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

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]]
> 
> ______________________________________________
> 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]]

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 <
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)),
>
> 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]]
>> >
>> > ______________________________________________
>> > 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
>> <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
>> <http://www.r-project.org/posting-guide.html>
>> and provide commented, minimal, self-contained, reproducible code.
>
>
>
>
	[[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)),
> 
Why not simply numeric(n)?

Berend Hasselman

> 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.

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 <ligges at
statistik.tu-dortmund.de
> 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 <
>> 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)),
>>>
>>> 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]]
>>>>>
>>>>> ______________________________________________
>>>>> 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
>>>>>
>>>> <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
>>>> <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]]