[Rnomads-user] Problems with MacOS

Thu Dec 10 03:57:35 CET 2015

Hello Again,

I think I have found a way around this problem from the RStudio support
page.  You set $PATH in .bash_profile and then start RStudio from the
command line.  R then picks up the path including wgrib.  I prefer
navigating via terminal windows anyway.

> system("wgrib2")
wgrib2 v0.2.0.3 11/2015 Wesley Ebisuzaki, .....

Hopefully I can do some of my plots tomorrow.

Apparently this has something to do with Mac increasing their security.  I
also had troubles installing McIDAS-X because of similar changes.

Pat

On Thu, Dec 10, 2015 at 2:22 AM, Patrick King <king.pws at gmail.com> wrote:

> Thanks for your response Danny.
>
> Here is the response to the pwd command:
> > system("wgrib2")
> sh: wgrib2: command not found
> > system("pwd", intern=TRUE)
> [1] "/Users/pking/SCI/rNomads"
> >
>
> I tried setting the path in both bash_profile and /etc/environment, but R
> could not see it in either case.  Apparently Mac OS X does not consult
> /etc/environment.  This article (
> https://support.enthought.com/hc/en-us/articles/204469160-How-do-I-set-PYTHONPATH-and-other-environment-variables-for-Canopy-)
> suggests a way of doing it.  I will try to figure that out and report later.
>
> pat
>
> On Thu, Dec 10, 2015 at 12:46 AM, Bowman, Daniel <haksaeng at live.unc.edu>
> wrote:
>
>> Hi Patrick,
>>
>>
>> Thank you, I'm glad rNOMADS has been useful.  First of all, where are you
>> adding wgrib2 to the path variable?  If you're using your local bash user
>> profile, it could be that R never calls bash and thus never uses it.  In
>> Linux, I always set it in /etc/environment, so that the variable is set for
>> all users in all environments.
>>
>>
>> What does system("pwd", intern=TRUE) give you?
>>
>>
>> Keep me posted!
>>
>> Danny
>>
>>
>> Daniel C. Bowman
>> Doctoral Candidate in Geophysics
>> UNC Chapel Hill
>> phone: 575-418-8555
>> *curriculum vitae*:
>> http://www.unc.edu/~haksaeng/curriculum_vitae/bowman_cv.pdf
>> *LinkedIn*:  https://www.linkedin.com/in/dannycbowman
>> web:http://geosci.unc.edu/page/daniel-c-bowman
>> twitter: @dannycbowman
>>
>>
>>
>> ------------------------------
>> *From:* rnomads-user-bounces at lists.r-forge.r-project.org <
>> rnomads-user-bounces at lists.r-forge.r-project.org> on behalf of Patrick
>> King <king.pws at gmail.com>
>> *Sent:* Wednesday, December 9, 2015 7:28 AM
>> *To:* Announcements, feature requests, and help using rNOMADS
>> *Subject:* Re: [Rnomads-user] rNOMADS 2.1.6 released
>>
>> Hello Danny,
>>
>> Thank you very much for your nomads work.  I have used it to extract GFS
>> data and plot cross-sections using RAOB. I enjoy looking at your balloon
>> work.  I was the forecaster for a research project studying stratospheric
>> ozone based in Saskatchewan in 1975 and the pictures bring back memories of
>> the ballon launches. We even had some go astray too.
>>
>> I am migrating from a dual Linux/Windows system to a Macintosh and I
>> cannot get rNomads to work.  The problem seems to be in accessing wgrib2.
>>
>> Here is a snippet from my bash terminal:
>>
>> ~/SCI/rNomads $ echo $PATH
>>
>> /Users/pking/ ...   n:/usr/local/wgrib2:/usr/local/wgrib
>>
>> ~/SCI/rNomads $ wgrib2 fcst.grb
>>
>> 1:0:d=2015120900:TMP:800 mb:6 hour fcst:
>>
>> 2:131801:d=2015120900:RH:800 mb:6 hour fcst:
>>
>> 3:378897:d=2015120900:TMP:2 m above ground:6 hour fcst:
>>
>> 4:627907:d=2015120900:RH:2 m above ground:6 hour fcst:
>>
>> ~/SCI/rNomads $
>>
>> So wgrib2 is on my path and it does find 'fcst.grb' downloaded by
>> rNomads.  However rNomads can't find wgrib2 from within R:
>>
>> [Workspace loaded from ~/SCI/rnomads/.RData]
>>
>> > system("wgrib2")
>> sh: wgrib2: command not found
>> >
>>
>> DO you have any idea where I should look now?
>>
>> Thanks
>>
>> Pat
>>
>> On Sun, Nov 15, 2015 at 12:30 AM, Bowman, Daniel <haksaeng at live.unc.edu>
>> wrote:
>>
>>> Hello all,
>>>
>>>
>>> I've just released rNOMADS 2.1.6.  It now allows you to define a region
>>> to return data from in ReadGrib.  This should speed up data processing by
>>> orders of magnitude for those of you who are using archived grib data (such
>>> as gfs-anl), since those don't give an option to subset server-side.
>>>
>>>
>>> Let me know if you have any questions or suggestions for further work.
>>>
>>>
>>> Best,
>>>
>>>
>>> Danny
>>>
>>>
>>> Daniel C. Bowman
>>> Doctoral Candidate in Geophysics
>>> UNC Chapel Hill
>>> phone: 575-418-8555
>>> *curriculum vitae*:
>>> http://www.unc.edu/~haksaeng/curriculum_vitae/bowman_cv.pdf
>>> *LinkedIn*:  https://www.linkedin.com/in/dannycbowman
>>> web:http://geosci.unc.edu/page/daniel-c-bowman
>>> twitter: @dannycbowman
>>>
>>>
>>> _______________________________________________
>>> Rnomads-user mailing list
>>> Rnomads-user at lists.r-forge.r-project.org
>>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rnomads-user
>>>
>>>
>>
>>
>> --
>> Patrick King
>> Mobile: +1 647 525 6738
>>
>> _______________________________________________
>> Rnomads-user mailing list
>> Rnomads-user at lists.r-forge.r-project.org
>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rnomads-user
>>
>>
>
>
> --
> Patrick King
> Mobile: +1 647 525 6738
>

-- 
Patrick King
Mobile: +1 647 525 6738
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