[Bioc-devel] linking LAPACK in windows

Dear Martin,

That was it! Thanks a lot. I was completely fooled by the no errors in
the compilation.

Alejandro

-----Mensaje original-----
De: Martin Morgan [mailto:mtmorgan at fhcrc.org]
Enviado el: viernes, 01 de abril de 2011 19:48
Para: "C?ceres Dom?nguez, Alejandro"
CC: bioc-devel at r-project.org
Asunto: Re: [Bioc-devel] linking LAPACK in windows

On 04/01/2011 10:07 AM, C?ceres Dom?nguez, 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]]
 >
 > _______________________________________________
 > Bioc-devel at r-project.org mailing list
 > https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

Location: M1-B861
Telephone: 206 667-2793