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affyio: stack trace shows R error function is called, rather than bio…

…lib's
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1 parent 13ec197 commit 5ab5b7aa062fcc33dc59a56d41b2ea31ab413792 @pjotrp committed Nov 16, 2008
Showing with 27 additions and 0 deletions.
  1. +19 −0 TODO
  2. +4 −0 src/clibs/affyio-1.8/src/read_celfile_generic.h
  3. +4 −0 src/clibs/affyio-1.8/src/read_generic.h
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19 TODO
@@ -4,6 +4,25 @@ Problems - to be fixed before release 0.9:
- RMA unit tests
- R library errors not caught properly (biolib-core handler is not
found)
+ Program received signal SIGSEGV, Segmentation fault.
+0x00000000 in ?? ()
+(gdb) backtrace
+#0 0x00000000 in ?? ()
+#1 0xb7e76937 in R_WriteConsole () from /usr/lib/R/lib/libR.so
+#2 0xb7dd3508 in REvprintf () from /usr/lib/R/lib/libR.so
+#3 0xb7dd3687 in REprintf () from /usr/lib/R/lib/libR.so
+#4 0xb7d321ae in Rf_jump_to_toplevel () from /usr/lib/R/lib/libR.so
+#5 0xb7d313b7 in Rf_errorcall () from /usr/lib/R/lib/libR.so
+#6 0xb7d3187a in Rf_error () from /usr/lib/R/lib/libR.so
+#7 0xb7f627ef in isTextCelFile ()
+ from /home/wrk/izip/git/opensource/biolib/src/clibs/affyio-1.8/src/libbiolib_affyio-0.0.1.so
+#8 0xb7f6b0d2 in read_cel_file ()
+ from /home/wrk/izip/git/opensource/biolib/src/clibs/affyio-1.8/src/libbiolib_affyio-0.0.1.so
+#9 0xb7f5ffee in open_celfile ()
+ from /home/wrk/izip/git/opensource/biolib/src/clibs/affyio-1.8/src/libbiolib_affyio-0.0.1.so
+#10 0x0804869a in main (argc=1, argv=0xbfd2d4e8)
+ at /home/wrk/izip/git/opensource/biolib/doc/examples/c/affy.c:16
+
- Python and Perl now broken - need to locate biolib.so
Features:
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4 src/clibs/affyio-1.8/src/read_celfile_generic.h
@@ -1,6 +1,10 @@
#ifndef READ_CELFILE_GENERIC_H
#define READ_CELFILE_GENERIC_H
+#ifdef BIOLIB
+ #include <biolib_R_map.h>
+#endif
+
#include "read_abatch.h"
int isGenericCelFile(const char *filename);
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4 src/clibs/affyio-1.8/src/read_generic.h
@@ -1,4 +1,8 @@
+#ifdef BIOLIB
+ #include <biolib_R_map.h>
+#endif
+
#include <zlib.h>
/******

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