[Ifeffit] Regarding installation of demeter on Mac Mavericks system

pushkar shejwalkar pshejwalkar2004 at gmail.com
Wed Sep 3 00:17:38 CDT 2014


Dear All
thank you very much for your help. The athena is working well now.
Pushkar


On Tue, Sep 2, 2014 at 11:55 PM, Schima, Frank <frank.schima at nist.gov>
wrote:

>  This error just came up on the list a week ago and I posted the solution
> there:
>
>  <
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-August/012068.html
> >
>
>  In your case, after running the cited code, then continue your install
> of demeter-devel.
>
>  sudo port install demeter-devel
>
>  In the future, if you or anyone else is having Macports specific issues,
> you should instead use the Macports users mailing list for tech support.
>
>  <https://lists.macosforge.org/mailman/listinfo/macports-users>
>
>  Also, under no circumstances is attaching a Word document an acceptable
> way to post an error log from Terminal. You should instead attach a text
> file. In the case of Macports, just directly attach the main.log file cited
> in your output.
>
>
>  -Frank
>
>   On Sep 1, 2014, at 6:48 PM, pushkar shejwalkar <
> pshejwalkar2004 at gmail.com> wrote:
>
>     Dear Alison/ and All,
>          As you suggested I tried to install the demeter and xorg
> separately. As you expected the xorg installation went very well and was
> complete. However, when i tried to install demeter-devel it did not go well
> and I had following error.
>  Attempting to fetch 1.2.final.tar.gz from
> http://cjj.kr.distfiles.macports.org/ifeffit
> --->  Verifying checksums for
> p5.16-ifeffit
> --->  Extracting p5.16-ifeffit
> --->  Configuring p5.16-ifeffit
> --->  Building p5.16-ifeffit
> Error: org.macports.build for port p5.16-ifeffit returned: command
> execution failed
> Error: Failed to install p5.16-ifeffit
>
>  Then there was log file which is attached to this email including other
> steps i did. and then following error again.
>
> To report a bug, follow the instructions in the guide:
>     http://guide.macports.org/#project.tickets
> Error: Processing of port demeter-devel failed
>
>  So as you expected there was a problem installing demeter-devel.
>  any help in this aspect will be highly appreciated. I am not sure if this
> is a bug and can be fixed easily? shoudl I just try once more? I am afraid
> that i would mess up again by multiple installation.
>  Thank you very much for help and pursuing this prooblem to be solved.
>
>  Sincerely
>  Pushkar
>
>
> On Tue, Sep 2, 2014 at 2:16 AM, Alison Tebo <agtebo at umich.edu> wrote:
>
>> Hi Pushkar,
>> I messed up and said athena is its own port--it's not, Athena, Artemis,
>> and Hephaestus all go with demeter-devel. Sorry about that! xorg-server
>> and demeter-devel are two separate ports. Since you're having trouble
>> installing them, I would highly recommend that you do them separately so
>> you know which one is broken.  I'm not sure if libgcc is a dependency of
>> X11 or Demeter, probably Demeter though. Either way, if you get a
>> truncation of the installation like that, then Athena, Artemis, and
>> Hephaestus won't work.
>>
>>  Best,
>> Alison
>>
>>
>> On Mon, Sep 1, 2014 at 11:33 AM, pushkar shejwalkar <
>> pshejwalkar2004 at gmail.com> wrote:
>>
>>>  Dear Alison,
>>>      Thank you very much for the response. Sorry for the earlier email
>>> not being detailed. I will try to explain everything in detail this time.
>>>  As you suggested, I uninstalled macports and then  XQuartz (Essentially
>>> I googled how to do it and followed the steps they said)
>>>
>>> sudo rm -rf \
>>>     /opt/local \
>>>     /Applications/DarwinPorts \
>>>     /Applications/MacPorts \
>>>     /Library/LaunchDaemons/org.macports.* \
>>>     /Library/Receipts/DarwinPorts*.pkg \
>>>     /Library/Receipts/MacPorts*.pkg \
>>>     /Library/StartupItems/DarwinPortsStartup \
>>>     /Library/Tcl/darwinports1.0 \
>>>     /Library/Tcl/macports1.0 \
>>>     ~/.macports
>>>
>>> after this I reinstalled macports by double clicking my earlier downloaded file. After that I
>>> reinstalled xorg by typing the sudo port install xorg-server demeter-devel command. this time it took too
>>>
>>>
>>>
>>>  long to install. Essentially I could see individual things getting checked downloaded and cleaned
>>>
>>> etc. but the error message occured towards the end
>>>
>>>
>>>
>>>
>>> -->  Attempting to fetch
>>> libmpc-1.0.2_0.darwin_13.x86_64.tbz2.rmd160 fromhttp://packages.macports.org/libmpc
>>>
>>> --->  Installing libmpc @1.0.2_0
>>>
>>> --->  Activating libmpc @1.0.2_0
>>>
>>> --->  Cleaning libmpc
>>>
>>> --->  Fetching archive for libgcc
>>>
>>> --->  Attempting to fetch libgcc-4.9.1_0.darwin_13.x86_64.tbz2 from
>>> http://packages.macports.org/libgcc
>>>
>>> --->  Attempting to fetch libgcc-4.9.1_0.darwin_13.x86_64.tbz2.rmd160
>>> from http://packages.macports.org/libgcc
>>>
>>> Error: org.macports.archivefetch for port libgcc returned: Failed to
>>> fetch signature for archive: Connection timed out after 30023 milliseconds
>>>
>>> Error: Failed to install libgcc
>>>
>>> Please see the log file for port libgcc for details:
>>>
>>> The log file is attached to this email. neverthless I still logged out by typing logout in terminal
>>>
>>> (if thats what it means) and clicked terminal again. this time I checked the $DISPLAY command and it
>>>
>>>
>>>
>>>  showed the following message.
>>>
>>> Last login: Mon Sep  1 23:18:41 on ttys000
>>>
>>> Pushkar-Shejwalkars-MacBook:~ Pushkar$ echo $DISPLAY
>>>
>>> /tmp/launch-WZNfFS/org.macosforge.xquartz:0
>>>
>>> after this I typed
>>> sudo port install athena
>>>
>>> and error read as
>>> Error: Port athena not found
>>>
>>> Pushkar-Shejwalkars-MacBook:~ Pushkar$ athena
>>>
>>> -bash: athena: command not found
>>>
>>> Pushkar-Shejwalkars-MacBook:~ Pushkar$ sudo port install athena
>>>
>>> Error: Port athena not found
>>>
>>> Pushkar-Shejwalkars-MacBook:~ Pushkar$
>>>
>>> Please tell me what did I do wrong? I am sure I am missing something here very important step.
>>>
>>> Thanks a lot for your help. Hope to hear back with some possible suggestions.
>>>
>>> Best
>>>
>>>
>>>  Pushkar
>>>
>>>
>>>
>>> On Mon, Sep 1, 2014 at 11:49 AM, Alison Tebo <agtebo at umich.edu> wrote:
>>>
>>>> Hi Pushkar,
>>>>
>>>>  It's a little hard to tell what you did and in what order. When you
>>>> activated Macports and then installed athena did you type something like 'sudo
>>>> port install xorg-server athena'? Is that when you first came across
>>>> the library duplicate? When you tried to run athena, what error did you
>>>> get? You didn't report this. It sounds like you might have installed
>>>> xorg-server (which is the same thing you downloaded from the XQuartz site)
>>>> and didn't logout and then back in to reset your DISPLAY variable and then
>>>> downloaded it again manually, messing up your ports. I can't really tell
>>>> from the information you gave. What is the output of typing echo
>>>> $DISPLAY?
>>>>
>>>>  What I would do: start over. Uninstall all of your X11s. For the
>>>> XQuartz one start here:
>>>> http://xquartz.macosforge.org/trac/wiki/X11-UsersFAQ. For the Macports
>>>> one, uninstall and clean both the 'athena' and 'xorg-server' ports. Then,
>>>> reinstall xorg-server by itself. Log out and then back in. Then type echo
>>>> $DISPLAY. Your DISPLAY variable should be something like
>>>> /tmp/launch-XXXXXX/org.macports:0.  Then install athena (sudo port
>>>> install athena). Are there any errors? If so, what are they?
>>>>
>>>>  I'm not very knowledgable about this stuff but this seems like a
>>>> pretty reasonable first step to me. Since I'm on an older Mac OS, if
>>>> there's 10.9-specific issues I won't be much help. Hopefully this resolves
>>>> your issues.
>>>>
>>>>  Best,
>>>> Alison
>>>>
>>>>
>>>>  On Sun, Aug 31, 2014 at 1:50 AM, pushkar shejwalkar <
>>>> pshejwalkar2004 at gmail.com> wrote:
>>>>
>>>>>  Dear All,
>>>>>              I am new to the mac and mac apps as well as not a techie
>>>>> either. I am trying to install the latest version of demeter (artemis,
>>>>> athena and heph) on my macbook using Mavericks OS. For this I followed the
>>>>> steps given on the site with Macports installation, then its activation
>>>>> step. and then I used terminal to connect and download the athena. However
>>>>> there was error which I thought might because of not having the windowing
>>>>> environment ( I am using all the words from site and dont know anything
>>>>> what it means). So I clicked to download X11 from XQuartz site. After that
>>>>> I logged out from terminal and logged in again. to check if anything
>>>>> changes but the following message was observed (the complete message is
>>>>> attached as word document but some part essentially the last portion
>>>>> talking about the error is pasted below.
>>>>>
>>>>> --->  Activating xorg-libXau @1.0.8_0
>>>>>
>>>>> Error: org.macports.activate for port xorg-libXau returned: Image
>>>>> error: /opt/local/lib/libXau.6.dylib already exists and does not belong to
>>>>> a registered port.  Unable to activate port xorg-libXau. Use 'port -f
>>>>> activate xorg-libXau' to force the activation.
>>>>>
>>>>> Error: Failed to install xorg-libXau
>>>>>
>>>>> Please see the log file for port xorg-libXau for details:
>>>>>
>>>>>
>>>>> /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_x11_xorg-libXau/xorg-libXau/main.log
>>>>>
>>>>> Error: The following dependencies were not installed: quartz-wm
>>>>> xorg-libAppleWM xorg-libXext xorg-libX11 xorg-libXau xorg-libXdmcp
>>>>> xorg-libxcb python27 bzip2 db46 db_select gettext expat libiconv ncurses
>>>>> libedit openssl zlib python_select sqlite3 xorg-libpthread-stubs
>>>>> xorg-xcb-proto libxml2 xz xorg-xextproto xorg-libXinerama
>>>>> xorg-xineramaproto xorg-libXrandr xorg-randrproto xrender xorg-renderproto
>>>>> xinit mkfontdir mkfontscale freetype libpng xorg-libfontenc xauth
>>>>> xorg-libXmu xorg-libXt xorg-libsm xorg-libice xrdb xset xorg-libXfontcache
>>>>> xorg-fontcacheproto xorg-libXp xorg-printproto xorg-libXxf86misc
>>>>> xorg-xf86miscproto xkeyboard-config xkbcomp xorg-libxkbfile xorg-fonts
>>>>> font-adobe-100dpi fontconfig font-adobe-75dpi font-adobe-utopia-100dpi
>>>>> font-adobe-utopia-75dpi font-adobe-utopia-type1 font-alias font-arabic-misc
>>>>> font-bh-100dpi font-bh-75dpi font-bh-lucidatypewriter-100dpi
>>>>> font-bh-lucidatypewriter-75dpi font-bh-ttf font-bh-type1
>>>>> font-bitstream-100dpi font-bitstream-75dpi font-bitstream-speedo
>>>>> font-bitstream-type1 font-cronyx-cyrillic font-cursor-misc font-daewoo-misc
>>>>> font-dec-misc font-ibm-type1 font-isas-misc font-jis-misc font-micro-misc
>>>>> font-misc-cyrillic font-misc-ethiopic font-misc-meltho font-misc-misc
>>>>> font-mutt-misc font-schumacher-misc font-screen-cyrillic font-sony-misc
>>>>> font-sun-misc font-winitzki-cyrillic font-xfree86-type1 xorg-encodings
>>>>> xorg-libXfixes xorg-fixesproto xorg-libXfont xorg-fontsproto
>>>>>
>>>>> To report a bug, follow the instructions in the guide:
>>>>>
>>>>>     http://guide.macports.org/#project.tickets
>>>>>
>>>>> Error: Processing of port xorg-server failed
>>>>>
>>>>> Pushkar-Shejwalkars-MacBook:~ Pushkar$
>>>>>
>>>>>  Please help me installing it properly. Really very sorry for the long
>>>>> email but I thought it will be more helpful this way.
>>>>>  Waiting for the replies.
>>>>>  Thank you very much
>>>>>
>>>>>  --
>>>>> Best Regards,
>>>>> Pushkar Shejwalkar.
>>>>> Post-doctoral -Researcher,JSPS Fellow
>>>>> Hokkaido University,
>>>>> Sapporo,
>>>>> Japan
>>>>>
>>>>>
>>>>>  _______________________________________________
>>>>> Ifeffit mailing list
>>>>> Ifeffit at millenia.cars.aps.anl.gov
>>>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> Ifeffit mailing list
>>>> Ifeffit at millenia.cars.aps.anl.gov
>>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>>>
>>>>
>>>
>>>
>>> --
>>> Best Regards,
>>> Pushkar Shejwalkar.
>>> Post-doctoral -Researcher,JSPS Fellow
>>> Hokkaido University,
>>> Sapporo,
>>> Japan
>>>
>>>
>>> _______________________________________________
>>> Ifeffit mailing list
>>> Ifeffit at millenia.cars.aps.anl.gov
>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>>
>>>
>>
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>> Ifeffit at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>
>>
>
>
> --
> Best Regards,
> Pushkar Shejwalkar.
> Post-doctoral -Researcher,JSPS Fellow
> Hokkaido University,
> Sapporo,
> Japan
>
>   <Attempt 3 sept 2 Demeter installation.docx>
> _______________________________________________
>
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
>
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>


-- 
Best Regards,
Pushkar Shejwalkar.
Post-doctoral -Researcher,JSPS Fellow
Hokkaido University,
Sapporo,
Japan
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