#85 gcc/make warnings during compilation process

[Torsten Seemann]

When I compile Staden from source on Linux Centos 5.5 x86_64 I notice a lot of gcc warnings. Many of these are probably fine, but some are a bit worrying. I have attached a .TXT of the relevant lines from the make process stderr, and pasted in a few below for examples.

make[1]: [/bio/src/staden/staden.svn/staden/trunk/src/lib/libmutlib.so] Error 1 (ignored)
io_utils.c: In function ‘template_name_to_number’:
io_utils.c:38: warning: cast from pointer to integer of different size
sheet.c:51: warning: incompatible implicit declaration of built-in function
‘memset’
tman_display.c:72: warning: incompatible implicit declaration of built-in function ‘memmove’
convert/main.c:77: warning: the Gets' function is dangerous and should not be used.
tman_interface.c:340: warning: assignment makes pointer from integer without a cast

Compilation process:

% cd staden.svn/staden/trunk/src
% ./configure --enable-64bit --prefix=/bio/sw/staden.svn --with-samtools=/bio/sw/samtools --with-io_lib=/bio/sw/io_lib
External packages used:
curl: via /usr/bin/curl-config
zlib: DIR (system)
ncurses: DIR (system)
liblzma: DIR
samtools: DIR /bio/sw/samtools
io_lib: via /bio/sw/io_lib/bin/io_lib-config
Tcl: via /usr/lib/tclConfig.sh
Tk: via /usr/lib/tkConfig.sh
tklib: /usr/share/tklib0.4
Iwidgets: /usr/share/iwidgets4.0.1
Itcl: /usr/lib64/itcl3.3
Itk: /usr/lib64/itk3.3
% make 1> make.stdout 2> make.stderr

[Torsten Seemann]

Staden compilation warning messages

[James Bonfield]

I notice that some of these are warnings about Tcl prototypes (eg those in vseqs.c). What version of Tcl do you have installed? The code has #include <tcl.h> so I'm suprised to see these prototype problems.

Some of the others are certainly real and need looking at though. I don't believe any will cause bugs, but we should fix them regardless.

[James Bonfield]

I think the vast majority of these should have been address in the 2.0.0b8 now. I spent a lot of time removing warnings, although not from some of the older cruftier code. (I figure that's been there so long most real problems would have surfaced by now.)

James