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brew upgrade fails on open-mpi #15452

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rhaynes74 opened this Issue Oct 14, 2012 · 7 comments

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@rhaynes74

Hi folks, did a brew update, brew install today and things failed on open-mpi, things seem to fail on
the config step with gfortran with some problem with -lgcc, see output from config.log at the bottom of the message.

Brew doctor is all clear. If I do

 brew install gfortran

I get

Error: gfortran-4.2.4-5666.3 already installed

Yet

gfortran -v

gives:

gfortran -v
Using built-in specs.
Target: i686-apple-darwin11
Configured with: /Volumes/Media/Builds/gcc-5666.3/build/obj/src/configure --disable-checking --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c++,obj-c++,fortran --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib --build=i686-apple-darwin11 --program-prefix=i686-apple-darwin11- --host=x86_64-apple-darwin11 --target=i686-apple-darwin11 --with-gxx-include-dir=/include/c++/4.2.1
Thread model: posix
gcc version 4.2.1 (Apple Inc. build 5666) (dot 3)

echo $PATH

gives

/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin

It seems like the most recent gfortran from homebrew is not being seen. Any suggestions?

config.log from brew install open-mpi

https://gist.github.com/3890167

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2bits Oct 14, 2012

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Please read and follow [this wiki.][1] We need your gist urls. Also please edit your original post to remove all that output even though you did a good job trying to present this. The information we need, however, will be in the gists you create by following the wiki. (We can't trust what you place directly into the issue comments like that because the text gets interpreted by github. Check the GitHub Flavored Markdown link above the comments box to read about things like that.)

Please also paste for us the output of

brew list -f gfortran --verbose | grep gcc.a

I use tripple backticks above and below my text to get it into non-interpreted code-box like that above.

Contributor

2bits commented Oct 14, 2012

Please read and follow [this wiki.][1] We need your gist urls. Also please edit your original post to remove all that output even though you did a good job trying to present this. The information we need, however, will be in the gists you create by following the wiki. (We can't trust what you place directly into the issue comments like that because the text gets interpreted by github. Check the GitHub Flavored Markdown link above the comments box to read about things like that.)

Please also paste for us the output of

brew list -f gfortran --verbose | grep gcc.a

I use tripple backticks above and below my text to get it into non-interpreted code-box like that above.

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rhaynes74 Oct 14, 2012

2bits - is there supposed to be a link to the wiki in message ? - something got lost in translation!

brew list -f gfortran --verbose | grep gcc.a

gives absolutely nothing for me.

2bits - is there supposed to be a link to the wiki in message ? - something got lost in translation!

brew list -f gfortran --verbose | grep gcc.a

gives absolutely nothing for me.

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2bits Oct 15, 2012

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Ooops. https://github.com/mxcl/homebrew/wiki/Troubleshooting is the link.
Also I gave you a broken command. I meant

brew rm -f gfortran
brew install gfortran
brew list --verbose gfortran | grep gcc.a

That should give you something. If not, paste in the output of brew info gfortran

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2bits commented Oct 15, 2012

Ooops. https://github.com/mxcl/homebrew/wiki/Troubleshooting is the link.
Also I gave you a broken command. I meant

brew rm -f gfortran
brew install gfortran
brew list --verbose gfortran | grep gcc.a

That should give you something. If not, paste in the output of brew info gfortran

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adamv Jan 7, 2013

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Did the last comment here provide any useful output?

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adamv commented Jan 7, 2013

Did the last comment here provide any useful output?

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rhaynes74 Jan 7, 2013

Hi Adam - to be honest I forget how this issue was rectified.

Best,
R Haynes

Dr. Ronald D. Haynes (PhD)
Associate Professor
Department of Mathematics & Statistics
Memorial University of Newfoundland
St. John's, NL, Canada
A1C 5S7
(P) 709-864-8825
(F) 709-864-3010

On 2013-01-07, at 5:23 PM, Adam Vandenberg notifications@github.com wrote:

Did the last comment here provide any useful output?


Reply to this email directly or view it on GitHub.

Hi Adam - to be honest I forget how this issue was rectified.

Best,
R Haynes

Dr. Ronald D. Haynes (PhD)
Associate Professor
Department of Mathematics & Statistics
Memorial University of Newfoundland
St. John's, NL, Canada
A1C 5S7
(P) 709-864-8825
(F) 709-864-3010

On 2013-01-07, at 5:23 PM, Adam Vandenberg notifications@github.com wrote:

Did the last comment here provide any useful output?


Reply to this email directly or view it on GitHub.

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adamv Jan 7, 2013

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Fair enough.

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adamv commented Jan 7, 2013

Fair enough.

@adamv adamv closed this Jan 7, 2013

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rhaynes74 Jan 7, 2013

Thanks for following up Adam.

Best,
R Haynes

Dr. Ronald D. Haynes (PhD)
Associate Professor
Department of Mathematics & Statistics
Memorial University of Newfoundland
St. John's, NL, Canada
A1C 5S7
(P) 709-864-8825
(F) 709-864-3010

On 2013-01-07, at 6:04 PM, Adam Vandenberg notifications@github.com wrote:

Fair enough.


Reply to this email directly or view it on GitHub.

Thanks for following up Adam.

Best,
R Haynes

Dr. Ronald D. Haynes (PhD)
Associate Professor
Department of Mathematics & Statistics
Memorial University of Newfoundland
St. John's, NL, Canada
A1C 5S7
(P) 709-864-8825
(F) 709-864-3010

On 2013-01-07, at 6:04 PM, Adam Vandenberg notifications@github.com wrote:

Fair enough.


Reply to this email directly or view it on GitHub.

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