan 8, 2014

Don't think that could be it - that package doesn't have a copy of the tool that's been overwritten and unless you're running a root-owned Homebrew install it wouldn't have the permissions to overwrite it either.

osx-gcc-installer or railsinstaller would be my guess, but could be something else.

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The install_name_tool is OK after running rescue and reinstallation. R with gfortran and dependencies installed OK without any issues.

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bonkey commented Jan 13, 2014

The install_name_tool is OK after running rescue and reinstallation. R with gfortran and dependencies installed OK without any issues.

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Closing, hope you can get your system install repaired.

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adamv commented Jan 14, 2014

Closing, hope you can get your system install repaired.

@adamv adamv closed this Jan 14, 2014

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jatinganhotra Jan 18, 2014

@bonkey Could you please elaborate what you meant by running rescue and then reinstallation?
Should I re-download the OS X Mavericks from the App Store and re-install it like I did before? OR does the re-install has to be a clean install?

Regarding the clean install by making a bootable USB drive, I had a concern. Won't a clean install via bootable USB wipe out all my data and settings so far? I have tons of configuration for various apps and lot of other things and I don't want to go through the pain of doing it again.

jatinganhotra commented Jan 18, 2014

@bonkey Could you please elaborate what you meant by running rescue and then reinstallation?
Should I re-download the OS X Mavericks from the App Store and re-install it like I did before? OR does the re-install has to be a clean install?

Regarding the clean install by making a bootable USB drive, I had a concern. Won't a clean install via bootable USB wipe out all my data and settings so far? I have tons of configuration for various apps and lot of other things and I don't want to go through the pain of doing it again.

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@silverspoon There's actually not much to elaborate and I can't guarantee it will work correctly, but I've never ever had any problems with such an operation before. You need to get into Recovery mode (sorry, I mixed the name) by keeping Cmd-R pressed in the boot stage and than choose Reinstall, wait around an hour and that's all. If you don't do clean install, you shouldn't loose a single thing. More about that here: http://support.apple.com/kb/PH10763.

In my situation almost nothing had changed, eg. iTerm2 window was opened in the same state, like there was not only even any reinstallation, but it looked like the system had been just waken from standby and everything else worked without issues. The only difference I noticed I had to accept running few unsigned apps.

HTH.

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bonkey commented Jan 18, 2014

@silverspoon There's actually not much to elaborate and I can't guarantee it will work correctly, but I've never ever had any problems with such an operation before. You need to get into Recovery mode (sorry, I mixed the name) by keeping Cmd-R pressed in the boot stage and than choose Reinstall, wait around an hour and that's all. If you don't do clean install, you shouldn't loose a single thing. More about that here: http://support.apple.com/kb/PH10763.

In my situation almost nothing had changed, eg. iTerm2 window was opened in the same state, like there was not only even any reinstallation, but it looked like the system had been just waken from standby and everything else worked without issues. The only difference I noticed I had to accept running few unsigned apps.

HTH.

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jatinganhotra Jan 18, 2014

Sorry to spam this thread with irrelevant details, but I had one more quick query...

@bonkey Thanks for your quick response. I really appreciate it :) But if I get it right, the Reinstall option from Recovery mode would re-download the whole 5.3GB installer. I have already downloaded the installer using the AppStore and don't want to re-download it again.

Should I just go ahead and re-install using the Installer.app file downloaded from the AppStore? Would it make any difference? Please correct me if I am wrong but unless I want to change the disk partitions it should not matter, right?

jatinganhotra commented Jan 18, 2014

Sorry to spam this thread with irrelevant details, but I had one more quick query...

@bonkey Thanks for your quick response. I really appreciate it :) But if I get it right, the Reinstall option from Recovery mode would re-download the whole 5.3GB installer. I have already downloaded the installer using the AppStore and don't want to re-download it again.

Should I just go ahead and re-install using the Installer.app file downloaded from the AppStore? Would it make any difference? Please correct me if I am wrong but unless I want to change the disk partitions it should not matter, right?

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bonkey Jan 18, 2014

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@silverspoon I can't tell you if it would work as I don't remember if I've ever done it that way. When I have an installer of OS X I usually put it on a pen drive, but I haven't done it for long, so I don't even remember what is the correct way of doing it now. Last time I did it, I used a "manual way" described here: http://mashable.com/2013/10/23/clean-install-os-x-mavericks/
I wouldn't be afraid that anything would break, unless you touch partitions as you wrote so.
BTW. It's always good to have a Time Machine backup around. It fully restored my system many times when I had issues with SSD drive.

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bonkey commented Jan 18, 2014

@silverspoon I can't tell you if it would work as I don't remember if I've ever done it that way. When I have an installer of OS X I usually put it on a pen drive, but I haven't done it for long, so I don't even remember what is the correct way of doing it now. Last time I did it, I used a "manual way" described here: http://mashable.com/2013/10/23/clean-install-os-x-mavericks/
I wouldn't be afraid that anything would break, unless you touch partitions as you wrote so.
BTW. It's always good to have a Time Machine backup around. It fully restored my system many times when I had issues with SSD drive.

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jatinganhotra Jan 18, 2014

@bonkey It worked!!! I re-installed OS X Mavericks using the Installer.app that is downloaded from the AppStore without making a clean install.

Now, when I run the same commands as @mistydemeo asked me to while running diagnostics, I am getting expected results:

bash-3.2$ ls -l $(which install_name_tool)
-rwxr-xr-x  1 root  wheel  14272 Jan 18 23:17 /usr/bin/install_name_tool
bash-3.2$ brew irb
==> Interactive Homebrew Shell
Example commands available with: brew irb --help
1.9.3p194 :001 > MacOS.locate('install_name_tool')
 => #<Pathname:/usr/bin/install_name_tool> 
1.9.3p194 :002 > exit
bash-3.2$ otool -L /usr/bin/install_name_tool
/usr/bin/install_name_tool:
    /usr/lib/libxcselect.dylib (compatibility version 1.0.0, current version 1.0.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)

Now, when I tried brew install gfortran again after uninstalling the dependencies, it ran just fine.
Thanks @bonkey and @mistydemeo again for your help :)

jatinganhotra commented Jan 18, 2014

@bonkey It worked!!! I re-installed OS X Mavericks using the Installer.app that is downloaded from the AppStore without making a clean install.

Now, when I run the same commands as @mistydemeo asked me to while running diagnostics, I am getting expected results:

bash-3.2$ ls -l $(which install_name_tool)
-rwxr-xr-x  1 root  wheel  14272 Jan 18 23:17 /usr/bin/install_name_tool
bash-3.2$ brew irb
==> Interactive Homebrew Shell
Example commands available with: brew irb --help
1.9.3p194 :001 > MacOS.locate('install_name_tool')
 => #<Pathname:/usr/bin/install_name_tool> 
1.9.3p194 :002 > exit
bash-3.2$ otool -L /usr/bin/install_name_tool
/usr/bin/install_name_tool:
    /usr/lib/libxcselect.dylib (compatibility version 1.0.0, current version 1.0.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)

Now, when I tried brew install gfortran again after uninstalling the dependencies, it ran just fine.
Thanks @bonkey and @mistydemeo again for your help :)

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Glad it's all okay now!

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mistydemeo commented Jan 18, 2014

Glad it's all okay now!

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shahalpk Feb 1, 2014

Another better solution would be to copy install_name_tool from Xcode.app to /usr/bin.

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This worked for me :)

shahalpk commented Feb 1, 2014

Another better solution would be to copy install_name_tool from Xcode.app to /usr/bin.

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This worked for me :)

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That works in the short term, but it still means that your install_name_tool will be out of date with future Xcode updates. You should restore the shim if you can.

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mistydemeo commented Feb 1, 2014

That works in the short term, but it still means that your install_name_tool will be out of date with future Xcode updates. You should restore the shim if you can.

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krzyzanowskim Apr 8, 2014

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Oh I just stuck with that, is there any known solution (without reinstalling the whole system?). I don't have gcc package installed

$ ls -l $(which install_name_tool)
-rwxr-xr-x 1 root wheel 251868 Jan 13 10:34 /usr/bin/install_name_tool

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krzyzanowskim commented Apr 8, 2014

Oh I just stuck with that, is there any known solution (without reinstalling the whole system?). I don't have gcc package installed

$ ls -l $(which install_name_tool)
-rwxr-xr-x 1 root wheel 251868 Jan 13 10:34 /usr/bin/install_name_tool

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zhiyuanfirst Apr 11, 2014

@shahalpk great! This worked for me too.
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zhiyuanfirst commented Apr 11, 2014

@shahalpk great! This worked for me too.
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Sorry, I'm editing comments that advise removing or replacing stuff in /usr/bin. If you do that you will likely have issues with OSX updates so I don't want to encourage people to do it.

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MikeMcQuaid commented Apr 11, 2014

Sorry, I'm editing comments that advise removing or replacing stuff in /usr/bin. If you do that you will likely have issues with OSX updates so I don't want to encourage people to do it.

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andryblack Sep 29, 2014

need use command 'xcrun install_name_tool' instead 'install_name_tool'

andryblack commented Sep 29, 2014

need use command 'xcrun install_name_tool' instead 'install_name_tool'

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