[Bioperl-l] makefile on alpha

Elia Stupka elia@fugu-sg.org
Sat, 24 Aug 2002 02:30:19 +0800 (SGT)

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.fugu-sg.org/~elia *
* tel:    +65 6874 1467        *
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---------- 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

[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... 


* http://www.fugu-sg.org/~elia *
* tel:    +65 6874 1467        *
* mobile: +65 9030 7613        *
* fax:    +65 6779 1117        *