[Bioc-devel] linking LAPACK in windows

[Martin Morgan]

On 04/04/2011 12:03 AM, Cáceres Domínguez, Alejandro wrote:
> Dear Martin,
>
> That was it! Thanks a lot. I was completely fooled by the no errors in
> the compilation.
>
> Alejandro

Glad that fixed it! I should have said that I compiled with warnings 
enabled, and this can be very helpful

   CFLAGS="-Wall"  R CMD INSTALL inveRsion

or ~/.R/Makevars
CFLAGS += -Wall -g -O0

which also disables optimizations and compiles with debugging symbols 
enabled.

Martin

>
>
> -----Mensaje original-----
> De: Martin Morgan [mailto:mtmorgan at fhcrc.org]
> Enviado el: viernes, 01 de abril de 2011 19:48
> Para: "Cáceres Domínguez, Alejandro"
> CC: bioc-devel at r-project.org
> Asunto: Re: [Bioc-devel] linking LAPACK in windows
>
> On 04/01/2011 10:07 AM, Cáceres Domínguez, Alejandro wrote:
>  > Dear list,
>  >
>  > I am a new contributor to Bioconductor looking for guidance. My package
>  > (inveRsion) does not pass the R CMD check in liverpool. Basically,
> when it
>  > compiles the vignette, one of the functions returns NaNs when it should
>  > not. I traced back the bug on a windows machine. Although the package
>  > installs and compiles the c code without errors, I found that an R
>  > function ultimately relying on a LAPACK call returns the NaNs (source of
>  > the bug), when in Mac and Linux it does not. Would this be a problem of
>  > linking LAPACK in windows?
>  >
>  > I've got a Makevars file with the line
>  >
>  > PKG_LIBS = $(SUBLIBS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
>
> Hi Alejandro --
>
> This looks correct to me. When I compile the code below I see
>
> newFreq.c: In function ‘newFreq’:
> newFreq.c:36:5: warning: statement with no effect
>
> did you mean
>
> maxfreq = -1.0;
>
> ? Otherwise maxfreq is used uninitialized. I see this also in
> inversionModel.c:94 and when running your test code under valgrind
>
> R -d valgrind -f test.R
>
> Martin
>
>  >
>  > that seems to work in lamb1 and pelham. I've been back and forth the
>  > R-extension manual and feel a bit out of my depth. I cannot figure out
>  > what I should do. I imagine that a way out would be to provide the LAPACK
>  > routines with the package and compile them with it. My question is: Is
>  > this an acceptable practice? Otherwise, some light into which sort of
>  > things I would have to do in the Makevars (Makevars.win?) file will be
>  > much appreciated. Or am I missing something else?
>  >
>  > Please see bellow for particulars.
>  >
>  > Many thanks,
>  > Alejandro
>  >
>  > Alejandro Caceres
>  > Centre de Recerca en Epidemiologia Ambiental
>  > Doctor Aiguader 88, 0803
>  > Barcelona, Spain
>  >
>  >
>  > -------------
>  > newFreq.c compiled with
>  > -------------
>  >
>  > R CMD SHLIB newFreq.c
>  >
>  > (with a Makevars in the local dir having the line:
>  > PKG_LIBS = $(SUBLIBS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS))
>  >
>  > --------
>  > R code
>  > --------
>  >
>  > Resp<-c(0.93,0.98,1,0.97,1,1,1,1,0.93,1)
>  > block<-c(4,1,7,2,5,1,5,1,4,1)
>  > nsub<-10
>  > lev<-7
>  > nlev<-7
>  >
>  > dyn.load("newFreq.dll")
>  > # dyn.load("newFreq.so")
>  >
>  > .C("newFreq", as.double(Resp), as.double(block), as.double(lev),
>  > as.integer(nlev),as.integer(nsub), as.double(rep(0,nlev)))[[6]]
>  >
>  > ---------
>  > C code, file: newFreq.c
>  > ----------
>  > #include<stdio.h>
>  > #include<R.h>
>  > #include<R_ext/Lapack.h>
>  > #include<R_ext/BLAS.h>
>  >
>  >
>  > void newFreq( double *Resp, double *block, double *lev, int *nlev, int
>  > *nsub, double *out)
>  > {
>  >
>  > int level, subject, row, col, inx;
>  > double freqLev[*nlev];
>  > double bb[*nlev];
>  >
>  > double *AA= (double *)malloc(((*nsub)*(*nsub))*sizeof(*AA));
>  >
>  > double maxfreq;
>  >
>  > /* compute freqLev */
>  > for (level=0; level<*nlev; ++level)
>  > freqLev[level]=0.0;
>  >
>  >
>  > for (subject=0; subject<*nsub; ++subject)
>  > {
>  > for (level=0; level<*nlev; ++level)
>  > {
>  > if(block[subject]==lev[level])
>  > {
>  > freqLev[level]=freqLev[level]+Resp[subject];
>  > }
>  > }
>  > }
>  >
>  > /*register max freq*/
>  > maxfreq==-1.0;
>  > inx=0;
>  > for (level=0; level<*nlev; ++level)
>  > {
>  > if(freqLev[level]>maxfreq)
>  > {
>  > maxfreq=freqLev[level];
>  > inx=level;
>  > }
>  > }
>  >
>  >
>  > for (row=0; row<*nlev; ++row)
>  > {
>  > for (col=0; col<*nlev; ++col)
>  > {
>  > if (row==col)
>  > {
>  > AA[row*(*nlev)+col]=1.0;
>  > }
>  > else
>  > {
>  > AA[row*(*nlev)+col]=0.0;
>  > }
>  >
>  > if (row==inx)
>  > {
>  > AA[row*(*nlev)+col]=-freqLev[col]/maxfreq;
>  > }
>  >
>  > if (col==inx)
>  > {
>  > AA[row*(*nlev)+col]=1;
>  > }
>  > }
>  >
>  > }
>  >
>  > /*define bb*/
>  > for (row=0; row<*nlev; ++row)
>  > {
>  > bb[row]=0.0;
>  > if(row==inx)
>  > bb[inx]=1;
>  > }
>  >
>  >
>  > /*solve linear algebra*/
>  > int nr=1;
>  > int *pnr;
>  > pnr=&nr;
>  > *pnr=nr;
>  >
>  > int inf=0;
>  > int *pinf;
>  > pinf=&inf;
>  > *pinf=inf;
>  >
>  > int ipiv[*nlev];
>  >
>  > F77_NAME(dgesv)(nlev, pnr, AA, nlev, ipiv, bb, nlev, pinf);
>  >
>  > for (row=0; row<*nlev; ++row)
>  > out[row]=bb[row];
>  >
>  > free(AA);
>  > AA=NULL;
>  >
>  > }
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>  > [[alternative HTML version deleted]]
>  >
>  > _______________________________________________
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>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793