[Bioc-devel] linking LAPACK in windows

[Kasper Daniel Hansen]

2011/4/1 Martin Morgan <mtmorgan at fhcrc.org>:
> 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

As far as I know LAPACK routines cannot deal with NA's in their input
values (and possibly Nan etc, but I am less clear on that);  I did not
fully understand the OP, but he seemed to indicate the presence of
NA's, and that may be why there are problems?

Kasper

>> 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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>
>
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