From king.pws at gmail.com Wed Dec 9 13:28:40 2015 From: king.pws at gmail.com (Patrick King) Date: Wed, 9 Dec 2015 12:28:40 +0000 Subject: [Rnomads-user] rNOMADS 2.1.6 released In-Reply-To: References: Message-ID: 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 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From haksaeng at live.unc.edu Thu Dec 10 01:46:28 2015 From: haksaeng at live.unc.edu (Bowman, Daniel) Date: Thu, 10 Dec 2015 00:46:28 +0000 Subject: [Rnomads-user] Problems with MacOS In-Reply-To: References: , Message-ID: 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 on behalf of Patrick King 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 > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From king.pws at gmail.com Thu Dec 10 03:22:46 2015 From: king.pws at gmail.com (Patrick King) Date: Thu, 10 Dec 2015 02:22:46 +0000 Subject: [Rnomads-user] Problems with MacOS In-Reply-To: References: Message-ID: 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 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 > *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 > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From king.pws at gmail.com Thu Dec 10 03:57:35 2015 From: king.pws at gmail.com (Patrick King) Date: Thu, 10 Dec 2015 02:57:35 +0000 Subject: [Rnomads-user] Problems with MacOS In-Reply-To: References: Message-ID: 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 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 > 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 >> *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 >> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From haksaeng at live.unc.edu Thu Dec 10 04:36:37 2015 From: haksaeng at live.unc.edu (Bowman, Daniel) Date: Thu, 10 Dec 2015 03:36:37 +0000 Subject: [Rnomads-user] Problems with MacOS In-Reply-To: References: , Message-ID: 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 on behalf of Patrick King 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 > 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 > 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

> on behalf of Patrick King > 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 > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From haksaeng at live.unc.edu Thu Dec 31 01:33:43 2015 From: haksaeng at live.unc.edu (Bowman, Daniel) Date: Thu, 31 Dec 2015 00:33:43 +0000 Subject: [Rnomads-user] Work around for XML_PARSE_HUGE errors Message-ID: Hi all, An rNOMADS user had an issue a while back parsing grib repositories: Error: Excessive depth in document: 256 use XML_PARSE_HUGE option [1] After a lot of back and forth, head scratching, etc, the best I can do at this point is suggest using a forked version of the xml2 package that makes the problem go away: library(drat) drat:::add("shabbychef") install.packages('xml2') I will be considering how to fix the error in the official rNOMADS library (without requiring users to install non-CRAN libraries), but please use this work around for now. 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: