7 files changed, 35 insertions, 31 deletions

diff --git a/src/aggregator.c b/src/aggregator.c
index 4c4ca8e..200de7d 100644
--- a/src/aggregator.c
+++ b/src/aggregator.c
@@ -9,8 +9,8 @@
 #include <stdio.h>
 
 #define H5FILE "influenza.h5"
-#define INFLUENZA_AA_DAT "/home/don/exp004/genomes/INFLUENZA/influenza_aa.dat"
-#define INFLUENZA_FAA "/home/don/exp004/genomes/INFLUENZA/influenza.faa"
+#define INFLUENZA_AA_DAT "/u/ac/dpellegr/Documents/exp004/genomes/INFLUENZA/influenza_aa.dat"
+#define INFLUENZA_FAA "/u/ac/dpellegr/Documents/exp004/genomes/INFLUENZA/influenza.faa"
 
 int
 main ()
@@ -25,14 +25,14 @@ main ()
     {
       file_id = H5Fcreate (H5FILE, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
       if (file_id < 0)
-        check_h5_error (file_id, __FILE__, __LINE__);
+        check_h5_error (__FILE__, __LINE__);
     }
   else
     {
       fclose (f);
       file_id = H5Fopen (H5FILE, H5F_ACC_RDWR, H5P_DEFAULT);
       if (file_id < 0)
-        check_h5_error (file_id, __FILE__, __LINE__);
+        check_h5_error (__FILE__, __LINE__);
     }
 
   /*
@@ -53,7 +53,7 @@ main ()
    */
   herr_t status = H5Fclose (file_id);
   if (status < 0)
-    check_h5_error (status, __FILE__, __LINE__);
+    check_h5_error (__FILE__, __LINE__);
 
   return 0;
 }
diff --git a/src/assign/assign_protein_type.c b/src/assign/assign_protein_type.c
index 1df4c8d..065880f 100644
--- a/src/assign/assign_protein_type.c
+++ b/src/assign/assign_protein_type.c
@@ -19,12 +19,12 @@
 /*
  * BLAST database containing all of the influenza protein sequences.
  */
-#define SEQDB "/home/don/exp004/influenzadb/influenzadb"
+#define SEQDB "/u/ac/dpellegr/Documents/exp004/influenzadb/influenzadb"
 
 /*
  * BLAST reference database of prototypical protein types.
  */
-#define REFDB "/home/don/exp004/influenzadb/proteinnames"
+#define REFDB "/u/ac/dpellegr/Documents/exp004/influenzadb/proteinnames"
 
 #define BUFFER_LEN 50
 
@@ -68,7 +68,7 @@ assign_protein_type (hid_t file_id)
   herr_t status = H5TBget_table_info (file_id, "influenza.faa", &faa_nfields,
                                       &faa_nrecords);
   if (status < 0)
-    check_h5_error (status, __FILE__, __LINE__);
+    check_h5_error (__FILE__, __LINE__);
 
   sequence_data *faa_buf = malloc (sizeof (sequence_data) * faa_nrecords);
 
@@ -81,7 +81,7 @@ assign_protein_type (hid_t file_id)
   status = H5TBread_table (file_id, "influenza.faa", faa_size, faa_offset,
                            faa_sizes, faa_buf);
   if (status < 0)
-    check_h5_error (status, __FILE__, __LINE__);
+    check_h5_error (__FILE__, __LINE__);
 
   /*
    * Allocate memory for the new table.
@@ -115,7 +115,7 @@ assign_protein_type (hid_t file_id)
       status = H5TBget_table_info (file_id, "gi_type_data", &gi_nfields,
                                    &gi_nrecords);
       if (status < 0)
-        check_h5_error (status, __FILE__, __LINE__);
+        check_h5_error (__FILE__, __LINE__);
 
       printf ("  Using gi_type_data cache of %i records.\n",
               (int) gi_nrecords);
@@ -125,11 +125,11 @@ assign_protein_type (hid_t file_id)
       status = H5TBread_table (file_id, "gi_type_data", gi_size, gi_offset,
                                gi_sizes, old_buf);
       if (status < 0)
-        check_h5_error (status, __FILE__, __LINE__);
+        check_h5_error (__FILE__, __LINE__);
 
       status = H5TBdelete_record (file_id, "gi_type_data", 0, gi_nrecords);
       if (status < 0)
-        check_h5_error (status, __FILE__, __LINE__);
+        check_h5_error (__FILE__, __LINE__);
 
     }
 
@@ -155,7 +155,7 @@ assign_protein_type (hid_t file_id)
                                gi_offset, gi_field_type,
                                chunk_size, fill_data, compress, NULL);
       if (status < 0)
-        check_h5_error (status, __FILE__, __LINE__);
+        check_h5_error (__FILE__, __LINE__);
 
     }
 
@@ -295,11 +295,11 @@ assign_protein_type (hid_t file_id)
                                        gi_size, gi_offset, gi_sizes,
                                        &new_buf[i - 1000]);
           if (status < 0)
-            check_h5_error (status, __FILE__, __LINE__);
+            check_h5_error (__FILE__, __LINE__);
 
           status = H5Fflush (file_id, H5F_SCOPE_GLOBAL);
           if (status < 0)
-            check_h5_error (status, __FILE__, __LINE__);
+            check_h5_error (__FILE__, __LINE__);
 
           written = i;
 
@@ -326,11 +326,11 @@ assign_protein_type (hid_t file_id)
     }
 
   if (status < 0)
-    check_h5_error (status, __FILE__, __LINE__);
+    check_h5_error (__FILE__, __LINE__);
 
   status = H5Fflush (file_id, H5F_SCOPE_GLOBAL);
   if (status < 0)
-    check_h5_error (status, __FILE__, __LINE__);
+    check_h5_error (__FILE__, __LINE__);
 
   free (faa_buf);
   free (old_buf);
diff --git a/src/error/check_h5_error.c b/src/error/check_h5_error.c
index d90b21f..30183fe 100644
--- a/src/error/check_h5_error.c
+++ b/src/error/check_h5_error.c
@@ -3,7 +3,7 @@
 #include <stdlib.h>
 
 void
-check_h5_error (herr_t status, const char *filename, unsigned int linenum)
+check_h5_error (const char *filename, unsigned int linenum)
 {
   error_at_line (EXIT_FAILURE, 0, filename, linenum,
                  "An error has been reported by the HDF5 API.");
diff --git a/src/error/check_h5_error.h b/src/error/check_h5_error.h
index e460e97..fa93c6b 100644
--- a/src/error/check_h5_error.h
+++ b/src/error/check_h5_error.h
@@ -7,6 +7,6 @@
  * Handle errors from the HDF5 API.
  */
 void
-check_h5_error (herr_t status, const char *filename, unsigned int linenum);
+check_h5_error (const char *filename, unsigned int linenum);
 
 #endif // CHECK_H5_ERROR_H
diff --git a/src/load/load_influenza_aa_dat.c b/src/load/load_influenza_aa_dat.c
index b50fcab..bbd4f8b 100644
--- a/src/load/load_influenza_aa_dat.c
+++ b/src/load/load_influenza_aa_dat.c
@@ -5,12 +5,14 @@
  * todo: Handle NULL values occuring in numeric fields.
  */
 
+#define _GNU_SOURCE
 #include "load_influenza_aa_dat.h"
 #include "error/check_error.h"
 #include "error/check_h5_error.h"
 #include <hdf5_hl.h>
 #include <string.h>
 #include <stdlib.h>
+#include <stdio.h>
 
 #define NFIELDS (hsize_t) 11
 
@@ -223,18 +225,18 @@ load_influenza_aa_dat (hid_t file_id, const char *file_name)
               herr_t status = H5TBget_table_info (file_id, "influenza_aa.dat",
                                                   &nfields, &nrecords);
               if (status < 0)
-                check_h5_error (status, __FILE__, __LINE__);
+                check_h5_error (__FILE__, __LINE__);
 
               status =
                 H5TBdelete_record (file_id, "influenza_aa.dat", 0, nrecords);
               if (status < 0)
-                check_h5_error (status, __FILE__, __LINE__);
+                check_h5_error (__FILE__, __LINE__);
 
               status =
                 H5TBappend_records (file_id, "influenza_aa.dat", 1, dst_size,
                                     dst_offset, dst_sizes, &p_data);
               if (status < 0)
-                check_h5_error (status, __FILE__, __LINE__);
+                check_h5_error (__FILE__, __LINE__);
             }
 
           /*
@@ -250,7 +252,7 @@ load_influenza_aa_dat (hid_t file_id, const char *file_name)
                                               chunk_size, fill_data, compress,
                                               &p_data);
               if (status < 0)
-                check_h5_error (status, __FILE__, __LINE__);
+                check_h5_error (__FILE__, __LINE__);
             }
         }
 
@@ -260,7 +262,7 @@ load_influenza_aa_dat (hid_t file_id, const char *file_name)
             H5TBappend_records (file_id, "influenza_aa.dat", 1, dst_size,
                                 dst_offset, dst_sizes, &p_data);
           if (status < 0)
-            check_h5_error (status, __FILE__, __LINE__);
+            check_h5_error (__FILE__, __LINE__);
         }
 
       if (running)
diff --git a/src/load/load_influenza_faa.c b/src/load/load_influenza_faa.c
index 80eb3ae..0026d11 100644
--- a/src/load/load_influenza_faa.c
+++ b/src/load/load_influenza_faa.c
@@ -1,3 +1,4 @@
+#define _GNU_SOURCE
 #include "error/check_error.h"
 #include "error/check_h5_error.h"
 #include "load_influenza_faa.h"
@@ -6,6 +7,7 @@
 #include <hdf5_hl.h>
 #include <string.h>
 #include <stdlib.h>
+#include <stdio.h>
 
 void
 load_influenza_faa (hid_t file_id, const char *file_name)
@@ -72,18 +74,18 @@ load_influenza_faa (hid_t file_id, const char *file_name)
                     H5TBget_table_info (file_id, "influenza.faa", &nfields,
                                         &nrecords);
                   if (status < 0)
-                    check_h5_error (status, __FILE__, __LINE__);
+                    check_h5_error (__FILE__, __LINE__);
 
                   status =
                     H5TBdelete_record (file_id, "influenza.faa", 0, nrecords);
                   if (status < 0)
-                    check_h5_error (status, __FILE__, __LINE__);
+                    check_h5_error (__FILE__, __LINE__);
 
                   status =
                     H5TBappend_records (file_id, "influenza.faa", 1, dst_size,
                                         dst_offset, dst_sizes, &p_data);
                   if (status < 0)
-                    check_h5_error (status, __FILE__, __LINE__);
+                    check_h5_error (__FILE__, __LINE__);
                 }
 
               /*
@@ -101,7 +103,7 @@ load_influenza_faa (hid_t file_id, const char *file_name)
                                                   compress,
                                                   &p_data);
                   if (status < 0)
-                    check_h5_error (status, __FILE__, __LINE__);
+                    check_h5_error (__FILE__, __LINE__);
                 }
             }
 
@@ -111,7 +113,7 @@ load_influenza_faa (hid_t file_id, const char *file_name)
                 H5TBappend_records (file_id, "influenza.faa", 1, dst_size,
                                     dst_offset, dst_sizes, &p_data);
               if (status < 0)
-                check_h5_error (status, __FILE__, __LINE__);
+                check_h5_error (__FILE__, __LINE__);
             }
 
           if (running)
diff --git a/src/updator.c b/src/updator.c
index 9a5ad18..f93e205 100644
--- a/src/updator.c
+++ b/src/updator.c
@@ -17,7 +17,7 @@ main ()
    */
   hid_t file_id = H5Fopen (FILE, H5F_ACC_RDWR, H5P_DEFAULT);
   if (file_id < 0)
-    check_h5_error (file_id, __FILE__, __LINE__);
+    check_h5_error (__FILE__, __LINE__);
 
   /*
    * Assign protein type values to the sequence records.
@@ -29,7 +29,7 @@ main ()
    */
   herr_t status = H5Fclose (file_id);
   if (status < 0)
-    check_h5_error (status, __FILE__, __LINE__);
+    check_h5_error (__FILE__, __LINE__);
 
   return 0;
 }