R help - Jun 2016 - Writing R package that call Fortran codes

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 <
emammendes at 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 <vwkv13 at
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 at 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]]

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 <vwkv13 at
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 <emammendes at
gmail.com <mailto:emammendes at 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
<https://github.com/emammendes/mittagleffler>
> 
> 
> 
>> On Jun 15, 2016, at 5:20 PM, Kodalore Vijayan, Vineetha W <vwkv13 at
mun.ca <mailto:vwkv13 at 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 at r-project.org <mailto:R-help at r-project.org> mailing
list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
<https://stat.ethz.ch/mailman/listinfo/r-help>
>> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
<http://www.r-project.org/posting-guide.html>
>> and provide commented, minimal, self-contained, reproducible code.
> 
> 

	[[alternative HTML version deleted]]

>  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 <
vwkv13 at 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 <
> emammendes at 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 <vwkv13
at 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 at 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 at 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]]

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 <wdunlap at tibco.com>
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 <
> vwkv13 at 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 <
>> emammendes at 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 <
>> vwkv13 at 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 at 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 at 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]]

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 <wdunlap at tibco.com>
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 <http://tibco.com/>
> On Thu, Jun 16, 2016 at 10:03 AM, Kodalore Vijayan, Vineetha W <vwkv13
at mun.ca <mailto:vwkv13 at 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 <
> emammendes at gmail.com <mailto:emammendes at 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
<https://github.com/emammendes/mittagleffler>
> >
> >
> >
> > On Jun 15, 2016, at 5:20 PM, Kodalore Vijayan, Vineetha W <vwkv13
at mun.ca <mailto:vwkv13 at 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 at r-project.org <mailto:R-help at r-project.org> mailing
list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
<https://stat.ethz.ch/mailman/listinfo/r-help>
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
> >
> >
> >
> 
>         [[alternative HTML version deleted]]
> 
> ______________________________________________
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