Re: [R-SIG-Mac] Issues with rj (requirement for StatET) since Mojave/3.5.1 update

2018-11-29 Thread Adrian Dușa 
On Sun, Nov 25, 2018 at 9:48 PM Jonathan Greenberg 
wrote:
>
> Ok, figured it out but it was non-trivial.  I found the solution here:
>
https://github.com/velocyto-team/velocyto.R/issues/2#issuecomment-352584213
>
> TLDR you need to use homebrew (https://brew.sh/):
> 1) Install homebrew as linked above
> 2) Install llvm (and maybe boost):
> brew install llvm
> brew install boost
> 3) Mod your ~/.R/Makevars (nano ~/.R/Makevars) to read:
>
> CC=/usr/local/clang4/bin/clang
> CXX=/usr/local/clang4/bin/clang++
> CXX11=/usr/local/clang4/bin/clang++
> CXX14=/usr/local/clang4/bin/clang++
> CXX17=/usr/local/clang4/bin/clang++
> CXX1X=/usr/local/clang4/bin/clang++
> LDFLAGS=-L/usr/local/clang4/lib


I've recently installed llvm via homebrew, after an upgrade to Mojave.
However my newly installed clang version is surely not 4 but 7, and it is
not found under /usr/local/.
Instead, I've edited the Makevars file with something like:

CC=/usr/local/Cellar/llvm/7.0.0/bin/clang
CXX=/usr/local/Cellar/llvm/7.0.0/bin/clang++
CXX1X=/usr/local/Cellar/llvm/7.0.0/bin/clang++
LDFLAGS=-L/usr/local/Cellar/llvm/7.0.0/lib
-Wl,-rpath,/usr/local/Cellar/llvm/7.0.0/lib
CXXFLAGS=-I/usr/local/Cellar/llvm/7.0.0/lib/clang/7.0.0/include/

This seems to work for me,
Adrian

--
Adrian Dusa
University of Bucharest
Romanian Social Data Archive
Soseaua Panduri nr. 90-92
050663 Bucharest sector 5
Romania
https://adriandusa.eu

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Re: [R-SIG-Mac] Issues with rj (requirement for StatET) since Mojave/3.5.1 update

2018-11-29 Thread Adrian Dușa 
On Thu, Nov 29, 2018 at 4:06 PM Simon Urbanek 
wrote:
>
> For posterity: both recommendations are plain wrong so don't use
(obviously, the settings didn't match the installed compilers). They are
not supported in the CRAN version of R which is compiled by the clang 6.0
compiler in /usr/local/clang6 that we supply on CRAN. You can compile your
own R or use homebrew, but don't expect CRAN packages to work with that.
You don't even need to touch Makevars, just setting PATH to start with
/usr/local/clang6/bin before compilation is sufficient.


Thanks very much Simon, will follow your instructions to be CRAN compliant.
Best,
Adrian

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Re: [R-SIG-Mac] Issues with rj (requirement for StatET) since Mojave/3.5.1 update

2018-11-29 Thread Simon Urbanek 
For posterity: both recommendations are plain wrong so don't use (obviously, 
the settings didn't match the installed compilers). They are not supported in 
the CRAN version of R which is compiled by the clang 6.0 compiler in 
/usr/local/clang6 that we supply on CRAN. You can compile your own R or use 
homebrew, but don't expect CRAN packages to work with that. You don't even need 
to touch Makevars, just setting PATH to start with /usr/local/clang6/bin before 
compilation is sufficient.

Cheers,
Simon


> On Nov 26, 2018, at 1:41 AM, Adrian Dușa  wrote:
> 
> On Sun, Nov 25, 2018 at 9:48 PM Jonathan Greenberg 
> wrote:
>> 
>> Ok, figured it out but it was non-trivial.  I found the solution here:
>> 
> https://github.com/velocyto-team/velocyto.R/issues/2#issuecomment-352584213
>> 
>> TLDR you need to use homebrew (https://brew.sh/):
>> 1) Install homebrew as linked above
>> 2) Install llvm (and maybe boost):
>> brew install llvm
>> brew install boost
>> 3) Mod your ~/.R/Makevars (nano ~/.R/Makevars) to read:
>> 
>> CC=/usr/local/clang4/bin/clang
>> CXX=/usr/local/clang4/bin/clang++
>> CXX11=/usr/local/clang4/bin/clang++
>> CXX14=/usr/local/clang4/bin/clang++
>> CXX17=/usr/local/clang4/bin/clang++
>> CXX1X=/usr/local/clang4/bin/clang++
>> LDFLAGS=-L/usr/local/clang4/lib
> 
> 
> I've recently installed llvm via homebrew, after an upgrade to Mojave.
> However my newly installed clang version is surely not 4 but 7, and it is
> not found under /usr/local/.
> Instead, I've edited the Makevars file with something like:
> 
> CC=/usr/local/Cellar/llvm/7.0.0/bin/clang
> CXX=/usr/local/Cellar/llvm/7.0.0/bin/clang++
> CXX1X=/usr/local/Cellar/llvm/7.0.0/bin/clang++
> LDFLAGS=-L/usr/local/Cellar/llvm/7.0.0/lib
> -Wl,-rpath,/usr/local/Cellar/llvm/7.0.0/lib
> CXXFLAGS=-I/usr/local/Cellar/llvm/7.0.0/lib/clang/7.0.0/include/
> 
> This seems to work for me,
> Adrian
> 
> --
> Adrian Dusa
> University of Bucharest
> Romanian Social Data Archive
> Soseaua Panduri nr. 90-92
> 050663 Bucharest sector 5
> Romania
> https://adriandusa.eu
> 
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> 
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Re: [R-SIG-Mac] Issues with rj (requirement for StatET) since Mojave/3.5.1 update

2018-11-25 Thread Adrian Dușa 
On Sun, Nov 25, 2018 at 9:48 PM Jonathan Greenberg 
wrote:
>
> Ok, figured it out but it was non-trivial.  I found the solution here:
>
https://github.com/velocyto-team/velocyto.R/issues/2#issuecomment-352584213
>
> TLDR you need to use homebrew (https://brew.sh/):
> 1) Install homebrew as linked above
> 2) Install llvm (and maybe boost):
> brew install llvm
> brew install boost
> 3) Mod your ~/.R/Makevars (nano ~/.R/Makevars) to read:
>
> CC=/usr/local/clang4/bin/clang
> CXX=/usr/local/clang4/bin/clang++
> CXX11=/usr/local/clang4/bin/clang++
> CXX14=/usr/local/clang4/bin/clang++
> CXX17=/usr/local/clang4/bin/clang++
> CXX1X=/usr/local/clang4/bin/clang++
> LDFLAGS=-L/usr/local/clang4/lib


I've recently installed llvm via homebrew, after an upgrade to Mojave.
However my newly installed clang version is surely not 4 but 7, and it is
not found under /usr/local/.
Instead, I've edited the Makevars file with something like:

CC=/usr/local/Cellar/llvm/7.0.0/bin/clang
CXX=/usr/local/Cellar/llvm/7.0.0/bin/clang++
CXX1X=/usr/local/Cellar/llvm/7.0.0/bin/clang++
LDFLAGS=-L/usr/local/Cellar/llvm/7.0.0/lib
-Wl,-rpath,/usr/local/Cellar/llvm/7.0.0/lib
CXXFLAGS=-I/usr/local/Cellar/llvm/7.0.0/lib/clang/7.0.0/include/

This seems to work for me,
Adrian

--
Adrian Dusa
University of Bucharest
Romanian Social Data Archive
Soseaua Panduri nr. 90-92
050663 Bucharest sector 5
Romania
https://adriandusa.eu

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Re: [R-SIG-Mac] Issues with rj (requirement for StatET) since Mojave/3.5.1 update

2018-11-25 Thread Jonathan Greenberg 
Ok, figured it out but it was non-trivial.  I found the solution here:
https://github.com/velocyto-team/velocyto.R/issues/2#issuecomment-352584213

TLDR you need to use homebrew (https://brew.sh/):
1) Install homebrew as linked above
2) Install llvm (and maybe boost):
brew install llvm
brew install boost
3) Mod your ~/.R/Makevars (nano ~/.R/Makevars) to read:

CC=/usr/local/clang4/bin/clang
CXX=/usr/local/clang4/bin/clang++
CXX11=/usr/local/clang4/bin/clang++
CXX14=/usr/local/clang4/bin/clang++
CXX17=/usr/local/clang4/bin/clang++
CXX1X=/usr/local/clang4/bin/clang++
LDFLAGS=-L/usr/local/clang4/lib

That allowed me to properly get rj and rj.gd working again which 
then allowed me to start using Stat-ET again.

I imagine this will solve other problems MacOS X Mojave package installs.

--jonathan

On Sat, Nov 17, 2018 at 5:50 AM Jonathan Greenberg 
mailto:jgreenb...@unr.edu>> wrote:
I'm aware rJava can be installed as a binary and that this is an OS issue, 
hence posting on r-sig-mac.  I assumed more people are familiar with rJava then 
rj and I'm fairly confident it's the same issue, hence my showing that error. 
rj is not on CRAN AFAIK so I'm trying to solve the source install issue for 
that particular package.

The manual and the website have not, this far, led me to getting this working.  
The clang and gfortran installers do not solve the issue.  I suspect there is a 
Makevars solution but, again, I haven't found one that works.

This happened post Mojave (I had everything working in High Sierra).

J

On Fri, Nov 16, 2018, 11:14 PM Prof Brian Ripley 
mailto:rip...@stats.ox.ac.uk>>>
 wrote:
BTW, reading the manual (in this case 'R Installation and
Administration') often helps, and would have here.

On 16/11/2018 19:10, Jonathan Greenberg wrote:
> I'm hoping to get some insight into seeing if I can get "rj" working again in 
> Mojave/R 3.5.1 -- this is a requirements for the Eclipse interface to R 
> "Stat-ET") -- I'm seeing similar issues when trying to get rJava working also 
> from source, e.g.:
>
> Rscript -e 'install.packages("rJava", repos="http://rforge.net;, 
> type="source")'

Why are you not installing from CRAN?  Discussing off-CRAN versions here
is frowned on, not least as we know the CRAN version works.

> and
>
> install.packages(c("rj", "rj.gd"), 
> repos="http://download.walware.de/rj-2.1",type="source;)
>
> All issues lead to:
>
> "clang: error: unsupported option '-fopenmp'"
>
> I've installed clang6 and gfortran61 from CRAN, but that doesn't seem to 
> work.  I've tried tweaking the ~/.R/Makevars, e.g.:
>
> FLIBS=-L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
> CC=/usr/local/clang6/bin/clang
> CXX=/usr/local/clang6/bin/clang++
> CXX1X=/usr/local/clang6/bin/clang++
> CXX98=/usr/local/clang6/bin/clang++
> CXX11=/usr/local/clang6/bin/clang++
> CXX14=/usr/local/clang6/bin/clang++
> CXX17=/usr/local/clang6/bin/clang++
> LDFLAGS=-L/usr/local/clang6/lib
>
> Which only results in a different error:
> ld: warning: text-based stub file 
> /System/Library/Frameworks//JavaVM.framework/JavaVM.tbd and library file 
> /System/Library/Frameworks//JavaVM.framework/JavaVM are out of sync. Falling 
> back to library file for linking.
> ld: library not found for -lomp
>
> Any ideas?

That is not an *error*!  It is a warning from the OS (ld is part of the
OS) about parts of the OS being out of step, and has been going on for
some time (AFAIR with High Sierra too).  You have not shown us the
complete output, but on my systems installation of CRAN rJava proceeds.

> --
> --
> Jonathan A. Greenberg, PhD
> Randall Endowed Professor and Associate Professor of Remote Sensing
> Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
> Natural Resources & 
> Environmental
>  Science
> University of Nevada, Reno
> 1664 N Virginia St MS/0186
> Reno, NV 89557
> Phone: 415-763-5476
> http://www.unr.edu/nres
> Gchat: 
> jgrn...@gmail.com>>>,
>  Skype: jgrn3007


--
Brian D. Ripley,  
rip...@stats.ox.ac.uk>
Emeritus Professor of Applied Statistics, University of Oxford

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Randall Endowed Professor and Associate Professor of Remote Sensing
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Natural Resources & Environmental Science
University of Nevada, Reno
1664 N Virginia St

Re: [R-SIG-Mac] Issues with rj (requirement for StatET) since Mojave/3.5.1 update

2018-11-17 Thread Jonathan Greenberg 
I'm aware rJava can be installed as a binary and that this is an OS issue, 
hence posting on r-sig-mac.  I assumed more people are familiar with rJava then 
rj and I'm fairly confident it's the same issue, hence my showing that error. 
rj is not on CRAN AFAIK so I'm trying to solve the source install issue for 
that particular package.

The manual and the website have not, this far, led me to getting this working.  
The clang and gfortran installers do not solve the issue.  I suspect there is a 
Makevars solution but, again, I haven't found one that works.

This happened post Mojave (I had everything working in High Sierra).

J

On Fri, Nov 16, 2018, 11:14 PM Prof Brian Ripley 
mailto:rip...@stats.ox.ac.uk>> wrote:
BTW, reading the manual (in this case 'R Installation and
Administration') often helps, and would have here.

On 16/11/2018 19:10, Jonathan Greenberg wrote:
> I'm hoping to get some insight into seeing if I can get "rj" working again in 
> Mojave/R 3.5.1 -- this is a requirements for the Eclipse interface to R 
> "Stat-ET") -- I'm seeing similar issues when trying to get rJava working also 
> from source, e.g.:
>
> Rscript -e 'install.packages("rJava", repos="http://rforge.net;, 
> type="source")'

Why are you not installing from CRAN?  Discussing off-CRAN versions here
is frowned on, not least as we know the CRAN version works.

> and
>
> install.packages(c("rj", "rj.gd"), 
> repos="http://download.walware.de/rj-2.1",type="source;)
>
> All issues lead to:
>
> "clang: error: unsupported option '-fopenmp'"
>
> I've installed clang6 and gfortran61 from CRAN, but that doesn't seem to 
> work.  I've tried tweaking the ~/.R/Makevars, e.g.:
>
> FLIBS=-L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
> CC=/usr/local/clang6/bin/clang
> CXX=/usr/local/clang6/bin/clang++
> CXX1X=/usr/local/clang6/bin/clang++
> CXX98=/usr/local/clang6/bin/clang++
> CXX11=/usr/local/clang6/bin/clang++
> CXX14=/usr/local/clang6/bin/clang++
> CXX17=/usr/local/clang6/bin/clang++
> LDFLAGS=-L/usr/local/clang6/lib
>
> Which only results in a different error:
> ld: warning: text-based stub file 
> /System/Library/Frameworks//JavaVM.framework/JavaVM.tbd and library file 
> /System/Library/Frameworks//JavaVM.framework/JavaVM are out of sync. Falling 
> back to library file for linking.
> ld: library not found for -lomp
>
> Any ideas?

That is not an *error*!  It is a warning from the OS (ld is part of the
OS) about parts of the OS being out of step, and has been going on for
some time (AFAIR with High Sierra too).  You have not shown us the
complete output, but on my systems installation of CRAN rJava proceeds.

> --
> --
> Jonathan A. Greenberg, PhD
> Randall Endowed Professor and Associate Professor of Remote Sensing
> Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
> Natural Resources & 
> Environmental
>  Science
> University of Nevada, Reno
> 1664 N Virginia St MS/0186
> Reno, NV 89557
> Phone: 415-763-5476
> http://www.unr.edu/nres
> Gchat: 
> jgrn...@gmail.com>,
>  Skype: jgrn3007


--
Brian D. Ripley,  
rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford

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--
Jonathan A. Greenberg, PhD
Randall Endowed Professor and Associate Professor of Remote Sensing
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Natural Resources & Environmental Science
University of Nevada, Reno
1664 N Virginia St MS/0186
Reno, NV 89557
Phone: 415-763-5476
http://www.unr.edu/nres
Gchat: jgrn...@gmail.com, Skype: jgrn3007

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Re: [R-SIG-Mac] Issues with rj (requirement for StatET) since Mojave/3.5.1 update

2018-11-16 Thread Prof Brian Ripley 
BTW, reading the manual (in this case 'R Installation and 
Administration') often helps, and would have here.


On 16/11/2018 19:10, Jonathan Greenberg wrote:

I'm hoping to get some insight into seeing if I can get "rj" working again in Mojave/R 
3.5.1 -- this is a requirements for the Eclipse interface to R "Stat-ET") -- I'm seeing 
similar issues when trying to get rJava working also from source, e.g.:

Rscript -e 'install.packages("rJava", repos="http://rforge.net;, type="source")'


Why are you not installing from CRAN?  Discussing off-CRAN versions here 
is frowned on, not least as we know the CRAN version works.



and

install.packages(c("rj", "rj.gd"), 
repos="http://download.walware.de/rj-2.1",type="source;)

All issues lead to:

"clang: error: unsupported option '-fopenmp'"

I've installed clang6 and gfortran61 from CRAN, but that doesn't seem to work.  
I've tried tweaking the ~/.R/Makevars, e.g.:

FLIBS=-L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CC=/usr/local/clang6/bin/clang
CXX=/usr/local/clang6/bin/clang++
CXX1X=/usr/local/clang6/bin/clang++
CXX98=/usr/local/clang6/bin/clang++
CXX11=/usr/local/clang6/bin/clang++
CXX14=/usr/local/clang6/bin/clang++
CXX17=/usr/local/clang6/bin/clang++
LDFLAGS=-L/usr/local/clang6/lib

Which only results in a different error:
ld: warning: text-based stub file 
/System/Library/Frameworks//JavaVM.framework/JavaVM.tbd and library file 
/System/Library/Frameworks//JavaVM.framework/JavaVM are out of sync. Falling 
back to library file for linking.
ld: library not found for -lomp

Any ideas?


That is not an *error*!  It is a warning from the OS (ld is part of the 
OS) about parts of the OS being out of step, and has been going on for 
some time (AFAIR with High Sierra too).  You have not shown us the 
complete output, but on my systems installation of CRAN rJava proceeds.



--
--
Jonathan A. Greenberg, PhD
Randall Endowed Professor and Associate Professor of Remote Sensing
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Natural Resources & Environmental Science
University of Nevada, Reno
1664 N Virginia St MS/0186
Reno, NV 89557
Phone: 415-763-5476
http://www.unr.edu/nres
Gchat: jgrn...@gmail.com, Skype: jgrn3007



--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford

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Re: [R-SIG-Mac] Issues with rj (requirement for StatET) since Mojave/3.5.1 update

2018-11-16 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac 
Check that you have the latest version of the clang compiler from the r-mac 
site.  I believe the present version supports -fopenmp, previous version did 
not.  If not,  I can point you to a different link to download the compiler, 
but I think using the officially approved versions the cleanest solution.

HTH,

-Roy


> On Nov 16, 2018, at 11:10 AM, Jonathan Greenberg  wrote:
> 
> I'm hoping to get some insight into seeing if I can get "rj" working again in 
> Mojave/R 3.5.1 -- this is a requirements for the Eclipse interface to R 
> "Stat-ET") -- I'm seeing similar issues when trying to get rJava working also 
> from source, e.g.:
> 
> Rscript -e 'install.packages("rJava", repos="http://rforge.net;, 
> type="source")'
> 
> and
> 
> install.packages(c("rj", "rj.gd"), 
> repos="http://download.walware.de/rj-2.1",type="source;)
> 
> All issues lead to:
> 
> "clang: error: unsupported option '-fopenmp'"
> 
> I've installed clang6 and gfortran61 from CRAN, but that doesn't seem to 
> work.  I've tried tweaking the ~/.R/Makevars, e.g.:
> 
> FLIBS=-L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
> CC=/usr/local/clang6/bin/clang
> CXX=/usr/local/clang6/bin/clang++
> CXX1X=/usr/local/clang6/bin/clang++
> CXX98=/usr/local/clang6/bin/clang++
> CXX11=/usr/local/clang6/bin/clang++
> CXX14=/usr/local/clang6/bin/clang++
> CXX17=/usr/local/clang6/bin/clang++
> LDFLAGS=-L/usr/local/clang6/lib
> 
> Which only results in a different error:
> ld: warning: text-based stub file 
> /System/Library/Frameworks//JavaVM.framework/JavaVM.tbd and library file 
> /System/Library/Frameworks//JavaVM.framework/JavaVM are out of sync. Falling 
> back to library file for linking.
> ld: library not found for -lomp
> 
> Any ideas?
> --
> --
> Jonathan A. Greenberg, PhD
> Randall Endowed Professor and Associate Professor of Remote Sensing
> Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
> Natural Resources & Environmental Science
> University of Nevada, Reno
> 1664 N Virginia St MS/0186
> Reno, NV 89557
> Phone: 415-763-5476
> http://www.unr.edu/nres
> Gchat: jgrn...@gmail.com, Skype: jgrn3007
> 
>   [[alternative HTML version deleted]]
> 
> ___
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> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

**
"The contents of this message do not reflect any position of the U.S. 
Government or NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

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[R-SIG-Mac] Issues with rj (requirement for StatET) since Mojave/3.5.1 update

2018-11-16 Thread Jonathan Greenberg 
I'm hoping to get some insight into seeing if I can get "rj" working again in 
Mojave/R 3.5.1 -- this is a requirements for the Eclipse interface to R 
"Stat-ET") -- I'm seeing similar issues when trying to get rJava working also 
from source, e.g.:

Rscript -e 'install.packages("rJava", repos="http://rforge.net;, type="source")'

and

install.packages(c("rj", "rj.gd"), 
repos="http://download.walware.de/rj-2.1",type="source;)

All issues lead to:

"clang: error: unsupported option '-fopenmp'"

I've installed clang6 and gfortran61 from CRAN, but that doesn't seem to work.  
I've tried tweaking the ~/.R/Makevars, e.g.:

FLIBS=-L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CC=/usr/local/clang6/bin/clang
CXX=/usr/local/clang6/bin/clang++
CXX1X=/usr/local/clang6/bin/clang++
CXX98=/usr/local/clang6/bin/clang++
CXX11=/usr/local/clang6/bin/clang++
CXX14=/usr/local/clang6/bin/clang++
CXX17=/usr/local/clang6/bin/clang++
LDFLAGS=-L/usr/local/clang6/lib

Which only results in a different error:
ld: warning: text-based stub file 
/System/Library/Frameworks//JavaVM.framework/JavaVM.tbd and library file 
/System/Library/Frameworks//JavaVM.framework/JavaVM are out of sync. Falling 
back to library file for linking.
ld: library not found for -lomp

Any ideas?
--
--
Jonathan A. Greenberg, PhD
Randall Endowed Professor and Associate Professor of Remote Sensing
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Natural Resources & Environmental Science
University of Nevada, Reno
1664 N Virginia St MS/0186
Reno, NV 89557
Phone: 415-763-5476
http://www.unr.edu/nres
Gchat: jgrn...@gmail.com, Skype: jgrn3007

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