Problems With Installing Tacg Package In Ubuntu

Question

[Lucas]

I was trying to install tacg package in the Ubuntu. And after "make check", I got this message.

gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"tacg\" -DVERSION=\"4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ALLOCA_H=1 -DHAVE_ALLOCA=1 -DHAVE_STRUCT_STAT_ST_BLKSIZE=1 -DHAVE_ST_BLKSIZE=1 -DHAVE_LIBM=1 -DHAVE_LIBNSL=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_PARAM_H=1 -DHAVE_GETPAGESIZE=1 -DHAVE_MMAP=1 -DHAVE_STRFTIME=1 -DHAVE_VPRINTF=1 -DHAVE_PUTENV=1 -DHAVE_RE_COMP=1 -DHAVE_REGCOMP=1 -DHAVE_SOCKET=1 -DHAVE_STRDUP=1 -DHAVE_STRSPN=1 -DHAVE_STRSTR=1 -DHAVE_UNAME=1 -I.     -g -O2 -MT Cutting.o -MD -MP -MF .deps/Cutting.Tpo -c -o Cutting.o Cutting.c
In file included from Cutting.c:17:0:
    tacg.h:152:27: error: array type has incomplete element type
    tacg.h:154:28: error: array type has incomplete element type
    tacg.h:635:7: warning: conflicting types for built-in function ‘fmax’ [enabled by default]
    tacg.h:787:28: error: array type has incomplete element type
    make: *** [Cutting.o] Error 1

Can anybody help explain what this means? And how I can install this tacg successfully? Thanks a lot.

Answer 1

[Neilfws]

If you search the Web for the phrase "array type has incomplete element type", you'll see that this is quite a common issue. Basically, it means that whoever wrote the C code for this software did not do a very good job.

I note that someone asked the same question 4 years ago, without a response.

You could troubleshoot this issue and edit the source code yourself, but - it seems to me that this is very old, poorly-maintained software. It's been around since at least 1998. There are sure to be newer and better alternatives; I'd look at the EMBOSS suite.

Answer 2

[Hamish]

The current version of tacg (4.1.0) does not support the current version of gcc and fails to compile with the error you observe

However you can build if you apply a set of patches contributed by Charles Plessy to enable builds with gcc 4: http://sourceforge.net/p/tacg/patches/1/

wget http://downloads.sourceforge.net/project/tacg/tacg/tacg-4.1/tacg-4.1.0-src.tar.bz2
tar zjf tacg-4.1.0-src.tar.bz2
cd tacg-4.1.0-src
wget http://sourceforge.net/p/tacg/patches/_discuss/thread/55725c46/3160/attachment/to-build-with-gcc4.patch
patch -p1 < to-build-with-gcc4.patch
./configure
make

You can then test that the build works with something like:

export TACGLIB=`pwd`/Data
./tacg -S -f1 -n3 -o1 -T 1,3 -C0 -c -L -F0 -D1 -w60 < ~/test/data/sequence/nuc_embl_L12345.tfa

In this case the input data file is EMBL:L12345.

On a Ubuntu 12.04 LTS the program generates the expected restriction map of the sequence before triggering a glibc error:

*** glibc detected *** ./tacg: free(): invalid pointer: 0x00007f20a7c33560 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7f20a71bbb96]
./tacg[0x403639]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f20a715e76d]
./tacg[0x404cbd]

You may have better luck with the version in CVS, rather than the release build (see http://sourceforge.net/p/tacg/code/?source=navbar).

For what it is worth, the last time I built a working version of tacg it was not the latest version, but instead the older 3.12. This still required a couple of changes (patch set provided below) but does not give the glibc error and accompanying segfault:

diff -Naur tacg-3.12-src/Makefile.in tacg-3.12-src_patched/Makefile.in
--- tacg-3.12-src/Makefile.in    2001-06-12 23:17:06.000000000 +0100
+++ tacg-3.12-src_patched/Makefile.in    2013-10-14 14:45:51.559741916 +0100
@@ -21,7 +21,7 @@
 # Simply edit CFLAGS for your local compiler/system
 #
 # -O2  will work for most systems
-CFLAGS = -O3 -m486  -Wall -fPIC
+CFLAGS = -O3 -Wall -fPIC
 # for gcc on intel, add -m486 to CFLAGS 
 # -fPIC for building Position Independent Code for dynamic lib

diff -Naur tacg-3.12-src/SeqFuncs.c tacg-3.12-src_patched/SeqFuncs.c
--- tacg-3.12-src/SeqFuncs.c    2001-08-20 23:20:21.000000000 +0100
+++ tacg-3.12-src_patched/SeqFuncs.c    2013-10-14 14:44:01.003739835 +0100
@@ -91,7 +91,7 @@
     should have been functionized long ago */

 void LinearMap(long seq_len, int basesPerLine, int NumREs, char *sequence, int max_okline, 
-                char Codons[][][], int codon_Table) {
+                char Codons[MAX_ORGS][N_CODONS][7], int codon_Table) {

     /* Declarations */
    int i, d, k, mm=0, rc, n_letters=0, Xn=0, okline, HTML, spacer, spacermod, nocuts, stanzaspace,
@@ -173,13 +173,13 @@

         /*write the correct numbering in Left margin  */
     if (F.NumStart < 1 && (((block_Cnt-1)*basesPerLine) + 1 + F.NumStart) == 0) {numstart++; tripclick++;}
-    sprintf((char *)s, "%7d",(((block_Cnt-1)*basesPerLine) + 1 + numstart)); /* numstart is just a + offset */
+    sprintf((char *)s, "%7ld",(((block_Cnt-1)*basesPerLine) + 1 + numstart)); /* numstart is just a + offset */
     memcpy(&O_txt[O_SEQ_LINE][0], s, 7);
         /* and in the right margin - combine with the above bit? */
     if (F.NumStart < 0 && (tripclick || (((block_Cnt)*basesPerLine + numstart)) > 0)) {
       if (!tripclick) {tripclick++; numstart++;}
     }
-        sprintf((char *)s, "%7d",(((block_Cnt)*basesPerLine + numstart)));
+        sprintf((char *)s, "%7ld",(((block_Cnt)*basesPerLine + numstart)));
         memcpy(&O_txt[O_SEQ_LINE][O_LMARG+basesPerLine], s, 7);
         /* and drop in the sequence directly after it. */

diff -Naur tacg-3.12-src/tacg.h tacg-3.12-src_patched/tacg.h
--- tacg-3.12-src/tacg.h    2001-09-07 00:57:45.000000000 +0100
+++ tacg-3.12-src_patched/tacg.h    2013-10-14 14:42:06.471737678 +0100
@@ -591,7 +591,7 @@

 /* fmax/imax return the float/int max of 2 values (mainly to save space) - it's another
     1 liner, but should be used relatively infrequently */
-float fmax(float v1, float v2);
+/* float fmax(float v1, float v2); */
 int imax(int v1, int v2);

 /* BitArray() is a 1st pass approx to doing interesting things with bit strings
@@ -740,7 +740,7 @@
     and functional enough to makeinto its own fn().  It takes the DD.Dat struct
    and parses the hit data out of it and composes a Linear Map out of it. */
 void LinearMap(long seq_len, int basesPerLine, int NumREs, char *sequence, 
-                     int max_okline, char Codons[][][], int codon_Table);  
+                     int max_okline, char Codons[MAX_ORGS][N_CODONS][7], int codon_Table);  

 /* Clone() goes thru RE[] and figures out which REs match the conditions of the option flag, where
    --clone '#_#,#x#,#x#,#_#' (up to MAX_NUM_CLONE_RANGES).  '_' indicates that the range cannot be cut;
diff -Naur tacg-3.12-src/udping.c tacg-3.12-src_patched/udping.c
--- tacg-3.12-src/udping.c    2001-08-21 03:56:49.000000000 +0100
+++ tacg-3.12-src_patched/udping.c    2013-10-14 14:38:30.059733637 +0100
@@ -54,7 +54,7 @@

 extern uid_t getuid();
 extern int socket();
-extern int sendto();
+/* extern int sendto(); */
 extern int close();

 int iamhere(char *progname)