genex-dev — GeneX developers

[GeneX-dev] xml2db, "No array data found!"

[<rb...@mw...>]

Dear genex team,

I still have problems loading data into genex with xml2db.pl. It loads for
quite a while and then ends with the last messages beeing:

parsing experiment_set elements...
No array data found!

I created the data set with the curration tool V01.50 on windows using the
testdata (whatfield_ecoli_ihf) that was included with the installation.


I have another question: Is the data within the controlfiles that are
downloaded by the curration tool created by the genex server on the fly
from the database, or does one have to create that data in advance? If I
change data on the data base, are those alterations automatically seen in
the controlfiles?

By the way, thank you very much for the quick and effective help on my
previous problems.

With best regards  Robert


    Robert Bell
    MWG Biotech AG
    Anzinger Strasse 7
    D-85560 Ebersberg; Germany
    email : rb...@mw...
    voice : +49-8092-8289 356
    fax   : +49-8092-8289 310

Re: [GeneX-dev] problem loading data with xml2db.pl

[Todd F. P. <tf...@nc...>]

Dear Robert:

This is due to a contact having no organization. To fix this problem, use
the Curation Tool to edit the contacts and fill in something (anything)
for any contacts that have a blank organization. Then save the experiment
and retry using xml2db. Alternatively, you can hand edit the xml file and
add the organization to the contacts.

Todd Peterson
NCGR GeneX Team

On Tue, 20 Nov 2001 rb...@mw... wrote:

> 
> Dear genex team,
> 
> I have a problem loading data with the xml2db.pl program into the genex
> database.
> I get the following messages:
> 
> Unrecognized escape \d passed through at
> /usr/lib/perl5/site_perl/5.6.0/i586-linux/XML/DOM.pm line 136.
> Using directory: ./.
> Reading GEML file: robtest4.xml...DONE.
> parsing contact elements...
> information already exists in table Contact.
> ...
> information already exists in table Contact.
> information already exists in table Contact.
> DBD::Pg::st execute failed: ERROR:  parser: parse error at or near "" at
> /usr/local/genex/bin/xml2db.pl line 1650.
> 7Contact: SELECT con_pk from Contact where contact_person = 'genex' AND
> at /usr/local/genex/bin/xml2db.pl line 1650.
> 
> Is this a problem due to the data base or the curation tool or are the DB
> and the tool versions incompatible or is it a user error?
> I would apreciate some help on this very much, since I feel quite stuck.
> 
> best regards Robert
> 
> 
>     Robert Bell
>     MWG Biotech AG
>     Anzinger Strasse 7
>     D-85560 Ebersberg; Germany
>     email : rb...@mw...
>     voice : +49-8092-8289 356
>     fax   : +49-8092-8289 310
> 
> 
> 
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genex-dev
> 

[GeneX-dev] problem loading data with xml2db.pl

[<rb...@mw...>]

Dear genex team,

I have a problem loading data with the xml2db.pl program into the genex
database.
I get the following messages:

Unrecognized escape \d passed through at
/usr/lib/perl5/site_perl/5.6.0/i586-linux/XML/DOM.pm line 136.
Using directory: ./.
Reading GEML file: robtest4.xml...DONE.
parsing contact elements...
information already exists in table Contact.
...
information already exists in table Contact.
information already exists in table Contact.
DBD::Pg::st execute failed: ERROR:  parser: parse error at or near "" at
/usr/local/genex/bin/xml2db.pl line 1650.
7Contact: SELECT con_pk from Contact where contact_person = 'genex' AND
at /usr/local/genex/bin/xml2db.pl line 1650.

Is this a problem due to the data base or the curation tool or are the DB
and the tool versions incompatible or is it a user error?
I would apreciate some help on this very much, since I feel quite stuck.

best regards Robert


    Robert Bell
    MWG Biotech AG
    Anzinger Strasse 7
    D-85560 Ebersberg; Germany
    email : rb...@mw...
    voice : +49-8092-8289 356
    fax   : +49-8092-8289 310

Re: [GeneX-dev] Project Management with Genex

[<ja...@op...>]

"Yong Liu" <y_...@ya...> writes:

> We are in the process of installing Genex on our system. One of the
> features we would like to have is that different projects can only
> view/edit their own data. Only for a few specific accounts can have
> access to all the data. Is there relatively simple way to modify the
> existing Genex to achieve this goal?

In the current Genex-1.0 release, you can do it, but you can only
protect Experiments, ArrayMeasurements, and Spots. The other meta-data
is public information. Michael Pear submitted a data normalization
framework that used this kind of protection. It is in its own branch
in the Genex CVS repository, and you can look at how he does it by
checking out his code. The CVS login instructions are at: 

  https://sourceforge.net/cvs/?group_id=16453

You will need to use the branch tag 'mpear_experimental_1_0_2' to get
his code:

  cvs -d :pserver:ano...@cv...:/cvsroot/genex \
    co -r mpear_experimental_1_0_2 genex-server

The good news is that Genex-2.0, which is now under heavy development
by me, will have this implemented. And, nearly all tables in the DB
will be protected, not just the three mentioned above. I will be
making a developers beta release of Genex-2.0 in a week or two.

jas.

[GeneX-dev] Project Management with Genex

[Yong L. <y_...@ya...>]

Hi, everybody,

We are in the process of installing Genex on our
system. One of the features we would like to have is
that different projects can only view/edit their own
data. Only for a few specific accounts can have access
to all the data. Is there relatively simple way to
modify the existing Genex to achieve this goal? 

Thanks for any input!

-Yong

Yong Liu, Ph.D.
Bioinformatics Unit
Biotechnology Center
University of Illinois at Urbana-Champaign
Urbana, IL 61801
Tel: 217-244-7355
Fax: 217-265-5066
Email: <Yo...@UI...>


__________________________________________________
Do You Yahoo!?
Find the one for you at Yahoo! Personals
http://personals.yahoo.com

[GeneX-dev] Curation tool

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

Hello

Thanks again all the help you have provided. i am now looking at the 
curation tool.

I have installed it and ran it after modifying the go.sh script to:

--------------------------
#!/bin/sh

JRE="../jre1.3.0"

# Start the Genex-Curation Tool from the genex.jar file on the Unix 
platform.

cd ../data

java -Xmx96m -Xms96m -classpath ../lib/genex.jar:../lib/xerces.jar 
org.ncgr.genex.curator.Curator
--------------------------

Cheers,

Nicolas

----------------------------------------------
Nicolas Bertrand
Department of Plant Sciences
University of Oxford
Oxford OX1 3RB

Tel: ++1865 275 116
----------------------------------------------

Re: [GeneX-dev] It works!

[Harry M. <man...@ho...>]

Hi Nicholas,

the following is now the Mac OSX section from the INSTALL file.  It will be included in the next release of GeneX and will be committed to the CVS tree today or tomorrow.


  * Mac OSX - as essentially BSD Unix under the hood, this should be a pretty
    straight port and as Daniel E Sabath <dsabath@u.washington.edu> discovered,
    it pretty much is.  
    - Gotchas are that since the g77 package isn't widely available for OSX,
    you may have to grab a binary package of R that has it built with another
    Fortran compiler, and due to a strange quirk of packaging, Apple has
    included the non-GNU version of several file utilities so you'll have to go
    get the utilities and compile them yourself.  The installer should catch
    this deviation and tell you in a (possibly hard to understand) error
    message that starts: 
    
         "Ugh!  What gibberish! The [app] you have certainly does not 
         taste like GNU [app]."
         
    and then it'll tell you where to get the appropriate one.
    - Daniel also mentioned that he had installed Fink:
        http://fink.sourceforge.net
      which is a collection of unix software and a modified version of the 
      Debian dpkg package maintenance tools.  This may have enabled him to
      build xgobi when others failed. 
      
    Nicolas Bertrand <nic...@pl...> also had some problems 
    using a binary installation of R to install the runa.so object file that
    CyberT uses.  If you're using such an installation, you will probably have 
    to modify the R_HOME/R/etc/Makeconf file so that these flags are defined as
    shown:
    
      SHLIB_CXXLDFLAGS  = -bundle -undefined suppress
      SHLIB_LDFLAGS     = -bundle -flat_namespace -undefined suppress
    
Thansk for the high wire act...

hjm



Nicolas Bertrand wrote:
> 
> Thanks for your help. And sorry I did not get what you meant earlier.
> 
> I modified ../R/etc/Makeconf
> 
> by adding the -flat_namespace  to SHLIB_LDFLAGS as follows:
> SHLIB_CXXLDFLAGS = -bundle -undefined suppress
> SHLIB_EXT = so
> SHLIB_FFLAGS =
> SHLIB_LD = gcc
> SHLIB_LDFLAGS = -bundle -flat_namespace -undefined suppress
>                                                         ^
> 
> Cheers!
> 
> That is perhaps one thing to add to the INSTALL file. It is a problem
> specific to MacOSX v10.1
> 
> Nicolas
> 
> On Thursday, November 15, 2001, at 10:15 PM, Harry Mangalam wrote:
> 
> > Nicolas Bertrand wrote:
> >>
> >> Hello
> >>
> >> On Thursday, November 15, 2001, at 09:47 , Harry Mangalam wrote:
> >>
> >>> OK - this is a Mac OSX-specific problem with R and gcc that I can't
> >>> really help you with except via the grungiest of suggestions.
> >>>
> >>> R's SHLIB command calls gcc with the arguments that you see echoed to
> >>> the screen, so somewhere you cshould be able to set them..
> >>>
> >>> AHA! Brian D. Ripley, one of R's authors, indicates:
> >>>
> >>> http://www.ens.gu.edu.au/robertk/R/help/01a/0881.html
> >>>
> >>> [don't forget that google is your friend..)
> >>>
> >>> that you have to enter these flags in R_HOME/etc/Makeconf as part of
> >>> the CFLAGS string, so you'll probably have to append  '-flat_namespace
> >>> -undefined suppress' to the CFLAGS string there.  It wasn't
> >>> cleear to me whether you'll have to recompile R to have this take
> >>> effect, but I'd try it without the recompile 1st.
> >>>
> >>> Helpful...?
> >>>
> >>> hjm
> >>>
> >>
> >> I don't exactly know... I installed R from binaries.
> >
> > OK - it should still have installed the R_HOME/etc/Makeconf - does it
> > exist?
> >
> > If so, edit it to add the the options recommended by the guy who gave
> > you the advice previously. ie:
> >
> > CFLAGS = -g -O2 -flat_namespace -undefined suppress
> >
> > Taking a longer look at the file, I see that there are a lot of
> > SHLIB-related flags which might benefit from those options as well.
> > I'm not an R expert, and certainly not on OSX, so your best bet
> > wold be to query the R user group to see if they have a solution:
> >
> > r-...@st...
> >
> > This group is EXCEPTIONALLY good at responding to questions.
> >
> >
> >> cc -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
> >>
> >> Doesn't it mean that runa.so could not be compiled because of a linker
> >> error? I have been advised by Keisuke Fujii to run cc with the
> >> -flat_namespace -undefined supress flags.
> >> That would give the following command to avoid this error:
> >> cc -bundle -flat_namespace -undefined suppress -o runa.so runa.o
> >> -L/usr/local/lib
> >
> > The linker is usually invoked automatically by the compiler if you ask
> > it to produce an object file requiring fn()s from system libs.  I THINK
> > that appro flags are essentially passed thru to the
> > linker in this case.  Hencve adding these
> >
> >> Which Make has to be modified to had this flag?
> >
> > Seee previous message
> >
> >> !! 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/)
> >>
> >> I suspect these errors pop up because runa.so failed to compile, right?
> >
> > Yup.
> >
> > --
> > Cheers, Harry
> >
> > Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho...
> >                     [plain text appreciated]
> >
> 
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genex-dev

-- 
Cheers, Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho... 
                    [plain text appreciated]

[GeneX-dev] It works!

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

Thanks for your help. And sorry I did not get what you meant earlier.

I modified ../R/etc/Makeconf

by adding the -flat_namespace  to SHLIB_LDFLAGS as follows:
SHLIB_CXXLDFLAGS = -bundle -undefined suppress
SHLIB_EXT = so
SHLIB_FFLAGS =
SHLIB_LD = gcc
SHLIB_LDFLAGS = -bundle -flat_namespace -undefined suppress
							^
							
Cheers!

That is perhaps one thing to add to the INSTALL file. It is a problem 
specific to MacOSX v10.1

Nicolas

On Thursday, November 15, 2001, at 10:15 PM, Harry Mangalam wrote:

> Nicolas Bertrand wrote:
>>
>> Hello
>>
>> On Thursday, November 15, 2001, at 09:47 , Harry Mangalam wrote:
>>
>>> OK - this is a Mac OSX-specific problem with R and gcc that I can't
>>> really help you with except via the grungiest of suggestions.
>>>
>>> R's SHLIB command calls gcc with the arguments that you see echoed to
>>> the screen, so somewhere you cshould be able to set them..
>>>
>>> AHA! Brian D. Ripley, one of R's authors, indicates:
>>>
>>> http://www.ens.gu.edu.au/robertk/R/help/01a/0881.html
>>>
>>> [don't forget that google is your friend..)
>>>
>>> that you have to enter these flags in R_HOME/etc/Makeconf as part of
>>> the CFLAGS string, so you'll probably have to append  '-flat_namespace
>>> -undefined suppress' to the CFLAGS string there.  It wasn't
>>> cleear to me whether you'll have to recompile R to have this take
>>> effect, but I'd try it without the recompile 1st.
>>>
>>> Helpful...?
>>>
>>> hjm
>>>
>>
>> I don't exactly know... I installed R from binaries.
>
> OK - it should still have installed the R_HOME/etc/Makeconf - does it 
> exist?
>
> If so, edit it to add the the options recommended by the guy who gave 
> you the advice previously. ie:
>
> CFLAGS = -g -O2 -flat_namespace -undefined suppress
>
> Taking a longer look at the file, I see that there are a lot of 
> SHLIB-related flags which might benefit from those options as well.  
> I'm not an R expert, and certainly not on OSX, so your best bet
> wold be to query the R user group to see if they have a solution:
>
> r-...@st...
>
> This group is EXCEPTIONALLY good at responding to questions.
>
>
>> cc -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
>>
>> Doesn't it mean that runa.so could not be compiled because of a linker
>> error? I have been advised by Keisuke Fujii to run cc with the
>> -flat_namespace -undefined supress flags.
>> That would give the following command to avoid this error:
>> cc -bundle -flat_namespace -undefined suppress -o runa.so runa.o
>> -L/usr/local/lib
>
> The linker is usually invoked automatically by the compiler if you ask 
> it to produce an object file requiring fn()s from system libs.  I THINK 
> that appro flags are essentially passed thru to the
> linker in this case.  Hencve adding these
>
>> Which Make has to be modified to had this flag?
>
> Seee previous message
>
>> !! 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/)
>>
>> I suspect these errors pop up because runa.so failed to compile, right?
>
> Yup.
>
> --
> Cheers, Harry
>
> Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho...
>                     [plain text appreciated]
>

Re: [GeneX-dev] Tail (2)

[Harry M. <man...@ho...>]

Nicolas Bertrand wrote:
> 
> Hello
> 
> On Thursday, November 15, 2001, at 09:47 , Harry Mangalam wrote:
> 
> > OK - this is a Mac OSX-specific problem with R and gcc that I can't
> > really help you with except via the grungiest of suggestions.
> >
> > R's SHLIB command calls gcc with the arguments that you see echoed to
> > the screen, so somewhere you cshould be able to set them..
> >
> > AHA! Brian D. Ripley, one of R's authors, indicates:
> >
> > http://www.ens.gu.edu.au/robertk/R/help/01a/0881.html
> >
> > [don't forget that google is your friend..)
> >
> > that you have to enter these flags in R_HOME/etc/Makeconf as part of
> > the CFLAGS string, so you'll probably have to append  '-flat_namespace
> > -undefined suppress' to the CFLAGS string there.  It wasn't
> > cleear to me whether you'll have to recompile R to have this take
> > effect, but I'd try it without the recompile 1st.
> >
> > Helpful...?
> >
> > hjm
> >
> 
> I don't exactly know... I installed R from binaries.

OK - it should still have installed the R_HOME/etc/Makeconf - does it exist?

If so, edit it to add the the options recommended by the guy who gave you the advice previously. ie:

CFLAGS = -g -O2 -flat_namespace -undefined suppress

Taking a longer look at the file, I see that there are a lot of SHLIB-related flags which might benefit from those options as well.  I'm not an R expert, and certainly not on OSX, so your best bet
wold be to query the R user group to see if they have a solution:

r-...@st...

This group is EXCEPTIONALLY good at responding to questions.


> cc -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
> 
> Doesn't it mean that runa.so could not be compiled because of a linker
> error? I have been advised by Keisuke Fujii to run cc with the
> -flat_namespace -undefined supress flags.
> That would give the following command to avoid this error:
> cc -bundle -flat_namespace -undefined suppress -o runa.so runa.o
> -L/usr/local/lib

The linker is usually invoked automatically by the compiler if you ask it to produce an object file requiring fn()s from system libs.  I THINK that appro flags are essentially passed thru to the
linker in this case.  Hencve adding these 

> Which Make has to be modified to had this flag?

Seee previous message

> !! 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/)
> 
> I suspect these errors pop up because runa.so failed to compile, right?

Yup.

-- 
Cheers, Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho... 
                    [plain text appreciated]

Re: [GeneX-dev] Tail (2)

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

Hello

On Thursday, November 15, 2001, at 09:47 , Harry Mangalam wrote:

> OK - this is a Mac OSX-specific problem with R and gcc that I can't 
> really help you with except via the grungiest of suggestions.
>
> R's SHLIB command calls gcc with the arguments that you see echoed to 
> the screen, so somewhere you cshould be able to set them..
>
> AHA! Brian D. Ripley, one of R's authors, indicates:
>
> http://www.ens.gu.edu.au/robertk/R/help/01a/0881.html
>
> [don't forget that google is your friend..)
>
> that you have to enter these flags in R_HOME/etc/Makeconf as part of 
> the CFLAGS string, so you'll probably have to append  '-flat_namespace 
> -undefined suppress' to the CFLAGS string there.  It wasn't
> cleear to me whether you'll have to recompile R to have this take 
> effect, but I'd try it without the recompile 1st.
>
> Helpful...?
>
> hjm
>

I don't exactly know... I installed R from binaries.

cc -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

Doesn't it mean that runa.so could not be compiled because of a linker 
error? I have been advised by Keisuke Fujii to run cc with the 
-flat_namespace -undefined supress flags.
That would give the following command to avoid this error:
cc -bundle -flat_namespace -undefined suppress -o runa.so runa.o 
-L/usr/local/lib

Which Make has to be modified to had this flag?


!! 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/)

I suspect these errors pop up because runa.so failed to compile, right?

>
>
> Nicolas Bertrand wrote:
>>
>> 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
----------------------------------------------
>>>>
>>>> _______________________________________________
>>>> Genex-dev mailing list
>>>> Gen...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/genex-dev
>>>
>>> --
>>> Cheers, Harry
>>>
>>> Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho...
>>>                     [plain text appreciated]
>>>
>>
>> _______________________________________________
>> Genex-dev mailing list
>> Gen...@li...
>> https://lists.sourceforge.net/lists/listinfo/genex-dev
>
> --
> Cheers, Harry
>
> Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho...
>                     [plain text appreciated]
>

Re: [GeneX-dev] Tail (2)

[<ja...@op...>]

"Nicolas Bertrand" <nic...@pl...> writes:

> 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.

Nor am I. Maybe Harry can help. It sounds like the R installation is
bad. The command used to compile runa.c into runa.so is:

  R SHLIB runa.c

We don't hard code any info at all, it's all up to R. So if it cannot
make the dynamic libraries it needs, it's not likely we can help.

jas.

Re: [GeneX-dev] Tail (2)

[Harry M. <man...@ho...>]

OK - this is a Mac OSX-specific problem with R and gcc that I can't really help you with except via the grungiest of suggestions.

R's SHLIB command calls gcc with the arguments that you see echoed to the screen, so somewhere you cshould be able to set them..

AHA! Brian D. Ripley, one of R's authors, indicates:

http://www.ens.gu.edu.au/robertk/R/help/01a/0881.html

[don't forget that google is your friend..)

that you have to enter these flags in R_HOME/etc/Makeconf as part of the CFLAGS string, so you'll probably have to append  '-flat_namespace -undefined suppress' to the CFLAGS string there.  It wasn't
cleear to me whether you'll have to recompile R to have this take effect, but I'd try it without the recompile 1st.

Helpful...?

hjm



Nicolas Bertrand wrote:
> 
> 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
> ----------------------------------------------
> >>
> >> _______________________________________________
> >> Genex-dev mailing list
> >> Gen...@li...
> >> https://lists.sourceforge.net/lists/listinfo/genex-dev
> >
> > --
> > Cheers, Harry
> >
> > Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho...
> >                     [plain text appreciated]
> >
> 
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genex-dev

-- 
Cheers, Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho... 
                    [plain text appreciated]

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
----------------------------------------------
>>
>> _______________________________________________
>> Genex-dev mailing list
>> Gen...@li...
>> https://lists.sourceforge.net/lists/listinfo/genex-dev
>
> --
> Cheers, Harry
>
> Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho...
>                     [plain text appreciated]
>

Re: [GeneX-dev] (no subject)

[Todd F. P. <tf...@nc...>]

Dear William:

There is a document on column def files at
http://genex.ncgr.org/download/tutorials/Curation_Tool_Importing_Validation.doc
This may help you out with these concepts. I'm currently in Denver at the
supercomputing conference so my email access is not the greatest. Please
excuse delays in response.

Todd Peterson
NCGR

On 11 Nov 2001, Jason E. Stewart wrote:

> "William Tam" <Ult...@jh...> writes:
> 
> >    Hello. I am trying to import an affymetrix file into
> >    GeneX. However, I have been having problems with how to define
> >    the columns. I tried to define the columns similar to how the
> >    sample data with the curation tool defined it.
> 
> I'm sorry, but Todd Peterson is really the only person who can help
> you with the curation tool. 
> 
> <opinion type='not shared with all members of the devo team'>
> 
> I'm afraid that the CT was a failed experiment. 
> 
> It will never be suited for bulk uploads of lab data into the DB. It
> is not automatable, and it makes assumptions about certain information
> being available that probably isn't.
> 
> Even though it's currently the only tool that we supply to get data
> into GeneX, I can't recommend that people use it.
> 
> </opinion>
> 
> We began a project in March to create an automatable, scriptable perl
> application for bulk data imports. Due to reorganization at NCGR this
> was never finished. Recently a group at U. Virginia at Bill Pearson's
> lab together with Jennifer Weller's group at Virginia Tech, and two
> other Virginia Universities have raised funds to finish the data
> loader. The drop dead date for UVA to get this working is end of
> January. They are retooling an Affy loader written in Perl by Michael
> Pear, while I'm finishing the work started in March.
> 
> I appologize for this serious problem, I wish it wasn't this
> way. GeneX is useless to anyone unless you can get your data into
> it. I believe that in 6 to 8 weeks we will have a really useful tool
> to do that. 
> 
> Until then, I'm afraid you haven't much choice.
> 
> jas.
> 
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genex-dev
> 

Re: [GeneX-dev] Tail (2)

[Harry M. <man...@ho...>]

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
> ----------------------------------------------
> 
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genex-dev

-- 
Cheers, Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho... 
                    [plain text appreciated]

Re: [GeneX-dev] Tail (2)

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

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
----------------------------------------------

Re: [GeneX-dev] Tail (2)

[Harry M. <man...@ho...>]

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..

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?

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).


> >
> >> !! 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.

> >> !! 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?

-- 
Cheers, Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho... 
                    [plain text appreciated]

Re: [GeneX-dev] Tail (2)

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

On Wednesday, November 14, 2001, at 06:30 , Harry Mangalam wrote:

> Nicolas Bertrand wrote:
>>
>> Hi
>>
>> I could compile GNU tail from source. I did placed it in 
>> /usr/local/bin/
>> The script was happier. The installation does not complete:
>
> I think this is because the 1st time you weren;t using the GNU tail 
> (from the text utils) - teh GNU utils have a specific response from the 
> --version query which is how we test for them.
>
> Your compile from scratch seems to have solved that.  Strange that it 
> didn;t complain about the thers tho, unless they DO use the rest of the 
> GNU utils.
>
> ANyway...
>
>> !! 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.

>
>> !! 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
>
>> !! 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/)
>
> Possibly having to do with the above; if there wasn't a R subdir made, 
> it couldn't copy things to it.  Does 
> '/usr/local/genex/lib/R/library/hdarray/R/' exist?

/usr/local/genex/lib/R/library/hdarray/R/ exists:

[localhost:Downloads/GeneX-Server-1.0.4/Genex] nicolasb% ls 
/usr/local/genex/lib/R/library/hdarray/
R



>
>> !! System Error: No such file or directory @ line: 2498
>> (/usr/bin/perl Makefile.PL)
>
> Hmm - this is odd - it SHOULD do this if you've gotten this far...
> Jason - is there anything in Makefile.PL which would generate this??
>
>> !! System Error: No such file or directory @ line: 2502  (make -s test)
>
> Ditto for Jason.
>
>> !! System Error: No such file or directory @ line: 2507  (make install)
>
> Ditto for Jason.
>
>> !! 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?
>
>
> Thanks for the feedback..
>
> Harry
>
>
>>   
>> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>                        Name: genex-errors.txt
>>    genex-errors.txt    Type: Plain Text (text/plain)
>>                    Encoding: 7bit
>>
>>   
>> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>
>> Any ideas?
>>
>> Best regards,
>>
>> Nicolas
>>
>> Begin forwarded message:
>>
>>> From: Nicolas Bertrand <nic...@pl...>
>>> Date: Wed Nov 14, 2001  11:44:04  Etc/GMT
>>> To: gen...@li...
>>> Subject:
>>>
>>> Hello
>>>
>>> I am installing genex server 1.0.4 on MacOSX10.1. The installation
>>> script stalls while checking tail. I was wondering if anybody had such
>>> problems.
>>>
>>>
>>> This a snapshot of the installation screen:
>>> [...]
>>> Testing for a GNU [tail] ...
>>> Unknown option: 1
>>> Usage: head [-options] <url>...
>>>     -m <method>   use method for the request (default is 'HEAD')
>>>     -f            make request even if head believes method is illegal
>>>     -b <base>     Use the specified URL as base
>>>     -t <timeout>  Set timeout value
>>>     -i <time>     Set the If-Modified-Since header on the request
>>>     -c <conttype> use this content-type for POST, PUT, CHECKIN
>>>     -a            Use text mode for content I/O
>>>     -p <proxyurl> use this as a proxy
>>>     -P            don't load proxy settings from environment
>>>     -H <header>   send this HTTP header (you can specify several)
>>>
>>>     -u            Display method and URL before any response
>>>     -U            Display request headers (implies -u)
>>>     -s            Display response status code
>>>     -S            Display response status chain
>>>     -e            Display response headers
>>>     -d            Do not display content
>>>     -o <format>   Process HTML content in various ways
>>>
>>>     -v            Show program version
>>>     -h            Print this message
>>>
>>>     -x            Extra debugging output
>>> Ugh!  What gibberish!
>>> The [tail] you have certainly does not taste like GNU [tail].  If you
>>> have
>>> a GNU [tail] stashed somewhere in your system, tell me its path below;
>>> otherwise cancel (^C) this installation, get a recent version of it 
>>> from
>>> ftp://www.fsf.org/gnu/textutils/
>>> compile & install it, then try this installation again.
>>> [/usr/bin/tail] ?
>>>
>>> The man page for version of tail installed is as follows:
>>> [localhost:local/bin/xgobi] nicolasb% man tail
>>> man: Formatting manual page...
>>>
>>> TAIL(1)                     System Reference Manual
>>> TAIL(1)
>>>
>>> NAME
>>>      tail - display the last part of a file
>>>
>>> SYNOPSIS
>>>      tail [-f | -F | -r] [-b number | -c number | -n number] 
>>> [file ...]
>>>
>>> DESCRIPTION
>>>      The tail utility displays the contents of file or, by default, 
>>> its
>>> stan-
>>>      dard input, to the standard output.
>>>
>>>      The display begins at a byte, line or 512-byte block location in
>>> the in-
>>>      put.  Numbers having a leading plus (``+'') sign are relative to
>>> the be-
>>>      ginning of the input, for example, ``-c +2'' starts the display 
>>> at
>>> the
>>>      second byte of the input.  Numbers having a leading minus (``-'')
>>> sign or
>>>      no explicit sign are relative to the end of the input, for
>>> example, ``-n
>>>      2'' displays the last two lines of the input.  The default
>>> starting loca-
>>>      tion is ``-n 10'', or the last 10 lines of the input.
>>>
>>>      The options are as follows:
>>>
>>>      -b number
>>>              The location is number 512-byte blocks.
>>>
>>>      -c number
>>>              The location is number bytes.
>>>
>>>      -f      The -f option causes tail to not stop when end of file is
>>>              reached, but rather to wait for additional data to be
>>> appended to
>>>              the input.  The -f option is ignored if the standard 
>>> input
>>> is a
>>>              pipe, but not if it is a FIFO.
>>>
>>>      -F      The -F option is the same as the -f option, except that
>>> every
>>>              five seconds tail will check to see if the file named on
>>> the com-
>>>              mand line has been shortened or moved (it is considered
>>> moved if
>>>              the inode or device number changes) and, if so, it will
>>> close the
>>>              current file, open the filename given, print out the
>>> entire con-
>>>              tents, and continue to wait for more data to be appended.
>>> This
>>>              option is used to follow log files though rotation by
>>> newsys-
>>>              log(8) or similar programs.
>>>
>>>      -n number
>>>              The location is number lines.
>>>
>>>      -r      The -r option causes the input to be displayed in reverse
>>> order,
>>>              by line.  Additionally, this option changes the meaning 
>>> of
>>> the
>>>              -b, -c and -n options.  When the -r option is specified,
>>> these
>>>              options specify the number of bytes, lines or 512-byte
>>> blocks to
>>>              display, instead of the bytes, lines or blocks from the
>>> beginning
>>>              or end of the input from which to begin the display.  The
>>> default
>>>              for the -r option is to display all of the input.
>>>
>>>      If more than a single file is specified, each file is preceded by
>>> a head-
>>>      er consisting of the string ``==> XXX <=='' where ``XXX'' is the
>>> name of
>>>      the file.
>>>
>>>      The tail utility exits 0 on success, and >0 if an error occurs.
>>>
>>> BUGS
>>>      When using the -F option, tail will not detect a file truncation
>>> if, be-
>>>      tween the truncation and the next check of the file size, data
>>> written to
>>>      the file make it larger than the last known file size.
>>>
>>> SEE ALSO
>>>      cat(1),  head(1),  sed(1)
>>>
>>> STANDARDS
>>>      The tail utility is expected to be a superset of the
>>> specification.  In
>>>      particular, the -b, -r and -F options are extensions to that
>>> standard.
>>>
>>>      The historic command line syntax of tail is supported by this
>>> implementa-
>>>      tion.  The only difference between this implementation and
>>> historic ver-
>>>      sions of , once the command line syntax translation has been 
>>> done,
>>> is
>>>      that the -b, -c and -n options modify the -r option, i.e. ``-r -c
>>> 4''
>>>      displays the last 4 characters of the last line of the input,
>>> while the
>>>      historic tail (using the historic syntax ``-4cr'') would ignore
>>> the -c
>>>      option and display the last 4 lines of the input.
>>>
>>> HISTORY
>>>      A tail command appeared in Version 7 AT&T UNIX.
>>>
>>> 4th Berkeley Distribution        June 6,
>>> 1993                                2
>>>
>>>
----------------------------------------------
Nicolas Bertrand
Department of Plant Sciences
University of Oxford
Oxford OX1 3RB

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

Re: [GeneX-dev] Tail (2)

[Harry M. <man...@ho...>]

Nicolas Bertrand wrote:
> 
> Hi
> 
> I could compile GNU tail from source. I did placed it in /usr/local/bin/
> The script was happier. The installation does not complete:

I think this is because the 1st time you weren;t using the GNU tail (from the text utils) - teh GNU utils have a specific response from the --version query which is how we test for them.

Your compile from scratch seems to have solved that.  Strange that it didn;t complain about the thers tho, unless they DO use the rest of the GNU utils.

ANyway...

> !! 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?

> !! 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

> !! 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/)

Possibly having to do with the above; if there wasn't a R subdir made, it couldn't copy things to it.  Does '/usr/local/genex/lib/R/library/hdarray/R/' exist?

> !! System Error: No such file or directory @ line: 2498  
> (/usr/bin/perl Makefile.PL)

Hmm - this is odd - it SHOULD do this if you've gotten this far...  
Jason - is there anything in Makefile.PL which would generate this??

> !! System Error: No such file or directory @ line: 2502  (make -s test)

Ditto for Jason.

> !! System Error: No such file or directory @ line: 2507  (make install)

Ditto for Jason.

> !! 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?  


Thanks for the feedback..

Harry


>   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>                        Name: genex-errors.txt
>    genex-errors.txt    Type: Plain Text (text/plain)
>                    Encoding: 7bit
> 
>   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> 
> Any ideas?
> 
> Best regards,
> 
> Nicolas
> 
> Begin forwarded message:
> 
> > From: Nicolas Bertrand <nic...@pl...>
> > Date: Wed Nov 14, 2001  11:44:04  Etc/GMT
> > To: gen...@li...
> > Subject:
> >
> > Hello
> >
> > I am installing genex server 1.0.4 on MacOSX10.1. The installation
> > script stalls while checking tail. I was wondering if anybody had such
> > problems.
> >
> >
> > This a snapshot of the installation screen:
> > [...]
> > Testing for a GNU [tail] ...
> > Unknown option: 1
> > Usage: head [-options] <url>...
> >     -m <method>   use method for the request (default is 'HEAD')
> >     -f            make request even if head believes method is illegal
> >     -b <base>     Use the specified URL as base
> >     -t <timeout>  Set timeout value
> >     -i <time>     Set the If-Modified-Since header on the request
> >     -c <conttype> use this content-type for POST, PUT, CHECKIN
> >     -a            Use text mode for content I/O
> >     -p <proxyurl> use this as a proxy
> >     -P            don't load proxy settings from environment
> >     -H <header>   send this HTTP header (you can specify several)
> >
> >     -u            Display method and URL before any response
> >     -U            Display request headers (implies -u)
> >     -s            Display response status code
> >     -S            Display response status chain
> >     -e            Display response headers
> >     -d            Do not display content
> >     -o <format>   Process HTML content in various ways
> >
> >     -v            Show program version
> >     -h            Print this message
> >
> >     -x            Extra debugging output
> > Ugh!  What gibberish!
> > The [tail] you have certainly does not taste like GNU [tail].  If you
> > have
> > a GNU [tail] stashed somewhere in your system, tell me its path below;
> > otherwise cancel (^C) this installation, get a recent version of it from
> > ftp://www.fsf.org/gnu/textutils/
> > compile & install it, then try this installation again.
> > [/usr/bin/tail] ?
> >
> > The man page for version of tail installed is as follows:
> > [localhost:local/bin/xgobi] nicolasb% man tail
> > man: Formatting manual page...
> >
> > TAIL(1)                     System Reference Manual
> > TAIL(1)
> >
> > NAME
> >      tail - display the last part of a file
> >
> > SYNOPSIS
> >      tail [-f | -F | -r] [-b number | -c number | -n number] [file ...]
> >
> > DESCRIPTION
> >      The tail utility displays the contents of file or, by default, its
> > stan-
> >      dard input, to the standard output.
> >
> >      The display begins at a byte, line or 512-byte block location in
> > the in-
> >      put.  Numbers having a leading plus (``+'') sign are relative to
> > the be-
> >      ginning of the input, for example, ``-c +2'' starts the display at
> > the
> >      second byte of the input.  Numbers having a leading minus (``-'')
> > sign or
> >      no explicit sign are relative to the end of the input, for
> > example, ``-n
> >      2'' displays the last two lines of the input.  The default
> > starting loca-
> >      tion is ``-n 10'', or the last 10 lines of the input.
> >
> >      The options are as follows:
> >
> >      -b number
> >              The location is number 512-byte blocks.
> >
> >      -c number
> >              The location is number bytes.
> >
> >      -f      The -f option causes tail to not stop when end of file is
> >              reached, but rather to wait for additional data to be
> > appended to
> >              the input.  The -f option is ignored if the standard input
> > is a
> >              pipe, but not if it is a FIFO.
> >
> >      -F      The -F option is the same as the -f option, except that
> > every
> >              five seconds tail will check to see if the file named on
> > the com-
> >              mand line has been shortened or moved (it is considered
> > moved if
> >              the inode or device number changes) and, if so, it will
> > close the
> >              current file, open the filename given, print out the
> > entire con-
> >              tents, and continue to wait for more data to be appended.
> > This
> >              option is used to follow log files though rotation by
> > newsys-
> >              log(8) or similar programs.
> >
> >      -n number
> >              The location is number lines.
> >
> >      -r      The -r option causes the input to be displayed in reverse
> > order,
> >              by line.  Additionally, this option changes the meaning of
> > the
> >              -b, -c and -n options.  When the -r option is specified,
> > these
> >              options specify the number of bytes, lines or 512-byte
> > blocks to
> >              display, instead of the bytes, lines or blocks from the
> > beginning
> >              or end of the input from which to begin the display.  The
> > default
> >              for the -r option is to display all of the input.
> >
> >      If more than a single file is specified, each file is preceded by
> > a head-
> >      er consisting of the string ``==> XXX <=='' where ``XXX'' is the
> > name of
> >      the file.
> >
> >      The tail utility exits 0 on success, and >0 if an error occurs.
> >
> > BUGS
> >      When using the -F option, tail will not detect a file truncation
> > if, be-
> >      tween the truncation and the next check of the file size, data
> > written to
> >      the file make it larger than the last known file size.
> >
> > SEE ALSO
> >      cat(1),  head(1),  sed(1)
> >
> > STANDARDS
> >      The tail utility is expected to be a superset of the
> > specification.  In
> >      particular, the -b, -r and -F options are extensions to that
> > standard.
> >
> >      The historic command line syntax of tail is supported by this
> > implementa-
> >      tion.  The only difference between this implementation and
> > historic ver-
> >      sions of , once the command line syntax translation has been done,
> > is
> >      that the -b, -c and -n options modify the -r option, i.e. ``-r -c
> > 4''
> >      displays the last 4 characters of the last line of the input,
> > while the
> >      historic tail (using the historic syntax ``-4cr'') would ignore
> > the -c
> >      option and display the last 4 lines of the input.
> >
> > HISTORY
> >      A tail command appeared in Version 7 AT&T UNIX.
> >
> > 4th Berkeley Distribution        June 6,
> > 1993                                2
> >
> >
> ----------------------------------------------
> Nicolas Bertrand
> Department of Plant Sciences
> University of Oxford
> Oxford OX1 3RB
> 
> Tel: ++1865 275 116
> ----------------------------------------------
> >

-- 
Cheers, Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho... 
                    [plain text appreciated]

Re: [GeneX-dev] Tail (2)

[<ja...@op...>]

"Nicolas Bertrand" <nic...@pl...> writes:

> I could compile GNU tail from source. I did placed it in
> /usr/local/bin/ The script was happier. The installation does not
> complete:
> 
> 
> 
> !! System Error:  @ line: 1829  ()
> 
> !! System Error: No such file or directory @ line: 2190  (cd /Users/Shared/Downloads/GeneX-Server-1.0.4/CyberT-dist; R SHLIB runa.c)
> 
> !! 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/)

It looks likes you don't have R installed.


> !! System Error: No such file or directory @ line: 2498  (/usr/bin/perl Makefile.PL)
> 
> !! System Error: No such file or directory @ line: 2502  (make -s test)
> 
> !! System Error: No such file or directory @ line: 2507  (make install)

This is trying to build the Perl API, but something goes wrong with
the command:

  '/usr/bin/perl Makefile.PL'

once that fails, you won't get a Makefile, so the make commands
fail. I need to check the return values...

Can you cd into the Genex/ sub-directory of the place where you
unpacked the GeneX-Server installation tarball, type that command
by hand, and send the output?

> !! System Error: No such file or directory @ line: 2631  (chmod ug+rw -R /usr/local/genex/rcluster/var/poqs)

Since R isn't installed, this probably won't work, Harry?

Cheers,
jas.

[GeneX-dev] Tail (2)

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

Hi

I could compile GNU tail from source. I did placed it in /usr/local/bin/
The script was happier. The installation does not complete:

[GeneX-dev] (no subject)

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

Hello

I am installing genex server 1.0.4 on MacOSX10.1. The installation 
script stalls while checking tail. I was wondering if anybody had such 
problems.


This a snapshot of the installation screen:
[...]
Testing for a GNU [tail] ...
Unknown option: 1
Usage: head [-options] <url>...
     -m <method>   use method for the request (default is 'HEAD')
     -f            make request even if head believes method is illegal
     -b <base>     Use the specified URL as base
     -t <timeout>  Set timeout value
     -i <time>     Set the If-Modified-Since header on the request
     -c <conttype> use this content-type for POST, PUT, CHECKIN
     -a            Use text mode for content I/O
     -p <proxyurl> use this as a proxy
     -P            don't load proxy settings from environment
     -H <header>   send this HTTP header (you can specify several)

     -u            Display method and URL before any response
     -U            Display request headers (implies -u)
     -s            Display response status code
     -S            Display response status chain
     -e            Display response headers
     -d            Do not display content
     -o <format>   Process HTML content in various ways

     -v            Show program version
     -h            Print this message

     -x            Extra debugging output
Ugh!  What gibberish!
The [tail] you have certainly does not taste like GNU [tail].  If you 
have
a GNU [tail] stashed somewhere in your system, tell me its path below;
otherwise cancel (^C) this installation, get a recent version of it from
ftp://www.fsf.org/gnu/textutils/
compile & install it, then try this installation again.
[/usr/bin/tail] ?

The man page for version of tail installed is as follows:
[localhost:local/bin/xgobi] nicolasb% man tail
man: Formatting manual page...

TAIL(1)                     System Reference Manual                    
TAIL(1)

NAME
      tail - display the last part of a file

SYNOPSIS
      tail [-f | -F | -r] [-b number | -c number | -n number] [file ...]

DESCRIPTION
      The tail utility displays the contents of file or, by default, its 
stan-
      dard input, to the standard output.

      The display begins at a byte, line or 512-byte block location in 
the in-
      put.  Numbers having a leading plus (``+'') sign are relative to 
the be-
      ginning of the input, for example, ``-c +2'' starts the display at 
the
      second byte of the input.  Numbers having a leading minus (``-'') 
sign or
      no explicit sign are relative to the end of the input, for 
example, ``-n
      2'' displays the last two lines of the input.  The default starting 
loca-
      tion is ``-n 10'', or the last 10 lines of the input.

      The options are as follows:

      -b number
              The location is number 512-byte blocks.

      -c number
              The location is number bytes.

      -f      The -f option causes tail to not stop when end of file is
              reached, but rather to wait for additional data to be 
appended to
              the input.  The -f option is ignored if the standard input 
is a
              pipe, but not if it is a FIFO.

      -F      The -F option is the same as the -f option, except that 
every
              five seconds tail will check to see if the file named on 
the com-
              mand line has been shortened or moved (it is considered 
moved if
              the inode or device number changes) and, if so, it will 
close the
              current file, open the filename given, print out the entire 
con-
              tents, and continue to wait for more data to be appended.  
This
              option is used to follow log files though rotation by 
newsys-
              log(8) or similar programs.

      -n number
              The location is number lines.

      -r      The -r option causes the input to be displayed in reverse 
order,
              by line.  Additionally, this option changes the meaning of 
the
              -b, -c and -n options.  When the -r option is specified, 
these
              options specify the number of bytes, lines or 512-byte 
blocks to
              display, instead of the bytes, lines or blocks from the 
beginning
              or end of the input from which to begin the display.  The 
default
              for the -r option is to display all of the input.

      If more than a single file is specified, each file is preceded by a 
head-
      er consisting of the string ``==> XXX <=='' where ``XXX'' is the 
name of
      the file.

      The tail utility exits 0 on success, and >0 if an error occurs.

BUGS
      When using the -F option, tail will not detect a file truncation 
if, be-
      tween the truncation and the next check of the file size, data 
written to
      the file make it larger than the last known file size.

SEE ALSO
      cat(1),  head(1),  sed(1)

STANDARDS
      The tail utility is expected to be a superset of the  
specification.  In
      particular, the -b, -r and -F options are extensions to that 
standard.

      The historic command line syntax of tail is supported by this 
implementa-
      tion.  The only difference between this implementation and historic 
ver-
      sions of , once the command line syntax translation has been done, 
is
      that the -b, -c and -n options modify the -r option, i.e. ``-r -c 
4''
      displays the last 4 characters of the last line of the input, while 
the
      historic tail (using the historic syntax ``-4cr'') would ignore 
the -c
      option and display the last 4 lines of the input.

HISTORY
      A tail command appeared in Version 7 AT&T UNIX.

4th Berkeley Distribution        June 6, 
1993                                2


----------------------------------------------
Nicolas Bertrand
Department of Plant Sciences
University of Oxford
Oxford OX1 3RB

Tel: ++1865 275 116
----------------------------------------------

Re: [GeneX-dev] Help

[<ja...@op...>]

"Harry Mangalam" <man...@ho...> writes:

> The original is probably still on your machine in: 
> 
> /your/install/dir/gxquery/fetch_spot.pl
> 
> If you're running on a Linux sys, use 'locate fetch_spot.pl'

Harry is correct, it is in the install dir, but that might be the one
you modified...

All .pl files are generated from a .pl.in file of the same name,
i.e. fetch_spot.pl.in, in the GeneX-Server installation package.

If you go to the directory where you untarred the package, you should
find a fresh copy of fetch_spot.pl. If this is the one you altered, no
problem, just delete the .pl file and run the configure.pl script. It
will recreate a fresh fetch_spot.pl for you.

jas.

Re: [GeneX-dev] Help

[Harry M. <man...@ho...>]

The original is probably still on your machine in: 

/your/install/dir/gxquery/fetch_spot.pl

If you're running on a Linux sys, use 'locate fetch_spot.pl'

hjm


> Matthew Lin wrote:
> 
> Hi,
>         I wonder if it is possible for you to send me a copy of "fetch_spot.pl" file. I tried to modify the file, but it turned out now that the file is not working. I forgot to backup the file
> before the modification. Please send me a copy of the file thank you. "fetch_spot.pl" at /var/www/cgi-bin/genex/gxquery/fetch_spot.pl
> I used all the default setting when I installed GeneX
> 
> 
> 
> Matt
> 11:09pm
> 11/11/2001

-- 
Cheers, Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho... 
                    [plain text appreciated]

[GeneX-dev] Help

[Matthew L. <ma...@jh...>]

Hi,
        I wonder if it is possible for you to send me a copy of =
"fetch_spot.pl" file. I tried to modify the file, but it turned out now =
that the file is not working. I forgot to backup the file before the =
modification. Please send me a copy of the file thank you. =
"fetch_spot.pl" at /var/www/cgi-bin/genex/gxquery/fetch_spot.pl
I used all the default setting when I installed GeneX



Matt
11:09pm
11/11/2001