For 4 years, I've not had many problems compiling the Staden package until Mavericks came around. Occasionally under Snow Leopard, Lion and Mountain Lion, we would have a bug, and I'd report it here and things would get fixed really fast, and all was good.
I was having huge problems with macports and Mavericks so I was using the compiled version from here, but it's getting long in the tooth, and I was hoping to use a newer version. The macports packages of Tcl and Tk are broken under Mavericks, and won't install, so I installed tcl and tk from source (using the unix section, as recommended). Then I successfully configured, made and installed io_lib, grabbed the latest staden package from svn, and did this:
$ cd ~/staden_install/staden.trunk/src
$ ./bootstrap
$ mkdir install.system
$ cd install.system
$ ../configure --with-png=/opt/local/ --with-lzma=/opt/local/ --with-tklib=/usr/local/lib/tklib0.5/ --prefix=/usr/local/staden --with-io_lib=/usr/local/staden --with-tcl=/usr/local/lib --with-tk=/usr/local/lib
$ make
'make' dies with this:
/Users/jnash/staden_install/staden.trunk/src/install.system/../gap5/str_finder.c:91:10: warning:
implicit declaration of function 'islower' is invalid in C99 [-Wimplicit-function-declaration]
if (islower(cons[i])) {
^
/Users/jnash/staden_install/staden.trunk/src/install.system/../gap5/str_finder.c:98:6: error: non-void
function 'add_rep' should return a value [-Wreturn-type]
return;
^
/Users/jnash/staden_install/staden.trunk/src/install.system/../gap5/str_finder.c:122:5: error:
non-void function 'add_rep' should return a value [-Wreturn-type]
return;
^
1 warning and 2 errors generated.
make[1]: [str_finder.o] Error 1
make: [gap5] Error 2
Any clues? In a sec, I'll check it on my Centos box to see if it's a Mac thing or not.
Or maybe I can beg for a new DMG release for the Mac?
Thanks heaps,
John
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
It looks like you have C99 enabled. I haven't tested everything under
the C99 strict mode, but will do so.
I have patched this and a variety of other things in Gap5 and io_lib
now, so maybe it is enough. I'm not going to go back through gap4 and
older code fixing that all though, so maybe you will want to build
with -std=c89.
--
James Bonfield (jkb@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae, https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi.
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Perfect! Trouble-free build and install of both io_lib and the main package. Thank you again.
Re C99 mode: I was not really paying much attention to my version of C as I was relying on Mavericks and macports to be seamless. I guess I'm more naive than I thought. Fortunately, I have not used gap4 since 2009 or so, having completely switched to gap5, and things appear to be working.
Last edit: John Nash 2014-09-23
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
For 4 years, I've not had many problems compiling the Staden package until Mavericks came around. Occasionally under Snow Leopard, Lion and Mountain Lion, we would have a bug, and I'd report it here and things would get fixed really fast, and all was good.
I was having huge problems with macports and Mavericks so I was using the compiled version from here, but it's getting long in the tooth, and I was hoping to use a newer version. The macports packages of Tcl and Tk are broken under Mavericks, and won't install, so I installed tcl and tk from source (using the unix section, as recommended). Then I successfully configured, made and installed io_lib, grabbed the latest staden package from svn, and did this:
$ cd ~/staden_install/staden.trunk/src
$ ./bootstrap
$ mkdir install.system
$ cd install.system
$ ../configure --with-png=/opt/local/ --with-lzma=/opt/local/ --with-tklib=/usr/local/lib/tklib0.5/ --prefix=/usr/local/staden --with-io_lib=/usr/local/staden --with-tcl=/usr/local/lib --with-tk=/usr/local/lib
$ make
'make' dies with this:
/Users/jnash/staden_install/staden.trunk/src/install.system/../gap5/str_finder.c:91:10: warning:
implicit declaration of function 'islower' is invalid in C99 [-Wimplicit-function-declaration]
if (islower(cons[i])) {
^
/Users/jnash/staden_install/staden.trunk/src/install.system/../gap5/str_finder.c:98:6: error: non-void
function 'add_rep' should return a value [-Wreturn-type]
return;
^
/Users/jnash/staden_install/staden.trunk/src/install.system/../gap5/str_finder.c:122:5: error:
non-void function 'add_rep' should return a value [-Wreturn-type]
return;
^
1 warning and 2 errors generated.
make[1]: [str_finder.o] Error 1
make: [gap5] Error 2
Any clues? In a sec, I'll check it on my Centos box to see if it's a Mac thing or not.
Or maybe I can beg for a new DMG release for the Mac?
Thanks heaps,
John
On Fri, Sep 19, 2014 at 06:17:36PM +0000, John Nash wrote:
It looks like you have C99 enabled. I haven't tested everything under
the C99 strict mode, but will do so.
I have patched this and a variety of other things in Gap5 and io_lib
now, so maybe it is enough. I'm not going to go back through gap4 and
older code fixing that all though, so maybe you will want to build
with -std=c89.
--
James Bonfield (jkb@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi.
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
Perfect! Trouble-free build and install of both io_lib and the main package. Thank you again.
Re C99 mode: I was not really paying much attention to my version of C as I was relying on Mavericks and macports to be seamless. I guess I'm more naive than I thought. Fortunately, I have not used gap4 since 2009 or so, having completely switched to gap5, and things appear to be working.
Last edit: John Nash 2014-09-23