Re: [GeneX-dev] Tail (2)

[Nicolas B. <nic...@pl...>]

OK I have installed the GNU utils into /usr/local/bin

Everything is fine except

Building runa.so for this architecture and installing it ..

gcc -bundle -undefined suppress  -o runa.so runa.o  -L/usr/local/lib
/usr/bin/ld: -undefined error must be used when -twolevel_namespace is 
in effect
make: *** [runa.so] Error 1

!! System Error: No such file or directory @ line: 2190  (cd 
/Users/Shared/Downloads/GeneX-Server-1.0.4/CyberT-dist; R SHLIB runa.c)
cp: cannot stat `runa.so': No such file or directory

!! System Error: No such file or directory @ line: 2195  (cd 
/Users/Shared/Downloads/GeneX-Server-1.0.4/CyberT-dist; cp hdarray 
runa.c runa.so /usr/local/genex/lib/R/library/hdarray/R/)

Talked to a developer, Keisuke Fujii, who ported some applications to 
Darwin. (http://www-jlc.kek.jp/~fujiik/macosx/10.1.X/)

He mentions that this compiling error can be circumvented by adding the 
following options to gcc:
-flat_namespace -undefined suppress

I am not sure on how to proceed next.

Sincerely,

Nicolas

On Wednesday, November 14, 2001, at 08:49 , Harry Mangalam wrote:

> OK - it looks like you're not using the rest of the GNU utils (head and 
> tail are supposed to be the GNU versions.  if your 'head' doesn't 
> understand the '-1' flag, then it's not a GNU head (and it
> should have been detected by the script..?)
>
> You'll have to get the entire GNU text util package:
> ftp://gatekeeper.dec.com/pub/GNU/textutils/textutils-1.22.tar.gz
> and compile and install them in a local bin. Then set that local dir 
> (/usr/local/bin/) in your PATH before the system dir so that when you 
> call tail from your shell, it picks up the GNU version rather
> than the system version (which is probably needed for system chores).
>  Many of the rest of the scripts require the GNU version.
>
> That should clear up a lot of the rest of your problems.
>
> Also, check your 'make'.  If it's not GNU make, you'll also have 
> problems.
> ftp://gatekeeper.dec.com/pub/GNU/make/make-3.79.1.tar.gz
>
> After doing that, try the install again and let us know what fails.
>
> hjm
>
>
>
> Nicolas Bertrand wrote:
>>
>> On Wednesday, November 14, 2001, at 07:27 , Harry Mangalam wrote:
>>
>>> Note that while we'll try to support Mac OSX, none of us have it
>>> running and so have not run thru the install on it obviously.  We're
>>> doing all this flying blind, so excuse the fumbling..
>>>
>>
>> I really appreciate your help. Thanks!
>>
>>> Nicolas Bertrand wrote:
>>>>>> !! System Error:  @ line: 1829  ()
>>>>>
>>>>> This seems to be a problem with your R distribution; either R did 
>>>>> not
>>>>> install properly or the installation script can't find it on the
>>>>> PATH -
>>>>> did your PATH environment variable include R's location?
>>>
>>>> R is installed and is indeed in my PATH: I can launch R from 
>>>> anywhere.
>>>
>>> OK - but is it in the PATH that the install-all script uses?
>>>
>>> Is it in the 'PATH=' line of the 'Options.Reminders' file that keeps
>>> track of all the variables?
>>>
>> Yes, it is:
>> R = /usr/local/bin/R
>>
>>> Can you execute the line from your shell script?
>>>
>>>    R --version |head -1
>>>
>>> it should give you something like:
>>>
>>> R 1.3.1 (2001-08-31).
>>>
>>
>> [localhost:~] nicolasb% R --version | head -1
>>
>> OK? R --version | heap -1? yes
>> Invalid process designation '-1'
>> [localhost:~] nicolasb% R --version | heap -1
>> Invalid process designation '-1'
>> [localhost:~] nicolasb% R --version
>> R 1.3.1 (2001-08-31).
>> Copyright (C) 2001 R Development Core Team
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under the terms of the GNU
>> General Public License.  For more information about these matters,
>> see http://www.gnu.org/copyleft/gpl.html.
>>
>>>>>
>>>>>> !! System Error: No such file or directory @ line: 2190
>>>>>> (cd /Users/Shared/Downloads/GeneX-Server-1.0.4/CyberT-dist; R SHLIB
>>>>>> runa.c)
>>>>>
>>>>> See above
>>>
>>> Can you also excute the above line from your shell?
>>> `cd /Users/Shared/Downloads/GeneX-Server-1.0.4/CyberT-dist; R SHLIB
>>> runa.c
>>>
>>> If you don't have an appro compiler it might also fail, but I assume
>>> that you have a working gcc onboard.
>>>
>> [localhost:Shared/Downloads/GeneX-Server-1.0.4] root# cd
>> /Users/Shared/Downloads/GeneX-Server-1.0.4/CyberT-dist; R SHLIB runa.c
>> gcc -bundle -undefined suppress  -o runa.so runa.o  -L/usr/local/lib
>> /usr/bin/ld: -undefined error must be used when -twolevel_namespace is
>> in effect
>> make: *** [runa.so] Error 1
>>
>> gcc got a problem with that...
>>
>>>>>> !! System Error: No such file or directory @ line: 2195
>>>>>> (cd /Users/Shared/Downloads/GeneX-Server-1.0.4/CyberT-dist; cp
>>>>>> hdarray
>>>>>> runa.c
>>>>>> runa.so /usr/local/genex/lib/R/library/hdarray/R/)
>>>
>>> If the line above didn't work, this one will fail b/c you didn't
>>> compile the runa.so.
>>>
>>>
>>> [stuff deleted]
>>>
>>>
>>>>>> !! System Error: No such file or directory @ line: 2631
>>>>>> (chmod ug+rw -R /usr/local/genex/rcluster/var/poqs)
>>>>>
>>>>> this looks like the installation of rcluster stopped prematurely.
>>>>> Jason - is this a possibility of the mkdir failing like you 
>>>>> mentioned
>>>>> yesterday?
>>>
>>> Did '/usr/local/genex/rcluster/var/poqs' get made correctly?
>>>
>>
>> It did but chmod does not like the option -R. Any reason why it should
>> not accept it?
>>
>> Cheers,
>>
>> Nicolas
>>
----------------------------------------------
Nicolas Bertrand
Department of Plant Sciences
University of Oxford
Oxford OX1 3RB

Tel: ++1865 275 116
----------------------------------------------
>>
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>
> --
> Cheers, Harry
>
> Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho...
>                     [plain text appreciated]
>