title: Using R_alloc in C
body: <p>I've got C code which I'm calling from R:</p>
  
  <pre><code>.C("giveProb",as.double(2),as.double(2),as.double(c(0,1,0,1,1,0,1,0)))
  </code></pre>
  
  <p>I'd like to call it a bunch (hundreds of thousands or millions) of times (with differing third arguments), and it works fine when I put it in a for loop for around 100 times, but anything above that crashes R.</p>
  
  <p>I've got a feeling that it's a memory problem from using R_alloc.  I've got six arrays allocated in C, e.g.:</p>
  
  <pre><code>newCoefArray = (double *)R_alloc(1,curSize * sizeof(double));
  </code></pre>
  
  <p>But according to the R Manual "Writing R Extensions":</p>
  
  <blockquote>
    <p>This memory is taken from the heap, and released at the end of the .C, .Call or .External call. </p>
  </blockquote>
  
  <p>which I took to mean that the memory would be freed during each iteration of the loop. But in the next sentence:</p>
  
  <blockquote>
    <p>Users can also manage it, by noting the current position with a call to vmaxget and clearing memory allocated subsequently by a call to vmaxset. This is only recommended for experts. </p>
  </blockquote>
  
  <p>As someone who is nowhere near an expert, I was hoping someone here could help. The C code, in its entirety is below.</p>
  
  <pre><code>#include &lt;R.h&gt;
  #include &lt;Rmath.h&gt;
  #include &lt;stdio.h&gt;
  void giveProb(double *k, double *q,double *order){
  double  curSize;
  double  tmpSize;
  double  *newCoefArray;
  double  *oldCoefArray;
  double  *newAArray;
  double  *oldAArray;
  double  *newBArray;
  double  *oldBArray;
  int     position=0;
  
  long int factorial(int n){
      if(n==0||n==1){
          return(1);
      }
      int tmp=1,i=1;
      while(i&lt;=n){
          tmp=tmp*i;
          i++;
      }
      return(tmp);
  } 
  
  void expander(double a, double b,double c,double d,double coeff){
      double leadingTerm=beta(a,b);
      int bb=b; 
      double index[bb], sumLeaders[bb];
      for(int i=0;i&lt;bb;i++){
          index[i]=a+i;
          sumLeaders[i]=factorial(a+b-1)/(factorial(index[i])*factorial(a+b-1-index[i]));
          newCoefArray[i+position]=coeff*leadingTerm*sumLeaders[i];
          newAArray[i+position]=index[i]+c+1;
          newBArray[i+position]=a+b+d-index[i];
      }
      position=position+bb;
      curSize=position;
  }
  
  void separator(double e, double f){
      double a, b, coeff;
      for(int i=0; i&lt;tmpSize; i++){
          coeff=oldCoefArray[i];
          a=oldAArray[i];
          b=oldBArray[i];
          expander(a,b,e,f,coeff);
      }
  }
  
  void condenser(){
      tmpSize=0;
      for(int i=1; i&lt;curSize; i++){
          for(int j=0; j&lt;i; j++){
              if(newAArray[j]==newAArray[i]){
                  newCoefArray[j]=newCoefArray[j]+newCoefArray[i];
                  newCoefArray[i]=0;
              }
          }
      }
      for(int i=0; i&lt;curSize; i++){
          tmpSize=tmpSize+(newCoefArray[i]!=0);
      }
      oldCoefArray =(double *) R_alloc(1,tmpSize * sizeof(double));
      oldAArray = (double *)R_alloc(1,tmpSize * sizeof(double));
      oldBArray = (double *)R_alloc(1,tmpSize * sizeof(double));
      for(int i=0; i&lt;tmpSize; i++){
          oldCoefArray[i]=newCoefArray[i];
          oldAArray[i]=newAArray[i];
          oldBArray[i]=newBArray[i];
      }
      curSize=tmpSize;    
  }
  
    long double coefficient=1;
    for(int i=0;i&lt;*k;i++){
      coefficient=coefficient*factorial(*k)/(factorial(i)*factorial(*k-i-1));
    }
    for(int i=0;i&lt;*q;i++){
      coefficient=coefficient*factorial(*q)/(factorial(i)*factorial(*q-i-1));
    }
  
    double numObs=*k+*q;
    double out=0;
    curSize=order[1]+1;
  
    newCoefArray = (double *)R_alloc(1,curSize * sizeof(double));
    newAArray = (double *)R_alloc(1,curSize * sizeof(double));
    newBArray = (double *)R_alloc(1,curSize * sizeof(double));
  
    expander(order[0]+1,order[1]+1,order[2],order[3],coefficient);
  
    oldCoefArray = (double *)R_alloc(1,curSize * sizeof(double));
    oldAArray = (double *)R_alloc(1,curSize * sizeof(double));
    oldBArray = (double *)R_alloc(1,curSize * sizeof(double));
  
    for(int i=0;i&lt;curSize; i++){
      oldCoefArray[i]=newCoefArray[i];
      oldAArray[i]=newAArray[i];
      oldBArray[i]=newBArray[i];
    }
  
    for(int i=4;i&lt;2*numObs;i+=2){ 
      position=0;
      tmpSize=curSize;
      separator(order[i],order[i+1]);
      condenser();
    }
    position=0;
    for(int i=0;i&lt;curSize;i++){
      out=out+newCoefArray[i]*beta(newAArray[i],newBArray[i]);
    }
    *k=out;
  
  }
  </code></pre>
  
  <p><strong>UPDATE:</strong>
  Using the suggestion in the comment below, I get the following (which sort of confirms what I had previously thought, right?):</p>
  
  <p>R -d valgrind -f test_script.R
      ==11131== Memcheck, a memory error detector
      ==11131== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.
      ==11131== Using Valgrind-3.6.0 and LibVEX; rerun with -h for copyright info
      ==11131== Command: /usr/lib64/R/bin/exec/R -f test_script.R
      ==11131==</p>
  
  <pre><code>R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
  Copyright (C) 2012 The R Foundation for Statistical Computing
  ISBN 3-900051-07-0
  Platform: x86_64-redhat-linux-gnu (64-bit)
  
  R is free software and comes with ABSOLUTELY NO WARRANTY.
  You are welcome to redistribute it under certain conditions.
  Type 'license()' or 'licence()' for distribution details.
  
  ==11131== Conditional jump or move depends on uninitialised value(s)
  ==11131==    at 0x3A6A685F80: __GI___strcasecmp_l (in /lib64/libc-2.12.so)
  ==11131==    by 0x3A6A61FF24: __gconv_open (in /lib64/libc-2.12.so)
  ==11131==    by 0x3A6A62D3B7: _nl_find_msg (in /lib64/libc-2.12.so)
  ==11131==    by 0x3A6A62DB83: __dcigettext (in /lib64/libc-2.12.so)
  ==11131==    by 0x3A6C3BD2DF: ??? (in /usr/lib64/R/lib/libR.so)
  ==11131==    by 0x3A6C313FC8: setup_Rmainloop (in /usr/lib64/R/lib/libR.so)
  ==11131==    by 0x3A6C315278: Rf_mainloop (in /usr/lib64/R/lib/libR.so)
  ==11131==    by 0x40084A: main (in /usr/lib64/R/bin/exec/R)
  ==11131==
  ==11131== Use of uninitialised value of size 8
  ==11131==    at 0x3A6A6863A4: __GI___strcasecmp_l (in /lib64/libc-2.12.so)
  ==11131==    by 0x3A6A61FF24: __gconv_open (in /lib64/libc-2.12.so)
  ==11131==    by 0x3A6A62D3B7: _nl_find_msg (in /lib64/libc-2.12.so)
  ==11131==    by 0x3A6A62DB83: __dcigettext (in /lib64/libc-2.12.so)
  ==11131==    by 0x3A6C3BD2DF: ??? (in /usr/lib64/R/lib/libR.so)
  ==11131==    by 0x3A6C313FC8: setup_Rmainloop (in /usr/lib64/R/lib/libR.so)
  ==11131==    by 0x3A6C315278: Rf_mainloop (in /usr/lib64/R/lib/libR.so)
  ==11131==    by 0x40084A: main (in /usr/lib64/R/bin/exec/R)
  ==11131==
  ==11131== Use of uninitialised value of size 8
  ==11131==    at 0x3A6A6863A8: __GI___strcasecmp_l (in /lib64/libc-2.12.so)
  ==11131==    by 0x3A6A61FF24: __gconv_open (in /lib64/libc-2.12.so)
  ==11131==    by 0x3A6A62D3B7: _nl_find_msg (in /lib64/libc-2.12.so)
  ==11131==    by 0x3A6A62DB83: __dcigettext (in /lib64/libc-2.12.so)
  ==11131==    by 0x3A6C3BD2DF: ??? (in /usr/lib64/R/lib/libR.so)
  ==11131==    by 0x3A6C313FC8: setup_Rmainloop (in /usr/lib64/R/lib/libR.so)
  ==11131==    by 0x3A6C315278: Rf_mainloop (in /usr/lib64/R/lib/libR.so)
  ==11131==    by 0x40084A: main (in /usr/lib64/R/bin/exec/R)
  ==11131==
    Natural language support but running in an English locale
  
  R is a collaborative project with many contributors.
  Type 'contributors()' for more information and
  'citation()' on how to cite R or R packages in publications.
  
  Type 'demo()' for some demos, 'help()' for on-line help, or
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  [Previously saved workspace restored]
  
  &gt; dyn.load("SchWolfenew.so")
  &gt; for(i in 1:1000){
  + .C("giveProb",as.double(2),as.double(2),as.double(c(0,1,0,1,1,0,1,0)))
  + }
  
  ==29371== Invalid read of size 1
  ==29371==    at 0x3A6C31A2E9: ??? (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C31CBC9: Rf_cons (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C2D2B74: ??? (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C2DD121: Rf_eval (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C2DF830: Rf_applyClosure (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C32B828: Rf_usemethod (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C32BAE7: ??? (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C2D290B: ??? (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C2DD121: Rf_eval (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C2DF830: Rf_applyClosure (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C2DD3F7: Rf_eval (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C2DEF4F: ??? (in /usr/lib64/R/lib/libR.so)
  ==29371==  Address 0x3ff0000000000003 is not stack'd, malloc'd or (recently) free'd
  ==29371==
  
   *** caught segfault ***
  address (nil), cause 'unknown'
  ==29371== Invalid read of size 1
  ==29371==    at 0x3A6C31AF0B: ??? (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C31CBC9: Rf_cons (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C31CC71: Rf_allocList (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C2C8CD4: R_GetTraceback (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C313472: ??? (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6B20F4FF: ??? (in /lib64/libpthread-2.12.so)
  ==29371==    by 0x3A6C31A2E8: ??? (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C31CBC9: Rf_cons (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C2D2B74: ??? (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C2DD121: Rf_eval (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C2DF830: Rf_applyClosure (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C32B828: Rf_usemethod (in /usr/lib64/R/lib/libR.so)
  ==29371==  Address 0x4020000000000003 is not stack'd, malloc'd or (recently) free'd
  ==29371==
  ==29371==
  ==29371== Process terminating with default action of signal 11 (SIGSEGV)
  ==29371==  General Protection Fault
  ==29371==    at 0x3A6C31AF0B: ??? (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C31CBC9: Rf_cons (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C31CC71: Rf_allocList (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C2C8CD4: R_GetTraceback (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C313472: ??? (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6B20F4FF: ??? (in /lib64/libpthread-2.12.so)
  ==29371==    by 0x3A6C31A2E8: ??? (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C31CBC9: Rf_cons (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C2D2B74: ??? (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C2DD121: Rf_eval (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C2DF830: Rf_applyClosure (in /usr/lib64/R/lib/libR.so)
  ==29371==    by 0x3A6C32B828: Rf_usemethod (in /usr/lib64/R/lib/libR.so)
  ==29371==
  ==29371== HEAP SUMMARY:
  ==29371==     in use at exit: 29,307,724 bytes in 12,896 blocks
  ==29371==   total heap usage: 28,845 allocs, 15,949 frees, 48,495,252 bytes allocated
  ==29371==
  ==29371== LEAK SUMMARY:
  ==29371==    definitely lost: 0 bytes in 0 blocks
  ==29371==    indirectly lost: 0 bytes in 0 blocks
  ==29371==      possibly lost: 0 bytes in 0 blocks
  ==29371==    still reachable: 29,307,724 bytes in 12,896 blocks
  ==29371==         suppressed: 0 bytes in 0 blocks
  ==29371== Rerun with --leak-check=full to see details of leaked memory
  ==29371==
  ==29371== For counts of detected and suppressed errors, rerun with: -v
  ==29371== Use --track-origins=yes to see where uninitialised values come from
  ==29371== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 21 from 9)
  Segmentation fault (core dumped)
  </code></pre>