[Rnomads-user] Problems with MacOS

[Bowman, Daniel]

Hi Pat,


I'm very glad you found the solution, and if I any one else contacts me with the same problem, I'll be able to pass along your wisdom!


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



________________________________
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 9:57 PM
To: Announcements, feature requests, and help using rNOMADS
Subject: Re: [Rnomads-user] Problems with MacOS

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<mailto: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<mailto: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<tel: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<mailto:rnomads-user-bounces at lists.r-forge.r-project.org> <rnomads-user-bounces at lists.r-forge.r-project.org<mailto:rnomads-user-bounces at lists.r-forge.r-project.org>> on behalf of Patrick King <king.pws at gmail.com<mailto: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<tel:2015120900>:TMP:800 mb:6 hour fcst:

2:131801:d=2015120900<tel:2015120900>:RH:800 mb:6 hour fcst:

3:378897:d=2015120900<tel:2015120900>:TMP:2 m above ground:6 hour fcst:

4:627907:d=2015120900<tel: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<mailto: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<tel: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


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--
Patrick King
Mobile: +1 647 525 6738<tel:%2B1%20647%20525%206738>

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--
Patrick King
Mobile: +1 647 525 6738<tel:%2B1%20647%20525%206738>



--
Patrick King
Mobile: +1 647 525 6738
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