Re: [R] Writing R package that call Fortran codes

[Kodalore Vijayan, Vineetha W]

Thanks for the comment. It resolved now. I have edited my namespace file.
-V

On Thu, Jun 16, 2016 at 3:20 PM, Uwe Ligges  wrote:

>
>
> On 16.06.2016 20:17, Kodalore Vijayan, Vineetha W wrote:
>
>> Hi,
>>
>>  Its running in R separately using dyn.load(). Thanks!
>>
>>  But my original issue is still there. I still can not build my package.
>> My
>> source code file name in SRC folder is "randomepi.f95" , the package name
>> is "NEpidemic". and the wrapper function in the R folder is "randomepi.r".
>> Not sure if I have to give the same file names.
>>
>> $R CMD BUILD NEpidemic
>>
>> Error in library.dynam(lib, package, package.lib) :
>>>
>>shared object ‘randomepi.so’ not found
>>Error: loading failed
>>
>> My namespace file has the following:
>>
>> exportPattern("^[[:alpha:]]+")
>> export(randomepi)
>> useDynLib(randomepi)
>>
>
> You probably need
>  useDynLib(NEpidemic)
> since the package mechanism will build a NEpidemic.so
>
> Best,
> Uwe Ligges
>
>
>
> import(graphics,grDevices,stats, utils)
>>
>>
>> Thanks,
>> Vineetha
>>
>>
>> On Thu, Jun 16, 2016 at 12:02 PM, Eduardo M. A. M.Mendes <
>> emammen...@gmail.com> wrote:
>>
>> Thanks  Bill for pointing this out.  I haven’t noticed it.
>>>
>>> Vineetha, try as.double(rep(0,n)) or as.matrix(rep(0,n)),
>>>
>>> Ed
>>>
>>> On Jun 16, 2016, at 2:54 PM, William Dunlap  wrote:
>>>
>>>  1: .Fortran("dataxy", n = as.integer(n), tmax = as.integer(tmax),

>>>  alpha = as.double(alpha), beta = as.double(beta), x = as.double(0,
>>>  length = n), y = as.double(0, length = n), tau = as.integer(0,
>>>  length = n))
>>>
>>> Are you expecting that
>>> as.integer(0, length=n)
>>> and
>>> as.double(0, length = n)
>>> will produce vectors of length 'n'?  They do not and short inputs will
>>> usually
>>> cause memory misuse and crashes in the Fortran code.
>>>
>>>
>>>
>>> Bill Dunlap
>>> TIBCO Software
>>> wdunlap tibco.com
>>>
>>> On Thu, Jun 16, 2016 at 10:03 AM, Kodalore Vijayan, Vineetha W <
>>> vwk...@mun.ca> wrote:
>>>
>>> Hi Eduardo,

  Thanks for your comments. I haven't tried the way you told me. Now
 when I
 tried, got the following error:

 *** caught segfault ***
 address 0x0, cause 'memory not mapped'

 Traceback:
  1: .Fortran("dataxy", n = as.integer(n), tmax = as.integer(tmax),
 alpha = as.double(alpha), beta = as.double(beta), x = as.double(0,
 length = n), y = as.double(0, length = n), tau = as.integer(0,
 length = n))
  2: out(NULL, NULL, NULL, NULL)

 Possible actions:
 1: abort (with core dump, if enabled)
 2: normal R exit
 3: exit R without saving workspace
 4: exit R saving workspace
 Selection:

 Any suggestions?

 Thanks,
 Vineetha

 On Wed, Jun 15, 2016 at 3:55 PM, Eduardo M. A. M.Mendes <
 emammen...@gmail.com> wrote:

 Hi
>
> Have you tried to load and run the fortran code using just a wrapper
> function in R?   I do that as the first step in order to build a
>
 package.

>
> Example:   fortran sources -> rk4_mod_r.f90 ,derive_henonheilles.f90,
> poincare_section.f90
>
> a) I use R CMD SHLIB rk4_mod_r.f90 ,derive_henonheilles.f90,
> poincare_section.f90 - o poincare_section_henonheilles_rk4.so
> b) Then I write a wrapper function in R, poinc_section_henonheilles.R
> ...
>  dyn.load("poincare_section_henonheilles_rk4.so")
>
>   out<-.Fortran("section_crossing",
> h=as.numeric(h),
> nphas=as.integer(nphas),..
> ...
> c) and call the function as usual.
>
> Please note that the function called by .Fortran is the name of the
> subroutine within poincare_section.f90 and not the filename.
>
> I take the opportunity to thank R-developers for making the calling of
> C
> and Fortran in R very easy.
>
> I hope this helps.
>
> regards
>
> Ed
>
> PS.  If you need an example of a package using Fortran90, please check
> https://github.com/emammendes/mittagleffler
>
>
>
> On Jun 15, 2016, at 5:20 PM, Kodalore Vijayan, Vineetha W <
>
 vwk...@mun.ca>

> wrote:
>
> Hi,
>
> I'm trying to write an R package that calls a Fortran subroutine on my
>
 Mac

> os x El Capitan with Xcode 7 and gfortran 6.1, R 3.3.0.   I can build
>
 and

> load the library but when I try to use it in R I get this error:
>
> library(NEpidemic)
> random_epi(variable_names)
>
>
> Error in .Fortran("random_epi", : "random_pi" not resolved from current
> namespace (NEpidemic).
>
> Then I  tried adding useDynLib(random_epi.f95) in the NAMESPACE file,
> additional to useDynLib(NEpidemic). After doing that I couldn't build
>
 the

> package and it gave me another error:
>
> Error in 

Re: [R] Writing R package that call Fortran codes

[Kodalore Vijayan, Vineetha W]

Thank you Don. I did send an email to R-sig-mac.

-Vineetha

On Thu, Jun 16, 2016 at 10:36 AM, MacQueen, Don  wrote:

> You might want to take this question to R-sig-mac.
>
> --
> Don MacQueen
>
> Lawrence Livermore National Laboratory
> 7000 East Ave., L-627
> Livermore, CA 94550
> 925-423-1062
>
>
>
>
>
> On 6/15/16, 1:20 PM, "R-help on behalf of Kodalore Vijayan, Vineetha W"
>  wrote:
>
> >Hi,
> >
> >I'm trying to write an R package that calls a Fortran subroutine on my
> >Mac
> >os x El Capitan with Xcode 7 and gfortran 6.1, R 3.3.0.   I can build and
> >load the library but when I try to use it in R I get this error:
> >>library(NEpidemic)
> >>random_epi(variable_names)
> >
> >Error in .Fortran("random_epi", : "random_pi" not resolved from current
> >namespace (NEpidemic).
> >
> >Then I  tried adding useDynLib(random_epi.f95) in the NAMESPACE file,
> >additional to useDynLib(NEpidemic). After doing that I couldn't build the
> >package and it gave me another error:
> >
> >Error in library.dynam(lib, package, package.lib) :
> >  shared object Œrandom_epi.so¹ not found
> >Error: loading failed
> >Execution halted
> >ERROR: loading failed
> >
> >When I checked my src folder, there is only random_epi.o file.  How can I
> >fix this issue? Any help would be much appreciated. I'm vey new to both R
> >and Fortran coding, especially in package building.
> >
> >Thanks in advance!
> >Vineetha
> >
> >   [[alternative HTML version deleted]]
> >
> >__
> >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >https://stat.ethz.ch/mailman/listinfo/r-help
> >PLEASE do read the posting guide
> >http://www.R-project.org/posting-guide.html
> >and provide commented, minimal, self-contained, reproducible code.
>
>

[[alternative HTML version deleted]]

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Writing R package that call Fortran codes

[Kodalore Vijayan, Vineetha W]

Thanks for the suggestion Berend. I just tried with numeric(n) and its
working for  x and y.

But my issue is different and its not resolved yet.

-Vineetha

On Thu, Jun 16, 2016 at 1:19 PM, Berend Hasselman  wrote:

>
> > On 16 Jun 2016, at 21:04, Eduardo M. A. M.Mendes 
> wrote:
> >
> >
> >> On Jun 16, 2016, at 3:50 PM, Berend Hasselman  wrote:
> >>
> >>
> >>> On 16 Jun 2016, at 20:02, Eduardo M. A. M.Mendes 
> wrote:
> >>>
> >>> Thanks  Bill for pointing this out.  I haven’t noticed it.
> >>>
> >>> Vineetha, try as.double(rep(0,n)) or as.matrix(rep(0,n)),
> >>>
> >>
> >> Why not simply numeric(n)?
> >>
> >> Berend Hasselman
> >>
> >
> > as.numeric(rep(0,n)) works too. Please remember that he wants a vector
> nor a scalar.
> >
>
> Indeed it does. And I certainly remembered that the OP wants a vector of
> length n.
> But so does numeric(n), which creates a length n vector. Just try
> numeric(2).
>
> Berend
>
>

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Writing R package that call Fortran codes

[Berend Hasselman]

> On 16 Jun 2016, at 21:04, Eduardo M. A. M.Mendes  wrote:
> 
> 
>> On Jun 16, 2016, at 3:50 PM, Berend Hasselman  wrote:
>> 
>> 
>>> On 16 Jun 2016, at 20:02, Eduardo M. A. M.Mendes  
>>> wrote:
>>> 
>>> Thanks  Bill for pointing this out.  I haven’t noticed it.
>>> 
>>> Vineetha, try as.double(rep(0,n)) or as.matrix(rep(0,n)),
>>> 
>> 
>> Why not simply numeric(n)?
>> 
>> Berend Hasselman
>> 
> 
> as.numeric(rep(0,n)) works too. Please remember that he wants a vector nor a 
> scalar.
> 

Indeed it does. And I certainly remembered that the OP wants a vector of length 
n.
But so does numeric(n), which creates a length n vector. Just try numeric(2).

Berend

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Writing R package that call Fortran codes

[Eduardo M. A. M.Mendes]

> On Jun 16, 2016, at 3:50 PM, Berend Hasselman  wrote:
> 
> 
>> On 16 Jun 2016, at 20:02, Eduardo M. A. M.Mendes  
>> wrote:
>> 
>> Thanks  Bill for pointing this out.  I haven’t noticed it.
>> 
>> Vineetha, try as.double(rep(0,n)) or as.matrix(rep(0,n)),
>> 
> 
> Why not simply numeric(n)?
> 
> Berend Hasselman
> 

as.numeric(rep(0,n)) works too. Please remember that he wants a vector nor a 
scalar.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Writing R package that call Fortran codes

[Berend Hasselman]

> On 16 Jun 2016, at 20:02, Eduardo M. A. M.Mendes  wrote:
> 
> Thanks  Bill for pointing this out.  I haven’t noticed it.
> 
> Vineetha, try as.double(rep(0,n)) or as.matrix(rep(0,n)),
> 

Why not simply numeric(n)?

Berend Hasselman

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Writing R package that call Fortran codes

[Kodalore Vijayan, Vineetha W]

Hi,

 Its running in R separately using dyn.load(). Thanks!

 But my original issue is still there. I still can not build my package. My
source code file name in SRC folder is "randomepi.f95" , the package name
is "NEpidemic". and the wrapper function in the R folder is "randomepi.r".
Not sure if I have to give the same file names.

$R CMD BUILD NEpidemic

> Error in library.dynam(lib, package, package.lib) :
   shared object ‘randomepi.so’ not found
   Error: loading failed

My namespace file has the following:

exportPattern("^[[:alpha:]]+")
export(randomepi)
useDynLib(randomepi)
import(graphics,grDevices,stats, utils)


Thanks,
Vineetha


On Thu, Jun 16, 2016 at 12:02 PM, Eduardo M. A. M.Mendes <
emammen...@gmail.com> wrote:

> Thanks  Bill for pointing this out.  I haven’t noticed it.
>
> Vineetha, try as.double(rep(0,n)) or as.matrix(rep(0,n)),
>
> Ed
>
> On Jun 16, 2016, at 2:54 PM, William Dunlap  wrote:
>
> >  1: .Fortran("dataxy", n = as.integer(n), tmax = as.integer(tmax),
>  alpha = as.double(alpha), beta = as.double(beta), x = as.double(0,
>  length = n), y = as.double(0, length = n), tau = as.integer(0,
>  length = n))
>
> Are you expecting that
> as.integer(0, length=n)
> and
> as.double(0, length = n)
> will produce vectors of length 'n'?  They do not and short inputs will
> usually
> cause memory misuse and crashes in the Fortran code.
>
>
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
> On Thu, Jun 16, 2016 at 10:03 AM, Kodalore Vijayan, Vineetha W <
> vwk...@mun.ca> wrote:
>
>> Hi Eduardo,
>>
>>  Thanks for your comments. I haven't tried the way you told me. Now when I
>> tried, got the following error:
>>
>> *** caught segfault ***
>> address 0x0, cause 'memory not mapped'
>>
>> Traceback:
>>  1: .Fortran("dataxy", n = as.integer(n), tmax = as.integer(tmax),
>> alpha = as.double(alpha), beta = as.double(beta), x = as.double(0,
>> length = n), y = as.double(0, length = n), tau = as.integer(0,
>> length = n))
>>  2: out(NULL, NULL, NULL, NULL)
>>
>> Possible actions:
>> 1: abort (with core dump, if enabled)
>> 2: normal R exit
>> 3: exit R without saving workspace
>> 4: exit R saving workspace
>> Selection:
>>
>> Any suggestions?
>>
>> Thanks,
>> Vineetha
>>
>> On Wed, Jun 15, 2016 at 3:55 PM, Eduardo M. A. M.Mendes <
>> emammen...@gmail.com> wrote:
>>
>> > Hi
>> >
>> > Have you tried to load and run the fortran code using just a wrapper
>> > function in R?   I do that as the first step in order to build a
>> package.
>> >
>> > Example:   fortran sources -> rk4_mod_r.f90 ,derive_henonheilles.f90,
>> > poincare_section.f90
>> >
>> > a) I use R CMD SHLIB rk4_mod_r.f90 ,derive_henonheilles.f90,
>> > poincare_section.f90 - o poincare_section_henonheilles_rk4.so
>> > b) Then I write a wrapper function in R, poinc_section_henonheilles.R
>> > ...
>> >  dyn.load("poincare_section_henonheilles_rk4.so")
>> >
>> >   out<-.Fortran("section_crossing",
>> > h=as.numeric(h),
>> > nphas=as.integer(nphas),..
>> > ...
>> > c) and call the function as usual.
>> >
>> > Please note that the function called by .Fortran is the name of the
>> > subroutine within poincare_section.f90 and not the filename.
>> >
>> > I take the opportunity to thank R-developers for making the calling of C
>> > and Fortran in R very easy.
>> >
>> > I hope this helps.
>> >
>> > regards
>> >
>> > Ed
>> >
>> > PS.  If you need an example of a package using Fortran90, please check
>> > https://github.com/emammendes/mittagleffler
>> >
>> >
>> >
>> > On Jun 15, 2016, at 5:20 PM, Kodalore Vijayan, Vineetha W <
>> vwk...@mun.ca>
>> > wrote:
>> >
>> > Hi,
>> >
>> > I'm trying to write an R package that calls a Fortran subroutine on my
>> Mac
>> > os x El Capitan with Xcode 7 and gfortran 6.1, R 3.3.0.   I can build
>> and
>> > load the library but when I try to use it in R I get this error:
>> >
>> > library(NEpidemic)
>> > random_epi(variable_names)
>> >
>> >
>> > Error in .Fortran("random_epi", : "random_pi" not resolved from current
>> > namespace (NEpidemic).
>> >
>> > Then I  tried adding useDynLib(random_epi.f95) in the NAMESPACE file,
>> > additional to useDynLib(NEpidemic). After doing that I couldn't build
>> the
>> > package and it gave me another error:
>> >
>> > Error in library.dynam(lib, package, package.lib) :
>> >  shared object ‘random_epi.so’ not found
>> > Error: loading failed
>> > Execution halted
>> > ERROR: loading failed
>> >
>> > When I checked my src folder, there is only random_epi.o file.  How can
>> I
>> > fix this issue? Any help would be much appreciated. I'm vey new to both
>> R
>> > and Fortran coding, especially in package building.
>> >
>> > Thanks in advance!
>> > Vineetha
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > __
>> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide
>> > 

Re: [R] Writing R package that call Fortran codes

[Kodalore Vijayan, Vineetha W]

Hi,

@Eduardo:  I do have statements like, double preciosion :: y(n) in my
fortran code. Will change the code and run again.

@ William :  Yes I was initializing X ,Y,and tau, each  have a vector of
length "n".

Thanks,
Vineetha

On Thu, Jun 16, 2016 at 11:54 AM, William Dunlap  wrote:

> >  1: .Fortran("dataxy", n = as.integer(n), tmax = as.integer(tmax),
>  alpha = as.double(alpha), beta = as.double(beta), x = as.double(0,
>  length = n), y = as.double(0, length = n), tau = as.integer(0,
>  length = n))
>
> Are you expecting that
> as.integer(0, length=n)
> and
> as.double(0, length = n)
> will produce vectors of length 'n'?  They do not and short inputs will
> usually
> cause memory misuse and crashes in the Fortran code.
>
>
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
> On Thu, Jun 16, 2016 at 10:03 AM, Kodalore Vijayan, Vineetha W <
> vwk...@mun.ca> wrote:
>
>> Hi Eduardo,
>>
>>  Thanks for your comments. I haven't tried the way you told me. Now when I
>> tried, got the following error:
>>
>> *** caught segfault ***
>> address 0x0, cause 'memory not mapped'
>>
>> Traceback:
>>  1: .Fortran("dataxy", n = as.integer(n), tmax = as.integer(tmax),
>> alpha = as.double(alpha), beta = as.double(beta), x = as.double(0,
>> length = n), y = as.double(0, length = n), tau = as.integer(0,
>> length = n))
>>  2: out(NULL, NULL, NULL, NULL)
>>
>> Possible actions:
>> 1: abort (with core dump, if enabled)
>> 2: normal R exit
>> 3: exit R without saving workspace
>> 4: exit R saving workspace
>> Selection:
>>
>> Any suggestions?
>>
>> Thanks,
>> Vineetha
>>
>> On Wed, Jun 15, 2016 at 3:55 PM, Eduardo M. A. M.Mendes <
>> emammen...@gmail.com> wrote:
>>
>> > Hi
>> >
>> > Have you tried to load and run the fortran code using just a wrapper
>> > function in R?   I do that as the first step in order to build a
>> package.
>> >
>> > Example:   fortran sources -> rk4_mod_r.f90 ,derive_henonheilles.f90,
>> > poincare_section.f90
>> >
>> > a) I use R CMD SHLIB rk4_mod_r.f90 ,derive_henonheilles.f90,
>> > poincare_section.f90 - o poincare_section_henonheilles_rk4.so
>> > b) Then I write a wrapper function in R, poinc_section_henonheilles.R
>> > ...
>> >  dyn.load("poincare_section_henonheilles_rk4.so")
>> >
>> >   out<-.Fortran("section_crossing",
>> > h=as.numeric(h),
>> > nphas=as.integer(nphas),..
>> > ...
>> > c) and call the function as usual.
>> >
>> > Please note that the function called by .Fortran is the name of the
>> > subroutine within poincare_section.f90 and not the filename.
>> >
>> > I take the opportunity to thank R-developers for making the calling of C
>> > and Fortran in R very easy.
>> >
>> > I hope this helps.
>> >
>> > regards
>> >
>> > Ed
>> >
>> > PS.  If you need an example of a package using Fortran90, please check
>> > https://github.com/emammendes/mittagleffler
>> >
>> >
>> >
>> > On Jun 15, 2016, at 5:20 PM, Kodalore Vijayan, Vineetha W <
>> vwk...@mun.ca>
>> > wrote:
>> >
>> > Hi,
>> >
>> > I'm trying to write an R package that calls a Fortran subroutine on my
>> Mac
>> > os x El Capitan with Xcode 7 and gfortran 6.1, R 3.3.0.   I can build
>> and
>> > load the library but when I try to use it in R I get this error:
>> >
>> > library(NEpidemic)
>> > random_epi(variable_names)
>> >
>> >
>> > Error in .Fortran("random_epi", : "random_pi" not resolved from current
>> > namespace (NEpidemic).
>> >
>> > Then I  tried adding useDynLib(random_epi.f95) in the NAMESPACE file,
>> > additional to useDynLib(NEpidemic). After doing that I couldn't build
>> the
>> > package and it gave me another error:
>> >
>> > Error in library.dynam(lib, package, package.lib) :
>> >  shared object ‘random_epi.so’ not found
>> > Error: loading failed
>> > Execution halted
>> > ERROR: loading failed
>> >
>> > When I checked my src folder, there is only random_epi.o file.  How can
>> I
>> > fix this issue? Any help would be much appreciated. I'm vey new to both
>> R
>> > and Fortran coding, especially in package building.
>> >
>> > Thanks in advance!
>> > Vineetha
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > __
>> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide
>> > http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>> >
>> >
>> >
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>
>

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- 

Re: [R] Writing R package that call Fortran codes

[Eduardo M. A. M.Mendes]

Thanks  Bill for pointing this out.  I haven’t noticed it.

Vineetha, try as.double(rep(0,n)) or as.matrix(rep(0,n)),

Ed

> On Jun 16, 2016, at 2:54 PM, William Dunlap  wrote:
> 
> >  1: .Fortran("dataxy", n = as.integer(n), tmax = as.integer(tmax), 
> > alpha = as.double(alpha), beta = as.double(beta), x = as.double(0, 
> > length = n), y = as.double(0, length = n), tau = as.integer(0, 
> > length = n))
> 
> Are you expecting that
> as.integer(0, length=n)
> and
> as.double(0, length = n)
> will produce vectors of length 'n'?  They do not and short inputs will usually
> cause memory misuse and crashes in the Fortran code.
> 
> 
> 
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com 
> On Thu, Jun 16, 2016 at 10:03 AM, Kodalore Vijayan, Vineetha W  > wrote:
> Hi Eduardo,
> 
>  Thanks for your comments. I haven't tried the way you told me. Now when I
> tried, got the following error:
> 
> *** caught segfault ***
> address 0x0, cause 'memory not mapped'
> 
> Traceback:
>  1: .Fortran("dataxy", n = as.integer(n), tmax = as.integer(tmax),
> alpha = as.double(alpha), beta = as.double(beta), x = as.double(0,
> length = n), y = as.double(0, length = n), tau = as.integer(0,
> length = n))
>  2: out(NULL, NULL, NULL, NULL)
> 
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
> 
> Any suggestions?
> 
> Thanks,
> Vineetha
> 
> On Wed, Jun 15, 2016 at 3:55 PM, Eduardo M. A. M.Mendes <
> emammen...@gmail.com > wrote:
> 
> > Hi
> >
> > Have you tried to load and run the fortran code using just a wrapper
> > function in R?   I do that as the first step in order to build a package.
> >
> > Example:   fortran sources -> rk4_mod_r.f90 ,derive_henonheilles.f90,
> > poincare_section.f90
> >
> > a) I use R CMD SHLIB rk4_mod_r.f90 ,derive_henonheilles.f90,
> > poincare_section.f90 - o poincare_section_henonheilles_rk4.so
> > b) Then I write a wrapper function in R, poinc_section_henonheilles.R
> > ...
> >  dyn.load("poincare_section_henonheilles_rk4.so")
> >
> >   out<-.Fortran("section_crossing",
> > h=as.numeric(h),
> > nphas=as.integer(nphas),..
> > ...
> > c) and call the function as usual.
> >
> > Please note that the function called by .Fortran is the name of the
> > subroutine within poincare_section.f90 and not the filename.
> >
> > I take the opportunity to thank R-developers for making the calling of C
> > and Fortran in R very easy.
> >
> > I hope this helps.
> >
> > regards
> >
> > Ed
> >
> > PS.  If you need an example of a package using Fortran90, please check
> > https://github.com/emammendes/mittagleffler 
> > 
> >
> >
> >
> > On Jun 15, 2016, at 5:20 PM, Kodalore Vijayan, Vineetha W  > >
> > wrote:
> >
> > Hi,
> >
> > I'm trying to write an R package that calls a Fortran subroutine on my  Mac
> > os x El Capitan with Xcode 7 and gfortran 6.1, R 3.3.0.   I can build and
> > load the library but when I try to use it in R I get this error:
> >
> > library(NEpidemic)
> > random_epi(variable_names)
> >
> >
> > Error in .Fortran("random_epi", : "random_pi" not resolved from current
> > namespace (NEpidemic).
> >
> > Then I  tried adding useDynLib(random_epi.f95) in the NAMESPACE file,
> > additional to useDynLib(NEpidemic). After doing that I couldn't build the
> > package and it gave me another error:
> >
> > Error in library.dynam(lib, package, package.lib) :
> >  shared object ‘random_epi.so’ not found
> > Error: loading failed
> > Execution halted
> > ERROR: loading failed
> >
> > When I checked my src folder, there is only random_epi.o file.  How can I
> > fix this issue? Any help would be much appreciated. I'm vey new to both R
> > and Fortran coding, especially in package building.
> >
> > Thanks in advance!
> > Vineetha
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org  mailing list -- To 
> > UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help 
> > 
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html 
> > 
> > and provide commented, minimal, self-contained, reproducible code.
> >
> >
> >
> 
> [[alternative HTML version deleted]]
> 
> __
> R-help@r-project.org  mailing list -- To 
> UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help 
> 
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html 
> 
> 

Re: [R] Writing R package that call Fortran codes

[William Dunlap via R-help]

>  1: .Fortran("dataxy", n = as.integer(n), tmax = as.integer(tmax),
 alpha = as.double(alpha), beta = as.double(beta), x = as.double(0,
 length = n), y = as.double(0, length = n), tau = as.integer(0,
 length = n))

Are you expecting that
as.integer(0, length=n)
and
as.double(0, length = n)
will produce vectors of length 'n'?  They do not and short inputs will
usually
cause memory misuse and crashes in the Fortran code.



Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Thu, Jun 16, 2016 at 10:03 AM, Kodalore Vijayan, Vineetha W <
vwk...@mun.ca> wrote:

> Hi Eduardo,
>
>  Thanks for your comments. I haven't tried the way you told me. Now when I
> tried, got the following error:
>
> *** caught segfault ***
> address 0x0, cause 'memory not mapped'
>
> Traceback:
>  1: .Fortran("dataxy", n = as.integer(n), tmax = as.integer(tmax),
> alpha = as.double(alpha), beta = as.double(beta), x = as.double(0,
> length = n), y = as.double(0, length = n), tau = as.integer(0,
> length = n))
>  2: out(NULL, NULL, NULL, NULL)
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
> Any suggestions?
>
> Thanks,
> Vineetha
>
> On Wed, Jun 15, 2016 at 3:55 PM, Eduardo M. A. M.Mendes <
> emammen...@gmail.com> wrote:
>
> > Hi
> >
> > Have you tried to load and run the fortran code using just a wrapper
> > function in R?   I do that as the first step in order to build a package.
> >
> > Example:   fortran sources -> rk4_mod_r.f90 ,derive_henonheilles.f90,
> > poincare_section.f90
> >
> > a) I use R CMD SHLIB rk4_mod_r.f90 ,derive_henonheilles.f90,
> > poincare_section.f90 - o poincare_section_henonheilles_rk4.so
> > b) Then I write a wrapper function in R, poinc_section_henonheilles.R
> > ...
> >  dyn.load("poincare_section_henonheilles_rk4.so")
> >
> >   out<-.Fortran("section_crossing",
> > h=as.numeric(h),
> > nphas=as.integer(nphas),..
> > ...
> > c) and call the function as usual.
> >
> > Please note that the function called by .Fortran is the name of the
> > subroutine within poincare_section.f90 and not the filename.
> >
> > I take the opportunity to thank R-developers for making the calling of C
> > and Fortran in R very easy.
> >
> > I hope this helps.
> >
> > regards
> >
> > Ed
> >
> > PS.  If you need an example of a package using Fortran90, please check
> > https://github.com/emammendes/mittagleffler
> >
> >
> >
> > On Jun 15, 2016, at 5:20 PM, Kodalore Vijayan, Vineetha W  >
> > wrote:
> >
> > Hi,
> >
> > I'm trying to write an R package that calls a Fortran subroutine on my
> Mac
> > os x El Capitan with Xcode 7 and gfortran 6.1, R 3.3.0.   I can build and
> > load the library but when I try to use it in R I get this error:
> >
> > library(NEpidemic)
> > random_epi(variable_names)
> >
> >
> > Error in .Fortran("random_epi", : "random_pi" not resolved from current
> > namespace (NEpidemic).
> >
> > Then I  tried adding useDynLib(random_epi.f95) in the NAMESPACE file,
> > additional to useDynLib(NEpidemic). After doing that I couldn't build the
> > package and it gave me another error:
> >
> > Error in library.dynam(lib, package, package.lib) :
> >  shared object ‘random_epi.so’ not found
> > Error: loading failed
> > Execution halted
> > ERROR: loading failed
> >
> > When I checked my src folder, there is only random_epi.o file.  How can I
> > fix this issue? Any help would be much appreciated. I'm vey new to both R
> > and Fortran coding, especially in package building.
> >
> > Thanks in advance!
> > Vineetha
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
> >
> >
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Writing R package that call Fortran codes

[Eduardo M. A. M.Mendes]

Hi Vineetha

It seems that there are some problems in the Fortran code as far as allocating 
memory is concerned.  If you have statements such as double preciosion :: y(n)  
 you will need to allocate memory for the vector within the Fortran code or in 
the R wrapper-function.  It is hard to pinpoint the error without seeing the 
source files.

Cheers

Ed



> On Jun 16, 2016, at 2:03 PM, Kodalore Vijayan, Vineetha W  
> wrote:
> 
> Hi Eduardo,
> 
>  Thanks for your comments. I haven't tried the way you told me. Now when I 
> tried, got the following error:
> 
> *** caught segfault ***
> address 0x0, cause 'memory not mapped'
> 
> Traceback:
>  1: .Fortran("dataxy", n = as.integer(n), tmax = as.integer(tmax), alpha 
> = as.double(alpha), beta = as.double(beta), x = as.double(0, length = 
> n), y = as.double(0, length = n), tau = as.integer(0, length = n))
>  2: out(NULL, NULL, NULL, NULL)
> 
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection: 
> 
> Any suggestions?
> 
> Thanks,
> Vineetha
> 
> On Wed, Jun 15, 2016 at 3:55 PM, Eduardo M. A. M.Mendes  > wrote:
> Hi
> 
> Have you tried to load and run the fortran code using just a wrapper function 
> in R?   I do that as the first step in order to build a package.  
> 
> Example:   fortran sources -> rk4_mod_r.f90 ,derive_henonheilles.f90, 
> poincare_section.f90
> 
> a) I use R CMD SHLIB rk4_mod_r.f90 ,derive_henonheilles.f90, 
> poincare_section.f90 - o poincare_section_henonheilles_rk4.so 
> b) Then I write a wrapper function in R, poinc_section_henonheilles.R
> ...
>  dyn.load("poincare_section_henonheilles_rk4.so")
>   
>   out<-.Fortran("section_crossing",
> h=as.numeric(h),
> nphas=as.integer(nphas),..
> ...
> c) and call the function as usual.
> 
> Please note that the function called by .Fortran is the name of the 
> subroutine within poincare_section.f90 and not the filename.
> 
> I take the opportunity to thank R-developers for making the calling of C and 
> Fortran in R very easy.   
> 
> I hope this helps.
> 
> regards
> 
> Ed
> 
> PS.  If you need an example of a package using Fortran90, please check 
> https://github.com/emammendes/mittagleffler 
> 
> 
> 
> 
>> On Jun 15, 2016, at 5:20 PM, Kodalore Vijayan, Vineetha W > > wrote:
>> 
>> Hi,
>> 
>> I'm trying to write an R package that calls a Fortran subroutine on my  Mac
>> os x El Capitan with Xcode 7 and gfortran 6.1, R 3.3.0.   I can build and
>> load the library but when I try to use it in R I get this error:
>>> library(NEpidemic)
>>> random_epi(variable_names)
>> 
>> Error in .Fortran("random_epi", : "random_pi" not resolved from current
>> namespace (NEpidemic).
>> 
>> Then I  tried adding useDynLib(random_epi.f95) in the NAMESPACE file,
>> additional to useDynLib(NEpidemic). After doing that I couldn't build the
>> package and it gave me another error:
>> 
>> Error in library.dynam(lib, package, package.lib) :
>>  shared object ‘random_epi.so’ not found
>> Error: loading failed
>> Execution halted
>> ERROR: loading failed
>> 
>> When I checked my src folder, there is only random_epi.o file.  How can I
>> fix this issue? Any help would be much appreciated. I'm vey new to both R
>> and Fortran coding, especially in package building.
>> 
>> Thanks in advance!
>> Vineetha
>> 
>>  
>> [[alternative HTML version deleted]]
>> 
>> __
>> R-help@r-project.org  mailing list -- To 
>> UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help 
>> 
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html 
>> 
>> and provide commented, minimal, self-contained, reproducible code.
> 
> 


[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Writing R package that call Fortran codes

[Kodalore Vijayan, Vineetha W]

Hi Eduardo,

 Thanks for your comments. I haven't tried the way you told me. Now when I
tried, got the following error:

*** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
 1: .Fortran("dataxy", n = as.integer(n), tmax = as.integer(tmax),
alpha = as.double(alpha), beta = as.double(beta), x = as.double(0,
length = n), y = as.double(0, length = n), tau = as.integer(0,
length = n))
 2: out(NULL, NULL, NULL, NULL)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:

Any suggestions?

Thanks,
Vineetha

On Wed, Jun 15, 2016 at 3:55 PM, Eduardo M. A. M.Mendes <
emammen...@gmail.com> wrote:

> Hi
>
> Have you tried to load and run the fortran code using just a wrapper
> function in R?   I do that as the first step in order to build a package.
>
> Example:   fortran sources -> rk4_mod_r.f90 ,derive_henonheilles.f90,
> poincare_section.f90
>
> a) I use R CMD SHLIB rk4_mod_r.f90 ,derive_henonheilles.f90,
> poincare_section.f90 - o poincare_section_henonheilles_rk4.so
> b) Then I write a wrapper function in R, poinc_section_henonheilles.R
> ...
>  dyn.load("poincare_section_henonheilles_rk4.so")
>
>   out<-.Fortran("section_crossing",
> h=as.numeric(h),
> nphas=as.integer(nphas),..
> ...
> c) and call the function as usual.
>
> Please note that the function called by .Fortran is the name of the
> subroutine within poincare_section.f90 and not the filename.
>
> I take the opportunity to thank R-developers for making the calling of C
> and Fortran in R very easy.
>
> I hope this helps.
>
> regards
>
> Ed
>
> PS.  If you need an example of a package using Fortran90, please check
> https://github.com/emammendes/mittagleffler
>
>
>
> On Jun 15, 2016, at 5:20 PM, Kodalore Vijayan, Vineetha W 
> wrote:
>
> Hi,
>
> I'm trying to write an R package that calls a Fortran subroutine on my  Mac
> os x El Capitan with Xcode 7 and gfortran 6.1, R 3.3.0.   I can build and
> load the library but when I try to use it in R I get this error:
>
> library(NEpidemic)
> random_epi(variable_names)
>
>
> Error in .Fortran("random_epi", : "random_pi" not resolved from current
> namespace (NEpidemic).
>
> Then I  tried adding useDynLib(random_epi.f95) in the NAMESPACE file,
> additional to useDynLib(NEpidemic). After doing that I couldn't build the
> package and it gave me another error:
>
> Error in library.dynam(lib, package, package.lib) :
>  shared object ‘random_epi.so’ not found
> Error: loading failed
> Execution halted
> ERROR: loading failed
>
> When I checked my src folder, there is only random_epi.o file.  How can I
> fix this issue? Any help would be much appreciated. I'm vey new to both R
> and Fortran coding, especially in package building.
>
> Thanks in advance!
> Vineetha
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
>

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Writing R package that call Fortran codes

[MacQueen, Don]

You might want to take this question to R-sig-mac.

-- 
Don MacQueen

Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062





On 6/15/16, 1:20 PM, "R-help on behalf of Kodalore Vijayan, Vineetha W"
 wrote:

>Hi,
>
>I'm trying to write an R package that calls a Fortran subroutine on my
>Mac
>os x El Capitan with Xcode 7 and gfortran 6.1, R 3.3.0.   I can build and
>load the library but when I try to use it in R I get this error:
>>library(NEpidemic)
>>random_epi(variable_names)
>
>Error in .Fortran("random_epi", : "random_pi" not resolved from current
>namespace (NEpidemic).
>
>Then I  tried adding useDynLib(random_epi.f95) in the NAMESPACE file,
>additional to useDynLib(NEpidemic). After doing that I couldn't build the
>package and it gave me another error:
>
>Error in library.dynam(lib, package, package.lib) :
>  shared object Œrandom_epi.so¹ not found
>Error: loading failed
>Execution halted
>ERROR: loading failed
>
>When I checked my src folder, there is only random_epi.o file.  How can I
>fix this issue? Any help would be much appreciated. I'm vey new to both R
>and Fortran coding, especially in package building.
>
>Thanks in advance!
>Vineetha
>
>   [[alternative HTML version deleted]]
>
>__
>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Writing R package that call Fortran codes

[Eduardo M. A. M.Mendes]

Hi

Have you tried to load and run the fortran code using just a wrapper function 
in R?   I do that as the first step in order to build a package.  

Example:   fortran sources -> rk4_mod_r.f90 ,derive_henonheilles.f90, 
poincare_section.f90

a) I use R CMD SHLIB rk4_mod_r.f90 ,derive_henonheilles.f90, 
poincare_section.f90 - o poincare_section_henonheilles_rk4.so 
b) Then I write a wrapper function in R, poinc_section_henonheilles.R
...
 dyn.load("poincare_section_henonheilles_rk4.so")
  
  out<-.Fortran("section_crossing",
h=as.numeric(h),
nphas=as.integer(nphas),..
...
c) and call the function as usual.

Please note that the function called by .Fortran is the name of the subroutine 
within poincare_section.f90 and not the filename.

I take the opportunity to thank R-developers for making the calling of C and 
Fortran in R very easy.   

I hope this helps.

regards

Ed

PS.  If you need an example of a package using Fortran90, please check 
https://github.com/emammendes/mittagleffler 




> On Jun 15, 2016, at 5:20 PM, Kodalore Vijayan, Vineetha W  
> wrote:
> 
> Hi,
> 
> I'm trying to write an R package that calls a Fortran subroutine on my  Mac
> os x El Capitan with Xcode 7 and gfortran 6.1, R 3.3.0.   I can build and
> load the library but when I try to use it in R I get this error:
>> library(NEpidemic)
>> random_epi(variable_names)
> 
> Error in .Fortran("random_epi", : "random_pi" not resolved from current
> namespace (NEpidemic).
> 
> Then I  tried adding useDynLib(random_epi.f95) in the NAMESPACE file,
> additional to useDynLib(NEpidemic). After doing that I couldn't build the
> package and it gave me another error:
> 
> Error in library.dynam(lib, package, package.lib) :
>  shared object ‘random_epi.so’ not found
> Error: loading failed
> Execution halted
> ERROR: loading failed
> 
> When I checked my src folder, there is only random_epi.o file.  How can I
> fix this issue? Any help would be much appreciated. I'm vey new to both R
> and Fortran coding, especially in package building.
> 
> Thanks in advance!
> Vineetha
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.