[Bioperl-l] makefile on alpha

[Jason Stajich]

did you upgrade your MakeMaker module on your system?
On Sat, 24 Aug 2002, Elia Stupka wrote:

> Since I hadn't received any nice "Oh just fix it like this" comments on
> the problem of the makefile for bioperl being too long for alpha, I set
> off on a mad search for a solution. You can read details in the mail
> below, which involved getting gnumake to compile on alpha which turns out
> to be a nightmare... anyway at the end of it all realised that make is not
> the only problem, the main problem is the 'sh' command itself which
> exceeds the number of arguments allowed by MAX_ARGS in the kernel.
>
> *BUT* the simplest, crazy as it sounds solution is to run make -i (for
> ignore errors) and make test will work nicely. Horrible hack but if all
> you want at the end of the day is to be able to run make test on systems
> were it's too complicated to get around the problem... use make -i
>
> If somebody is willing to look into this (I am dead by now) another fix at
> least for people who have gnumake version higher than 3.76 is to introduce
> the wordlist command in the makefile, as detailed here:
>
> http://www.geocrawler.com/mail/msg.php3?msg_id=2093588&list=380
>
> Elia
>
> ********************************
> * http://www.fugu-sg.org/~elia *
> * tel:    +65 6874 1467        *
> * mobile: +65 9030 7613        *
> * fax:    +65 6779 1117        *
> ********************************
>
>
> ---------- Forwarded message ----------
> Date: Sat, 24 Aug 2002 02:15:58 +0800 (SGT)
> From: Elia Stupka <elia@fugu-sg.org>
> To: Fugu Informatics mailing list <fugui@fugu-sg.org>
> Subject: Elia sysadmin ;) (fwd)
>
> Hi Chen Peng,
>
> I wanted to run make on bioperl-live in shaggy, but the make fails because
> it says "line too long".
>
> So I found out that we have the normal alpha unix make installed on
> shaggy, which is very bad, and that GNU make doesn't have this problem
>
> So I downloaded the source for GNU make and tried to install it.
>
> I tried a normal .configure, make, make install but it failed (explanation
> lower). So then I did a build from scratch by using sh ./build.sh and it
> also failed.
>
> It fails with the error "Invalid .stabs/.stabn directive", so it turns out
> (after a lot of reading" that gcc in alpha 4.1 is not very good and gives
> these problems sometimes (read
> http://www.geocrawler.com/archives/3/379/2002/2/0/7950008/) because of
> incompatibility with the newer version of the assembler...
>
> So for now the workaround is to add an option in the configure or build
> script like this:
>
> CC='gcc -Wa,-oldas'
>
> This tells the gcc compiler to invoke the assembler with the -oldas
> option, which makes it use the older (working) assembler instead of the
> new one.
>
> Thought I'd share this treasure hunt with you....
>
> ...if you want to copy gnumake to /usr/bin you can get it at
> /usr/home/elia/bin/gnumake
>
> [Apparently this problem has been fixed in the latest patch to the
> system, but I think we patched it recently and we still see it...]
>
> The worst part of the story is that even though I now have gnumake it
> still doesn't work on the bioperl-live makefile on alpha... grrrr...
>
> now I get /bin/sh Arg list too long...
>
> Elia
>
> ********************************
> * http://www.fugu-sg.org/~elia *
> * tel:    +65 6874 1467        *
> * mobile: +65 9030 7613        *
> * fax:    +65 6779 1117        *
> ********************************
>
>
>
>
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>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu