R devel - Sep 2019 - Calling a LAPACK subroutine from R

Berend,

I do not think this works with gfortran 7+. I am calling the BLAS 
subroutine dgemv from Fortran code in my package eha, and the check 
(with R-devel) gives:

gmlfun.f:223:1: warning: type of ?dgemv? does not match original 
declaration [-Wlto-type-mismatch]
       &     score, ione)
  ^
/home/gobr0002/R/src/R-devel/include/R_ext/BLAS.h:107:1: note: type 
mismatch in parameter 12
  F77_NAME(dgemv)(const char *trans, const int *m, const int *n,

Type of a Fortran subroutine is matched against type of a C function?! 
My conclusion is that it is impossible to call a BLAS subroutine with a 
character parameter from Fortran code (nowadays). Calling from C code is 
fine, on the other hand(!).

I have recently asked about this on R-pkg-devel, but not received any 
useful answers, and my submission to CRAN is rejected. I solve it by 
making a personal copy of dgemv and changing the character parameter to 
integer, and adding Jack Dongarra, Jeremy Du Croz, Sven Hammarling, and 
Richard Hanson as authors of eha. And a Copyright note, all in the 
DESCRIPTION file. Ugly but what can I do (except rewriting the Fortran 
code in C with f2c)?

G?ran

On 2019-09-11 21:38, Berend Hasselman wrote:
> 
> The Lapack library is loaded automatically by R itself when it needs it 
for doing some calculation.
> You can force it to do that with a (dummy) solve for example.
> Put this at start of your script:
> 
> <code>
> # dummy code to get LAPACK library loaded
> X1 <- diag(2,2)
> x1 <- rep(2,2)
> # X1;x1
> z <- solve(X1,x1)
> </code>
> 
> followed by the rest of your script.
> You will get a warning (I do) that  "passing a character vector  to
.Fortran is not portable".
> On other systems this may gave fatal errors. This is quick and very dirty.
Don't do it.
> 
> I believe there is a better and much safer way to achieve what you want.
> Here goes.
> 
> Create a folder (directory) src in the directory where your script resides.
> Create a wrapper for "dpbtrf" file in a file xdpbtrf.f that takes
an integer instead of character
> 
> <xdpbtrf.f>
> c intermediate for dpbtrf
> 
>        SUBROUTINE xDPBTRF( kUPLO, N, KD, AB, LDAB, INFO )
> 
> c      .. Scalar Arguments ..
>        integer         kUPLO
>        INTEGER         INFO, KD, LDAB, N
> 
> c  .. Array Arguments ..
>        DOUBLE PRECISION   AB( LDAB, * )
> 
>        character UPLO
> c     convert integer argument to character
>        if(kUPLO .eq. 1 ) then
>            UPLO = 'L'
>        else
>            UPLO = 'U'
>        endif
> 
>        call dpbtrf(UPLO,N,KD,AB,LDAB,INFO)
>        return
>        end
> </xdpbtrf.f>
> 
> 
> Instead of a character argument UPLO it takes an integer argument kUPLO.
> The meaning should be obvious from the code.
> 
> Now create a shell script in the folder of your script to generate a
dynamic library to be loaded in your script:
> 
> <mkso.sh>
> # Build a binary dynamic library for accessing Lapack dpbtrf
> 
> # syntax checking
>   
> SONAME=xdpbtrf.so
> 
> echo Strict syntax checking
> echo ----------------------
> gfortran -c -fsyntax-only -fimplicit-none -Wall src/*.f || exit 1
> 
> LAPACK=$(R CMD config LAPACK_LIBS)
> R CMD SHLIB --output=${SONAME} src/*.f ${LAPACK} || exit 1
> </mkso.sh>
> 
> To load the dynamic library xdpbtrf.so  change your script into this
> 
> <yourscript>
> dyn.load("xdpbtrf.so")
> n <- 4L
> phi <- 0.64
> AB <- matrix(0, 2, n)
> AB[1, ] <- c(1, rep(1 + phi^2, n-2), 1)
> AB[2, -n] <- -phi
> round(AB, 3)
> 
> AB.ch <- .Fortran("xdpbtrf", kUPLO=1L, N = as.integer(n),
>                              KD = 1L, AB = AB, LDAB = 2L, INFO =
as.integer(0))$AB
> AB.ch
> 
> </yourscript>
> 
> and you are good to go.
> 
> You should always do something  as described above when you need to pass
character arguments to Fortran code.
> 
> All of this was tested and run on macOS using the CRAN version of R.
> 
> Berend Hasselman
> 
>> On 11 Sep 2019, at 15:47, Giovanni Petris <gpetris at uark.edu>
wrote:
>>
>> Sorry for cross-posting, but I realized my question might be more
appropriate for r-devel...
>>
>> Thank you,
>> Giovanni
>>
>> ________________________________________
>> From: R-help <r-help-bounces at r-project.org> on behalf of
Giovanni Petris <gpetris at uark.edu>
>> Sent: Tuesday, September 10, 2019 16:44
>> To: r-help at r-project.org
>> Subject: [R] Calling a LAPACK subroutine from R
>>
>> Hello R-helpers!
>>
>> I am trying to call a LAPACK subroutine directly from my R code using
.Fortran(), but R cannot find the symbol name. How can I register/load the
appropriate library?
>>
>>> ### AR(1) Precision matrix
>>> n <- 4L
>>> phi <- 0.64
>>> AB <- matrix(0, 2, n)
>>> AB[1, ] <- c(1, rep(1 + phi^2, n-2), 1)
>>> AB[2, -n] <- -phi
>>> round(AB, 3)
>>       [,1]  [,2]  [,3] [,4]
>> [1,]  1.00  1.41  1.41    1
>> [2,] -0.64 -0.64 -0.64    0
>>>
>>> ### Cholesky factor
>>> AB.ch <- .Fortran("dpbtrf", UPLO = 'L', N =
as.integer(n),
>> +                  KD = 1L, AB = AB, LDAB = 2L, INFO =
as.integer(0))$AB
>> Error in .Fortran("dpbtrf", UPLO = "L", N =
as.integer(n), KD = 1L, AB = AB,  :
>>   Fortran symbol name "dpbtrf" not in load table
>>> sessionInfo()
>> R version 3.6.0 (2019-04-26)
>> Platform: x86_64-apple-darwin18.5.0 (64-bit)
>> Running under: macOS Mojave 10.14.6
>>
>> Matrix products: default
>> BLAS/LAPACK:
/usr/local/Cellar/openblas/0.3.6_1/lib/libopenblasp-r0.3.6.dylib
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> loaded via a namespace (and not attached):
>> [1] compiler_3.6.0 tools_3.6.0
>>
>> Thank you in advance for your help!
>>
>> Best,
>> Giovanni Petris
>>
>>
>>
>> --
>> Giovanni Petris, PhD
>> Professor
>> Director of Statistics
>> Department of Mathematical Sciences
>> University of Arkansas - Fayetteville, AR 72701
>>
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwICAg&c=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA&r=C3DNvy_azplKSvJKgvsgjA&m=C-MwKl__0xz-98RBbu7QNXJjqWkRr4xp6c0cz9Dck7A&s=a1vAu3mcXKObTLwP19vOmRPq55h6oQTh_vnS6BEibF0&e>>
PLEASE do read the posting guide
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html&d=DwICAg&c=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA&r=C3DNvy_azplKSvJKgvsgjA&m=C-MwKl__0xz-98RBbu7QNXJjqWkRr4xp6c0cz9Dck7A&s=qFGlplF9cOSmnDUvugsPRDn4iZS7v-LuWNAvfY69sbA&e>>
and provide commented, minimal, self-contained, reproducible code.
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

Can you write a small C function that calls LAPACK call that fro your
Fortran code? Yes, an extra step but maybe less traumatic than rewriting
parts of LAPACK directly.

Avi

On Wed, Sep 11, 2019 at 4:08 PM G?ran Brostr?m <goran.brostrom at umu.se>
wrote:
> Berend,
>
> I do not think this works with gfortran 7+. I am calling the BLAS
> subroutine dgemv from Fortran code in my package eha, and the check
> (with R-devel) gives:
>
> gmlfun.f:223:1: warning: type of ?dgemv? does not match original
> declaration [-Wlto-type-mismatch]
>        &     score, ione)
>   ^
> /home/gobr0002/R/src/R-devel/include/R_ext/BLAS.h:107:1: note: type
> mismatch in parameter 12
>   F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
>
> Type of a Fortran subroutine is matched against type of a C function?!
> My conclusion is that it is impossible to call a BLAS subroutine with a
> character parameter from Fortran code (nowadays). Calling from C code is
> fine, on the other hand(!).
>
> I have recently asked about this on R-pkg-devel, but not received any
> useful answers, and my submission to CRAN is rejected. I solve it by
> making a personal copy of dgemv and changing the character parameter to
> integer, and adding Jack Dongarra, Jeremy Du Croz, Sven Hammarling, and
> Richard Hanson as authors of eha. And a Copyright note, all in the
> DESCRIPTION file. Ugly but what can I do (except rewriting the Fortran
> code in C with f2c)?
>
> G?ran
>
> On 2019-09-11 21:38, Berend Hasselman wrote:
> >
> > The Lapack library is loaded automatically by R itself when it needs
it
> for doing some calculation.
> > You can force it to do that with a (dummy) solve for example.
> > Put this at start of your script:
> >
> > <code>
> > # dummy code to get LAPACK library loaded
> > X1 <- diag(2,2)
> > x1 <- rep(2,2)
> > # X1;x1
> > z <- solve(X1,x1)
> > </code>
> >
> > followed by the rest of your script.
> > You will get a warning (I do) that  "passing a character vector 
to
> .Fortran is not portable".
> > On other systems this may gave fatal errors. This is quick and very
> dirty. Don't do it.
> >
> > I believe there is a better and much safer way to achieve what you
want.
> > Here goes.
> >
> > Create a folder (directory) src in the directory where your script
> resides.
> > Create a wrapper for "dpbtrf" file in a file xdpbtrf.f that
takes an
> integer instead of character
> >
> > <xdpbtrf.f>
> > c intermediate for dpbtrf
> >
> >        SUBROUTINE xDPBTRF( kUPLO, N, KD, AB, LDAB, INFO )
> >
> > c      .. Scalar Arguments ..
> >        integer         kUPLO
> >        INTEGER         INFO, KD, LDAB, N
> >
> > c  .. Array Arguments ..
> >        DOUBLE PRECISION   AB( LDAB, * )
> >
> >        character UPLO
> > c     convert integer argument to character
> >        if(kUPLO .eq. 1 ) then
> >            UPLO = 'L'
> >        else
> >            UPLO = 'U'
> >        endif
> >
> >        call dpbtrf(UPLO,N,KD,AB,LDAB,INFO)
> >        return
> >        end
> > </xdpbtrf.f>
> >
> >
> > Instead of a character argument UPLO it takes an integer argument
kUPLO.
> > The meaning should be obvious from the code.
> >
> > Now create a shell script in the folder of your script to generate a
> dynamic library to be loaded in your script:
> >
> > <mkso.sh>
> > # Build a binary dynamic library for accessing Lapack dpbtrf
> >
> > # syntax checking
> >
> > SONAME=xdpbtrf.so
> >
> > echo Strict syntax checking
> > echo ----------------------
> > gfortran -c -fsyntax-only -fimplicit-none -Wall src/*.f || exit 1
> >
> > LAPACK=$(R CMD config LAPACK_LIBS)
> > R CMD SHLIB --output=${SONAME} src/*.f ${LAPACK} || exit 1
> > </mkso.sh>
> >
> > To load the dynamic library xdpbtrf.so  change your script into this
> >
> > <yourscript>
> > dyn.load("xdpbtrf.so")
> > n <- 4L
> > phi <- 0.64
> > AB <- matrix(0, 2, n)
> > AB[1, ] <- c(1, rep(1 + phi^2, n-2), 1)
> > AB[2, -n] <- -phi
> > round(AB, 3)
> >
> > AB.ch <- .Fortran("xdpbtrf", kUPLO=1L, N = as.integer(n),
> >                              KD = 1L, AB = AB, LDAB = 2L, INFO >
as.integer(0))$AB
> > AB.ch
> >
> > </yourscript>
> >
> > and you are good to go.
> >
> > You should always do something  as described above when you need to
pass
> character arguments to Fortran code.
> >
> > All of this was tested and run on macOS using the CRAN version of R.
> >
> > Berend Hasselman
> >
> >> On 11 Sep 2019, at 15:47, Giovanni Petris <gpetris at
uark.edu> wrote:
> >>
> >> Sorry for cross-posting, but I realized my question might be more
> appropriate for r-devel...
> >>
> >> Thank you,
> >> Giovanni
> >>
> >> ________________________________________
> >> From: R-help <r-help-bounces at r-project.org> on behalf of
Giovanni
> Petris <gpetris at uark.edu>
> >> Sent: Tuesday, September 10, 2019 16:44
> >> To: r-help at r-project.org
> >> Subject: [R] Calling a LAPACK subroutine from R
> >>
> >> Hello R-helpers!
> >>
> >> I am trying to call a LAPACK subroutine directly from my R code
using
> .Fortran(), but R cannot find the symbol name. How can I register/load the
> appropriate library?
> >>
> >>> ### AR(1) Precision matrix
> >>> n <- 4L
> >>> phi <- 0.64
> >>> AB <- matrix(0, 2, n)
> >>> AB[1, ] <- c(1, rep(1 + phi^2, n-2), 1)
> >>> AB[2, -n] <- -phi
> >>> round(AB, 3)
> >>       [,1]  [,2]  [,3] [,4]
> >> [1,]  1.00  1.41  1.41    1
> >> [2,] -0.64 -0.64 -0.64    0
> >>>
> >>> ### Cholesky factor
> >>> AB.ch <- .Fortran("dpbtrf", UPLO = 'L', N
= as.integer(n),
> >> +                  KD = 1L, AB = AB, LDAB = 2L, INFO =
as.integer(0))$AB
> >> Error in .Fortran("dpbtrf", UPLO = "L", N =
as.integer(n), KD = 1L, AB
> = AB,  :
> >>   Fortran symbol name "dpbtrf" not in load table
> >>> sessionInfo()
> >> R version 3.6.0 (2019-04-26)
> >> Platform: x86_64-apple-darwin18.5.0 (64-bit)
> >> Running under: macOS Mojave 10.14.6
> >>
> >> Matrix products: default
> >> BLAS/LAPACK:
> /usr/local/Cellar/openblas/0.3.6_1/lib/libopenblasp-r0.3.6.dylib
> >>
> >> locale:
> >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >>
> >> attached base packages:
> >> [1] stats     graphics  grDevices utils     datasets  methods  
base
> >>
> >> loaded via a namespace (and not attached):
> >> [1] compiler_3.6.0 tools_3.6.0
> >>
> >> Thank you in advance for your help!
> >>
> >> Best,
> >> Giovanni Petris
> >>
> >>
> >>
> >> --
> >> Giovanni Petris, PhD
> >> Professor
> >> Director of Statistics
> >> Department of Mathematical Sciences
> >> University of Arkansas - Fayetteville, AR 72701
> >>
> >>
> >> ______________________________________________
> >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more,
see
> >>
>
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwICAg&c=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA&r=C3DNvy_azplKSvJKgvsgjA&m=C-MwKl__0xz-98RBbu7QNXJjqWkRr4xp6c0cz9Dck7A&s=a1vAu3mcXKObTLwP19vOmRPq55h6oQTh_vnS6BEibF0&e>
>> PLEASE do read the posting guide
>
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html&d=DwICAg&c=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA&r=C3DNvy_azplKSvJKgvsgjA&m=C-MwKl__0xz-98RBbu7QNXJjqWkRr4xp6c0cz9Dck7A&s=qFGlplF9cOSmnDUvugsPRDn4iZS7v-LuWNAvfY69sbA&e>
>> and provide commented, minimal, self-contained, reproducible code.
> >>
> >> ______________________________________________
> >> R-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
-- 
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	[[alternative HTML version deleted]]

On 2019-09-11 22:16, Avraham Adler wrote:
> Can you write a small C function that calls LAPACK call that fro your 
> Fortran code? Yes, an extra step but maybe less traumatic than rewriting 
> parts of LAPACK directly.
Yes, I know how to do that, but I find it somewhat bizarre that it is 
impossible to call a Fortran subroutine from Fortran. And rewriting 
'dgemv' was simple: Just change character to integer and 'N' to
1. And
rename the subroutine. The hard (tedious) part was to include all the 
LAPACK authors in my DESCRIPTION file.

My guess is that the root cause is that BLAS/LAPACK is written in 
FORTRAN 77, which is said to be a subset of the current Fortran version 
but obviously isn't.

Thanks, G?ran
> 
> Avi
> 
> On Wed, Sep 11, 2019 at 4:08 PM G?ran Brostr?m <goran.brostrom at umu.se
> <mailto:goran.brostrom at umu.se>> wrote:
> 
>     Berend,
> 
>     I do not think this works with gfortran 7+. I am calling the BLAS
>     subroutine dgemv from Fortran code in my package eha, and the check
>     (with R-devel) gives:
> 
>     gmlfun.f:223:1: warning: type of ?dgemv? does not match original
>     declaration [-Wlto-type-mismatch]
>      ? ? ? ?&? ? ?score, ione)
>      ? ^
>     /home/gobr0002/R/src/R-devel/include/R_ext/BLAS.h:107:1: note: type
>     mismatch in parameter 12
>      ? F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
> 
>     Type of a Fortran subroutine is matched against type of a C function?!
>     My conclusion is that it is impossible to call a BLAS subroutine with a
>     character parameter from Fortran code (nowadays). Calling from C
>     code is
>     fine, on the other hand(!).
> 
>     I have recently asked about this on R-pkg-devel, but not received any
>     useful answers, and my submission to CRAN is rejected. I solve it by
>     making a personal copy of dgemv and changing the character parameter to
>     integer, and adding Jack Dongarra, Jeremy Du Croz, Sven Hammarling, and
>     Richard Hanson as authors of eha. And a Copyright note, all in the
>     DESCRIPTION file. Ugly but what can I do (except rewriting the Fortran
>     code in C with f2c)?
> 
>     G?ran
> 
>     On 2019-09-11 21:38, Berend Hasselman wrote:
>      >
>      > The Lapack library is loaded automatically by R itself when it
>     needs it? for doing some calculation.
>      > You can force it to do that with a (dummy) solve for example.
>      > Put this at start of your script:
>      >
>      > <code>
>      > # dummy code to get LAPACK library loaded
>      > X1 <- diag(2,2)
>      > x1 <- rep(2,2)
>      > # X1;x1
>      > z <- solve(X1,x1)
>      > </code>
>      >
>      > followed by the rest of your script.
>      > You will get a warning (I do) that? "passing a character
vector
>     to .Fortran is not portable".
>      > On other systems this may gave fatal errors. This is quick and
>     very dirty. Don't do it.
>      >
>      > I believe there is a better and much safer way to achieve what
>     you want.
>      > Here goes.
>      >
>      > Create a folder (directory) src in the directory where your
>     script resides.
>      > Create a wrapper for "dpbtrf" file in a file xdpbtrf.f
that takes
>     an integer instead of character
>      >
>      > <xdpbtrf.f>
>      > c intermediate for dpbtrf
>      >
>      >? ? ? ? SUBROUTINE xDPBTRF( kUPLO, N, KD, AB, LDAB, INFO )
>      >
>      > c? ? ? .. Scalar Arguments ..
>      >? ? ? ? integer? ? ? ? ?kUPLO
>      >? ? ? ? INTEGER? ? ? ? ?INFO, KD, LDAB, N
>      >
>      > c? .. Array Arguments ..
>      >? ? ? ? DOUBLE PRECISION? ?AB( LDAB, * )
>      >
>      >? ? ? ? character UPLO
>      > c? ? ?convert integer argument to character
>      >? ? ? ? if(kUPLO .eq. 1 ) then
>      >? ? ? ? ? ? UPLO = 'L'
>      >? ? ? ? else
>      >? ? ? ? ? ? UPLO = 'U'
>      >? ? ? ? endif
>      >
>      >? ? ? ? call dpbtrf(UPLO,N,KD,AB,LDAB,INFO)
>      >? ? ? ? return
>      >? ? ? ? end
>      > </xdpbtrf.f>
>      >
>      >
>      > Instead of a character argument UPLO it takes an integer argument
>     kUPLO.
>      > The meaning should be obvious from the code.
>      >
>      > Now create a shell script in the folder of your script to
>     generate a dynamic library to be loaded in your script:
>      >
>      > <mkso.sh>
>      > # Build a binary dynamic library for accessing Lapack dpbtrf
>      >
>      > # syntax checking
>      >
>      > SONAME=xdpbtrf.so
>      >
>      > echo Strict syntax checking
>      > echo ----------------------
>      > gfortran -c -fsyntax-only -fimplicit-none -Wall src/*.f || exit 1
>      >
>      > LAPACK=$(R CMD config LAPACK_LIBS)
>      > R CMD SHLIB --output=${SONAME} src/*.f ${LAPACK} || exit 1
>      > </mkso.sh>
>      >
>      > To load the dynamic library xdpbtrf.so? change your script into
this
>      >
>      > <yourscript>
>      > dyn.load("xdpbtrf.so")
>      > n <- 4L
>      > phi <- 0.64
>      > AB <- matrix(0, 2, n)
>      > AB[1, ] <- c(1, rep(1 + phi^2, n-2), 1)
>      > AB[2, -n] <- -phi
>      > round(AB, 3)
>      >
>      > AB.ch <- .Fortran("xdpbtrf", kUPLO=1L, N =
as.integer(n),
>      >? ? ? ? ? ? ? ? ? ? ? ? ? ? ? KD = 1L, AB = AB, LDAB = 2L, INFO
>     as.integer(0))$AB
>      > AB.ch
>      >
>      > </yourscript>
>      >
>      > and you are good to go.
>      >
>      > You should always do something? as described above when you need
>     to pass character arguments to Fortran code.
>      >
>      > All of this was tested and run on macOS using the CRAN version of
R.
>      >
>      > Berend Hasselman
>      >
>      >> On 11 Sep 2019, at 15:47, Giovanni Petris <gpetris at
uark.edu
>     <mailto:gpetris at uark.edu>> wrote:
>      >>
>      >> Sorry for cross-posting, but I realized my question might be
>     more appropriate for r-devel...
>      >>
>      >> Thank you,
>      >> Giovanni
>      >>
>      >> ________________________________________
>      >> From: R-help <r-help-bounces at r-project.org
>     <mailto:r-help-bounces at r-project.org>> on behalf of
Giovanni Petris
>     <gpetris at uark.edu <mailto:gpetris at uark.edu>>
>      >> Sent: Tuesday, September 10, 2019 16:44
>      >> To: r-help at r-project.org <mailto:r-help at
r-project.org>
>      >> Subject: [R] Calling a LAPACK subroutine from R
>      >>
>      >> Hello R-helpers!
>      >>
>      >> I am trying to call a LAPACK subroutine directly from my R
code
>     using .Fortran(), but R cannot find the symbol name. How can I
>     register/load the appropriate library?
>      >>
>      >>> ### AR(1) Precision matrix
>      >>> n <- 4L
>      >>> phi <- 0.64
>      >>> AB <- matrix(0, 2, n)
>      >>> AB[1, ] <- c(1, rep(1 + phi^2, n-2), 1)
>      >>> AB[2, -n] <- -phi
>      >>> round(AB, 3)
>      >>? ? ? ?[,1]? [,2]? [,3] [,4]
>      >> [1,]? 1.00? 1.41? 1.41? ? 1
>      >> [2,] -0.64 -0.64 -0.64? ? 0
>      >>>
>      >>> ### Cholesky factor
>      >>> AB.ch <- .Fortran("dpbtrf", UPLO =
'L', N = as.integer(n),
>      >> +? ? ? ? ? ? ? ? ? KD = 1L, AB = AB, LDAB = 2L, INFO >    
as.integer(0))$AB
>      >> Error in .Fortran("dpbtrf", UPLO = "L", N
= as.integer(n), KD >     1L, AB = AB,? :
>      >>? ?Fortran symbol name "dpbtrf" not in load table
>      >>> sessionInfo()
>      >> R version 3.6.0 (2019-04-26)
>      >> Platform: x86_64-apple-darwin18.5.0 (64-bit)
>      >> Running under: macOS Mojave 10.14.6
>      >>
>      >> Matrix products: default
>      >> BLAS/LAPACK:
>     /usr/local/Cellar/openblas/0.3.6_1/lib/libopenblasp-r0.3.6.dylib
>      >>
>      >> locale:
>      >> [1]
en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>      >>
>      >> attached base packages:
>      >> [1] stats? ? ?graphics? grDevices utils? ? ?datasets?
methods? ?base
>      >>
>      >> loaded via a namespace (and not attached):
>      >> [1] compiler_3.6.0 tools_3.6.0
>      >>
>      >> Thank you in advance for your help!
>      >>
>      >> Best,
>      >> Giovanni Petris
>      >>
>      >>
>      >>
>      >> --
>      >> Giovanni Petris, PhD
>      >> Professor
>      >> Director of Statistics
>      >> Department of Mathematical Sciences
>      >> University of Arkansas - Fayetteville, AR 72701
>      >>
>      >>
>      >> ______________________________________________
>      >> R-help at r-project.org <mailto:R-help at
r-project.org> mailing list
>     -- To UNSUBSCRIBE and more, see
>      >>
>    
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwICAg&c=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA&r=C3DNvy_azplKSvJKgvsgjA&m=C-MwKl__0xz-98RBbu7QNXJjqWkRr4xp6c0cz9Dck7A&s=a1vAu3mcXKObTLwP19vOmRPq55h6oQTh_vnS6BEibF0&e>
>> PLEASE do read the posting guide
>    
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html&d=DwICAg&c=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA&r=C3DNvy_azplKSvJKgvsgjA&m=C-MwKl__0xz-98RBbu7QNXJjqWkRr4xp6c0cz9Dck7A&s=qFGlplF9cOSmnDUvugsPRDn4iZS7v-LuWNAvfY69sbA&e>
>> and provide commented, minimal, self-contained, reproducible code.
>      >>
>      >> ______________________________________________
>      >> R-devel at r-project.org <mailto:R-devel at
r-project.org> mailing list
>      >> https://stat.ethz.ch/mailman/listinfo/r-devel
>      >
>      > ______________________________________________
>      > R-devel at r-project.org <mailto:R-devel at r-project.org>
mailing list
>      > https://stat.ethz.ch/mailman/listinfo/r-devel
>      >
> 
>     ______________________________________________
>     R-devel at r-project.org <mailto:R-devel at r-project.org>
mailing list
>     https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> -- 
> Sent from Gmail Mobile

I have tried what I proposed in a virtual Kubuntu 18.04 which uses gfortran 7.4.
I used the latest development version of R.

It worked just as on macOS.

Berend

> On 11 Sep 2019, at 22:07, G?ran Brostr?m <goran.brostrom at umu.se>
wrote:
> 
> Berend,
> 
> I do not think this works with gfortran 7+. I am calling the BLAS
subroutine dgemv from Fortran code in my package eha, and the check (with
R-devel) gives:
> 
> gmlfun.f:223:1: warning: type of ?dgemv? does not match original
declaration [-Wlto-type-mismatch]
>      &     score, ione)
> ^
> /home/gobr0002/R/src/R-devel/include/R_ext/BLAS.h:107:1: note: type
mismatch in parameter 12
> F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
> 
> Type of a Fortran subroutine is matched against type of a C function?! My
conclusion is that it is impossible to call a BLAS subroutine with a character
parameter from Fortran code (nowadays). Calling from C code is fine, on the
other hand(!).
> 
> I have recently asked about this on R-pkg-devel, but not received any
useful answers, and my submission to CRAN is rejected. I solve it by making a
personal copy of dgemv and changing the character parameter to integer, and
adding Jack Dongarra, Jeremy Du Croz, Sven Hammarling, and Richard Hanson as
authors of eha. And a Copyright note, all in the DESCRIPTION file. Ugly but what
can I do (except rewriting the Fortran code in C with f2c)?
> 
> G?ran
> 
> On 2019-09-11 21:38, Berend Hasselman wrote:
>> The Lapack library is loaded automatically by R itself when it needs it
for doing some calculation.
>> You can force it to do that with a (dummy) solve for example.
>> Put this at start of your script:
>> <code>
>> # dummy code to get LAPACK library loaded
>> X1 <- diag(2,2)
>> x1 <- rep(2,2)
>> # X1;x1
>> z <- solve(X1,x1)
>> </code>
>> followed by the rest of your script.
>> You will get a warning (I do) that  "passing a character vector 
to .Fortran is not portable".
>> On other systems this may gave fatal errors. This is quick and very
dirty. Don't do it.
>> I believe there is a better and much safer way to achieve what you
want.
>> Here goes.
>> Create a folder (directory) src in the directory where your script
resides.
>> Create a wrapper for "dpbtrf" file in a file xdpbtrf.f that
takes an integer instead of character
>> <xdpbtrf.f>
>> c intermediate for dpbtrf
>>       SUBROUTINE xDPBTRF( kUPLO, N, KD, AB, LDAB, INFO )
>> c      .. Scalar Arguments ..
>>       integer         kUPLO
>>       INTEGER         INFO, KD, LDAB, N
>> c  .. Array Arguments ..
>>       DOUBLE PRECISION   AB( LDAB, * )
>>       character UPLO
>> c     convert integer argument to character
>>       if(kUPLO .eq. 1 ) then
>>           UPLO = 'L'
>>       else
>>           UPLO = 'U'
>>       endif
>>       call dpbtrf(UPLO,N,KD,AB,LDAB,INFO)
>>       return
>>       end
>> </xdpbtrf.f>
>> Instead of a character argument UPLO it takes an integer argument
kUPLO.
>> The meaning should be obvious from the code.
>> Now create a shell script in the folder of your script to generate a
dynamic library to be loaded in your script:
>> <mkso.sh>
>> # Build a binary dynamic library for accessing Lapack dpbtrf
>> # syntax checking
>>  SONAME=xdpbtrf.so
>> echo Strict syntax checking
>> echo ----------------------
>> gfortran -c -fsyntax-only -fimplicit-none -Wall src/*.f || exit 1
>> LAPACK=$(R CMD config LAPACK_LIBS)
>> R CMD SHLIB --output=${SONAME} src/*.f ${LAPACK} || exit 1
>> </mkso.sh>
>> To load the dynamic library xdpbtrf.so  change your script into this
>> <yourscript>
>> dyn.load("xdpbtrf.so")
>> n <- 4L
>> phi <- 0.64
>> AB <- matrix(0, 2, n)
>> AB[1, ] <- c(1, rep(1 + phi^2, n-2), 1)
>> AB[2, -n] <- -phi
>> round(AB, 3)
>> AB.ch <- .Fortran("xdpbtrf", kUPLO=1L, N = as.integer(n),
>>                             KD = 1L, AB = AB, LDAB = 2L, INFO =
as.integer(0))$AB
>> AB.ch
>> </yourscript>
>> and you are good to go.
>> You should always do something  as described above when you need to
pass character arguments to Fortran code.
>> All of this was tested and run on macOS using the CRAN version of R.
>> Berend Hasselman
>>> On 11 Sep 2019, at 15:47, Giovanni Petris <gpetris at
uark.edu> wrote:
>>> 
>>> Sorry for cross-posting, but I realized my question might be more
appropriate for r-devel...
>>> 
>>> Thank you,
>>> Giovanni
>>> 
>>> ________________________________________
>>> From: R-help <r-help-bounces at r-project.org> on behalf of
Giovanni Petris <gpetris at uark.edu>
>>> Sent: Tuesday, September 10, 2019 16:44
>>> To: r-help at r-project.org
>>> Subject: [R] Calling a LAPACK subroutine from R
>>> 
>>> Hello R-helpers!
>>> 
>>> I am trying to call a LAPACK subroutine directly from my R code
using .Fortran(), but R cannot find the symbol name. How can I register/load the
appropriate library?
>>> 
>>>> ### AR(1) Precision matrix
>>>> n <- 4L
>>>> phi <- 0.64
>>>> AB <- matrix(0, 2, n)
>>>> AB[1, ] <- c(1, rep(1 + phi^2, n-2), 1)
>>>> AB[2, -n] <- -phi
>>>> round(AB, 3)
>>>      [,1]  [,2]  [,3] [,4]
>>> [1,]  1.00  1.41  1.41    1
>>> [2,] -0.64 -0.64 -0.64    0
>>>> 
>>>> ### Cholesky factor
>>>> AB.ch <- .Fortran("dpbtrf", UPLO = 'L', N
= as.integer(n),
>>> +                  KD = 1L, AB = AB, LDAB = 2L, INFO =
as.integer(0))$AB
>>> Error in .Fortran("dpbtrf", UPLO = "L", N =
as.integer(n), KD = 1L, AB = AB,  :
>>>  Fortran symbol name "dpbtrf" not in load table
>>>> sessionInfo()
>>> R version 3.6.0 (2019-04-26)
>>> Platform: x86_64-apple-darwin18.5.0 (64-bit)
>>> Running under: macOS Mojave 10.14.6
>>> 
>>> Matrix products: default
>>> BLAS/LAPACK:
/usr/local/Cellar/openblas/0.3.6_1/lib/libopenblasp-r0.3.6.dylib
>>> 
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>> 
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods  
base
>>> 
>>> loaded via a namespace (and not attached):
>>> [1] compiler_3.6.0 tools_3.6.0
>>> 
>>> Thank you in advance for your help!
>>> 
>>> Best,
>>> Giovanni Petris
>>> 
>>> 
>>> 
>>> --
>>> Giovanni Petris, PhD
>>> Professor
>>> Director of Statistics
>>> Department of Mathematical Sciences
>>> University of Arkansas - Fayetteville, AR 72701
>>> 
>>> 
>>> ______________________________________________
>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more,
see
>>>
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwICAg&c=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA&r=C3DNvy_azplKSvJKgvsgjA&m=C-MwKl__0xz-98RBbu7QNXJjqWkRr4xp6c0cz9Dck7A&s=a1vAu3mcXKObTLwP19vOmRPq55h6oQTh_vnS6BEibF0&e>>>
PLEASE do read the posting guide
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html&d=DwICAg&c=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA&r=C3DNvy_azplKSvJKgvsgjA&m=C-MwKl__0xz-98RBbu7QNXJjqWkRr4xp6c0cz9Dck7A&s=qFGlplF9cOSmnDUvugsPRDn4iZS7v-LuWNAvfY69sbA&e>>>
and provide commented, minimal, self-contained, reproducible code.
>>> 
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel

Followup:

I have checked my package nleqslv which uses dgemv only from Fortran, on Kubuntu
18.04 with the development version of R.
No errors or problems.

Berend

> On 12 Sep 2019, at 08:57, Berend Hasselman <bhh at xs4all.nl> wrote:
> 
> 
> I have tried what I proposed in a virtual Kubuntu 18.04 which uses gfortran
7.4.
> I used the latest development version of R.
> 
> It worked just as on macOS.
> 
> Berend
> 
> 
>> On 11 Sep 2019, at 22:07, G?ran Brostr?m <goran.brostrom at
umu.se> wrote:
>> 
>> Berend,
>> 
>> I do not think this works with gfortran 7+. I am calling the BLAS
subroutine dgemv from Fortran code in my package eha, and the check (with
R-devel) gives:
>> 
>> gmlfun.f:223:1: warning: type of ?dgemv? does not match original
declaration [-Wlto-type-mismatch]
>>     &     score, ione)
>> ^
>> /home/gobr0002/R/src/R-devel/include/R_ext/BLAS.h:107:1: note: type
mismatch in parameter 12
>> F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
>> 
>> Type of a Fortran subroutine is matched against type of a C function?!
My conclusion is that it is impossible to call a BLAS subroutine with a
character parameter from Fortran code (nowadays). Calling from C code is fine,
on the other hand(!).
>> 
>> I have recently asked about this on R-pkg-devel, but not received any
useful answers, and my submission to CRAN is rejected. I solve it by making a
personal copy of dgemv and changing the character parameter to integer, and
adding Jack Dongarra, Jeremy Du Croz, Sven Hammarling, and Richard Hanson as
authors of eha. And a Copyright note, all in the DESCRIPTION file. Ugly but what
can I do (except rewriting the Fortran code in C with f2c)?
>> 
>> G?ran
>> 
>> On 2019-09-11 21:38, Berend Hasselman wrote:
>>> The Lapack library is loaded automatically by R itself when it
needs it  for doing some calculation.
>>> You can force it to do that with a (dummy) solve for example.
>>> Put this at start of your script:
>>> <code>
>>> # dummy code to get LAPACK library loaded
>>> X1 <- diag(2,2)
>>> x1 <- rep(2,2)
>>> # X1;x1
>>> z <- solve(X1,x1)
>>> </code>
>>> followed by the rest of your script.
>>> You will get a warning (I do) that  "passing a character
vector  to .Fortran is not portable".
>>> On other systems this may gave fatal errors. This is quick and very
dirty. Don't do it.
>>> I believe there is a better and much safer way to achieve what you
want.
>>> Here goes.
>>> Create a folder (directory) src in the directory where your script
resides.
>>> Create a wrapper for "dpbtrf" file in a file xdpbtrf.f
that takes an integer instead of character
>>> <xdpbtrf.f>
>>> c intermediate for dpbtrf
>>>      SUBROUTINE xDPBTRF( kUPLO, N, KD, AB, LDAB, INFO )
>>> c      .. Scalar Arguments ..
>>>      integer         kUPLO
>>>      INTEGER         INFO, KD, LDAB, N
>>> c  .. Array Arguments ..
>>>      DOUBLE PRECISION   AB( LDAB, * )
>>>      character UPLO
>>> c     convert integer argument to character
>>>      if(kUPLO .eq. 1 ) then
>>>          UPLO = 'L'
>>>      else
>>>          UPLO = 'U'
>>>      endif
>>>      call dpbtrf(UPLO,N,KD,AB,LDAB,INFO)
>>>      return
>>>      end
>>> </xdpbtrf.f>
>>> Instead of a character argument UPLO it takes an integer argument
kUPLO.
>>> The meaning should be obvious from the code.
>>> Now create a shell script in the folder of your script to generate
a dynamic library to be loaded in your script:
>>> <mkso.sh>
>>> # Build a binary dynamic library for accessing Lapack dpbtrf
>>> # syntax checking
>>> SONAME=xdpbtrf.so
>>> echo Strict syntax checking
>>> echo ----------------------
>>> gfortran -c -fsyntax-only -fimplicit-none -Wall src/*.f || exit 1
>>> LAPACK=$(R CMD config LAPACK_LIBS)
>>> R CMD SHLIB --output=${SONAME} src/*.f ${LAPACK} || exit 1
>>> </mkso.sh>
>>> To load the dynamic library xdpbtrf.so  change your script into
this
>>> <yourscript>
>>> dyn.load("xdpbtrf.so")
>>> n <- 4L
>>> phi <- 0.64
>>> AB <- matrix(0, 2, n)
>>> AB[1, ] <- c(1, rep(1 + phi^2, n-2), 1)
>>> AB[2, -n] <- -phi
>>> round(AB, 3)
>>> AB.ch <- .Fortran("xdpbtrf", kUPLO=1L, N =
as.integer(n),
>>>                            KD = 1L, AB = AB, LDAB = 2L, INFO =
as.integer(0))$AB
>>> AB.ch
>>> </yourscript>
>>> and you are good to go.
>>> You should always do something  as described above when you need to
pass character arguments to Fortran code.
>>> All of this was tested and run on macOS using the CRAN version of
R.
>>> Berend Hasselman
>>>> On 11 Sep 2019, at 15:47, Giovanni Petris <gpetris at
uark.edu> wrote:
>>>> 
>>>> Sorry for cross-posting, but I realized my question might be
more appropriate for r-devel...
>>>> 
>>>> Thank you,
>>>> Giovanni
>>>> 
>>>> ________________________________________
>>>> From: R-help <r-help-bounces at r-project.org> on behalf
of Giovanni Petris <gpetris at uark.edu>
>>>> Sent: Tuesday, September 10, 2019 16:44
>>>> To: r-help at r-project.org
>>>> Subject: [R] Calling a LAPACK subroutine from R
>>>> 
>>>> Hello R-helpers!
>>>> 
>>>> I am trying to call a LAPACK subroutine directly from my R code
using .Fortran(), but R cannot find the symbol name. How can I register/load the
appropriate library?
>>>> 
>>>>> ### AR(1) Precision matrix
>>>>> n <- 4L
>>>>> phi <- 0.64
>>>>> AB <- matrix(0, 2, n)
>>>>> AB[1, ] <- c(1, rep(1 + phi^2, n-2), 1)
>>>>> AB[2, -n] <- -phi
>>>>> round(AB, 3)
>>>>     [,1]  [,2]  [,3] [,4]
>>>> [1,]  1.00  1.41  1.41    1
>>>> [2,] -0.64 -0.64 -0.64    0
>>>>> 
>>>>> ### Cholesky factor
>>>>> AB.ch <- .Fortran("dpbtrf", UPLO =
'L', N = as.integer(n),
>>>> +                  KD = 1L, AB = AB, LDAB = 2L, INFO =
as.integer(0))$AB
>>>> Error in .Fortran("dpbtrf", UPLO = "L", N =
as.integer(n), KD = 1L, AB = AB,  :
>>>> Fortran symbol name "dpbtrf" not in load table
>>>>> sessionInfo()
>>>> R version 3.6.0 (2019-04-26)
>>>> Platform: x86_64-apple-darwin18.5.0 (64-bit)
>>>> Running under: macOS Mojave 10.14.6
>>>> 
>>>> Matrix products: default
>>>> BLAS/LAPACK:
/usr/local/Cellar/openblas/0.3.6_1/lib/libopenblasp-r0.3.6.dylib
>>>> 
>>>> locale:
>>>> [1]
en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>> 
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods  
base
>>>> 
>>>> loaded via a namespace (and not attached):
>>>> [1] compiler_3.6.0 tools_3.6.0
>>>> 
>>>> Thank you in advance for your help!
>>>> 
>>>> Best,
>>>> Giovanni Petris
>>>> 
>>>> 
>>>> 
>>>> --
>>>> Giovanni Petris, PhD
>>>> Professor
>>>> Director of Statistics
>>>> Department of Mathematical Sciences
>>>> University of Arkansas - Fayetteville, AR 72701
>>>> 
>>>> 
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and
more, see
>>>>
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwICAg&c=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA&r=C3DNvy_azplKSvJKgvsgjA&m=C-MwKl__0xz-98RBbu7QNXJjqWkRr4xp6c0cz9Dck7A&s=a1vAu3mcXKObTLwP19vOmRPq55h6oQTh_vnS6BEibF0&e>>>>
PLEASE do read the posting guide
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html&d=DwICAg&c=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA&r=C3DNvy_azplKSvJKgvsgjA&m=C-MwKl__0xz-98RBbu7QNXJjqWkRr4xp6c0cz9Dck7A&s=qFGlplF9cOSmnDUvugsPRDn4iZS7v-LuWNAvfY69sbA&e>>>>
and provide commented, minimal, self-contained, reproducible code.
>>>> 
>>>> ______________________________________________
>>>> R-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel