Writing R package that call Fortran codes

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]]

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]]

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]]

 1: .Fortran("dataxy", n = as.integer(n), tmax = as.integer(tmax),

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]]

        [[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]]

        [[alternative HTML version deleted]]

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]]

        [[alternative HTML version deleted]]

Error in library.dynam(lib, package, package.lib) :

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

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]]

<http://www.r-project.org/posting-guide.html>

        [[alternative HTML version deleted]]

On 16 Jun 2016, at 20:02, Eduardo M. A. M.Mendes <emammendes at 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)),

On Jun 16, 2016, at 3:50 PM, Berend Hasselman <bhh at xs4all.nl> wrote:

On 16 Jun 2016, at 20:02, Eduardo M. A. M.Mendes <emammendes at 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)),

Why not simply numeric(n)?

Berend Hasselman

On 16 Jun 2016, at 21:04, Eduardo M. A. M.Mendes <emammendes at gmail.com> wrote:

On Jun 16, 2016, at 3:50 PM, Berend Hasselman <bhh at xs4all.nl> wrote:

On 16 Jun 2016, at 20:02, Eduardo M. A. M.Mendes <emammendes at 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)),

Why not simply numeric(n)?

Berend Hasselman

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

On 16 Jun 2016, at 21:04, Eduardo M. A. M.Mendes <emammendes at gmail.com>

wrote:

On Jun 16, 2016, at 3:50 PM, Berend Hasselman <bhh at xs4all.nl> wrote:

On 16 Jun 2016, at 20:02, Eduardo M. A. M.Mendes <emammendes at 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)),

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

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"
<r-help-bounces at r-project.org on behalf of 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]]