--- imach/src/imach.c	2015/08/04 07:17:42	1.193
+++ imach/src/imach.c	2015/08/18 16:28:39	1.195
@@ -1,6 +1,17 @@
-/* $Id: imach.c,v 1.193 2015/08/04 07:17:42 brouard Exp $
+/* $Id: imach.c,v 1.195 2015/08/18 16:28:39 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.195  2015/08/18 16:28:39  brouard
+  Summary: Adding a hack for testing purpose
+
+  After reading the title, ftol and model lines, if the comment line has
+  a q, starting with #q, the answer at the end of the run is quit. It
+  permits to run test files in batch with ctest. The former workaround was
+  $ echo q | imach foo.imach
+
+  Revision 1.194  2015/08/18 13:32:00  brouard
+  Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
+
   Revision 1.193  2015/08/04 07:17:42  brouard
   Summary: 0.98q4
 
@@ -685,6 +696,7 @@ typedef struct {
 #define YEARM 12. /**< Number of months per year */
 #define AGESUP 130
 #define AGEBASE 40
+#define AGEOVERFLOW 1.e20
 #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
 #ifdef _WIN32
 #define DIRSEPARATOR '\\'
@@ -696,11 +708,11 @@ typedef struct {
 #define ODIRSEPARATOR '\\'
 #endif
 
-/* $Id: imach.c,v 1.193 2015/08/04 07:17:42 brouard Exp $ */
+/* $Id: imach.c,v 1.195 2015/08/18 16:28:39 brouard Exp $ */
 /* $State: Exp $ */
 
-char version[]="Imach version 0.98q4, July 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
-char fullversion[]="$Revision: 1.193 $ $Date: 2015/08/04 07:17:42 $"; 
+char version[]="Imach version 0.98q5, August 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
+char fullversion[]="$Revision: 1.195 $ $Date: 2015/08/18 16:28:39 $"; 
 char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
@@ -5436,8 +5448,8 @@ int readdata(char datafile[], int firsto
 
 
   if((fic=fopen(datafile,"r"))==NULL)    {
-    printf("Problem while opening datafile: %s\n", datafile);return 1;
-    fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
+    printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
+    fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
   }
 
   i=1;
@@ -6272,7 +6284,8 @@ int main(int argc, char *argv[])
   /* FILE *ficgp;*/ /*Gnuplot File */
   struct stat info;
   double agedeb=0.;
-  double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+
+  double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
 
   double fret;
   double dum=0.; /* Dummy variable */
@@ -6284,9 +6297,11 @@ int main(int argc, char *argv[])
   char pathr[MAXLINE], pathimach[MAXLINE]; 
   char *tok, *val; /* pathtot */
   int firstobs=1, lastobs=10;
-  int c,  h , cpt;
+  int c,  h , cpt, c2;
   int jl=0;
   int i1, j1, jk, stepsize=0;
+  int count=0;
+
   int *tab; 
   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
   int mobilav=0,popforecast=0;
@@ -6477,7 +6492,7 @@ int main(int argc, char *argv[])
   ungetc(c,ficpar);
 
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
-  numlinepar++;
+  numlinepar=numlinepar+3; /* In general */
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
   if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
     model[strlen(model)-1]='\0';
@@ -6498,6 +6513,10 @@ int main(int argc, char *argv[])
     ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);
     numlinepar++;
+    if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
+      z[0]=line[1];
+    }
+    /* printf("****line [1] = %c \n",line[1]); */
     fputs(line, stdout);
     //puts(line);
     fputs(line,ficparo);
@@ -6654,12 +6673,22 @@ run imach with mle=-1 to get a correct t
     for(i=1; i <=npar; i++)
       for(j=1; j <=npar; j++) matcov[i][j]=0.;
       
+    /* Scans npar lines */
     for(i=1; i <=npar; i++){
-      fscanf(ficpar,"%s",str);
+      count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
+      if(count != 3){
+	printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
+This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
+Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
+	fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
+This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
+Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
+	exit(1);
+      }else
       if(mle==1)
-	printf("%s",str);
-      fprintf(ficlog,"%s",str);
-      fprintf(ficparo,"%s",str);
+	printf("%1d%1d%1d",i1,j1,jk);
+      fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
+      fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
       for(j=1; j <=i; j++){
 	fscanf(ficpar," %le",&matcov[i][j]);
 	if(mle==1){
@@ -6675,6 +6704,7 @@ run imach with mle=-1 to get a correct t
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
+    /* End of read covariance matrix npar lines */
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
 	matcov[i][j]=matcov[j][i];
@@ -7149,8 +7179,15 @@ Interval (in months) between two waves:
     
     
     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-    printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
-    
+    if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
+      	printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+      	fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+    }else
+      printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
 		     stepm, weightopt,\
 		     model,imx,p,matcov,agemortsup);
@@ -7413,7 +7450,15 @@ Interval (in months) between two waves:
     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
     
     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-    printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+    if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
+      	printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+      	fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+    }else
+      printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
     
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
 		 model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
@@ -7816,7 +7861,7 @@ Interval (in months) between two waves:
   }
   end:
   while (z[0] != 'q') {
-    printf("\nType  q for exiting: ");
+    printf("\nType  q for exiting: "); fflush(stdout);
     scanf("%s",z);
   }
 }