Installing Loaddap for Matlab 7.13 (R2011b)

[Marcello Magaldi]

Hello I am trying to build loaddap for my new version of Matlab,
specifically 7.13.0.564 (R2011b) on an Ubuntu 64 machine. I am using
correctly the "--with-matlab" and "--prefix" options. Anyhow the
configure script ends saying

"configure: error: cannot determine Matlab version number".

It seems to me that the macros used in ./configure to identify the
different versions of Matlab isn't working on Ubuntu.

Any help?

Thanks in advance,
Marcello

[Daniel Holloway]

James, or M4 gurus...

The problem is in the conf/matlabver.m4 file, (at least IMO).
Can you fix the regex's that identify matlab versions to allow the
version.

Dan

[Gallagher James]

Marcello,

I think this will fix your problem:

[Gallagher James]

On Nov 16, 2011, at 9:44 AM, Marcello Magaldi wrote:

> Dear James,
>
> Thank you for the new loaddap version. The configure script runs thru
> even if I am a little bit puzzled as I am getting at the end:
>
> checking for DAP... no
> checking for DAP_CLIENT... no
> checking for DAP_SERVER... no
> checking for dap-config...
> /home/magaldi/Softwares/Libdap/libdap_3_11_1/bin/dap-config
> checking for libdap version >= 3.8.0... yes

This is saying that DAP, DAP_CLIENT, ..., were not found in the package manager but the dap-config script was found and the verion of libdap it references is OK.

> configure: creating ./config.status
> config.status: creating Makefile
> config.status: creating config.h
> config.status: config.h is unchanged
> config.status: executing depfiles commands
> config.status: executing libtool commands
>
> Anyhow when I am then running "make check" I am getting the following error:

The tests are completely broken. We need to fix those ASAP.

>
> Warning: You are using gcc version "4.6.1-9ubuntu3)". The version
> currently supported with MEX is "4.3.4".
> For a list of currently supported compilers see:
> http://www.mathworks.com/support/compilers/current_release/
>
> ./loaddap.c: In function ‘mexFunction’:
> ./loaddap.c:600:9: warning: ignoring return value of ‘fread’, declared
> with attribute warn_unused_result [-Wunused-result]
> ./loaddap.c: In function ‘init’:
> ./loaddap.c:400:10: warning: ignoring return value of ‘fgets’,
> declared with attribute warn_unused_result [-Wunused-result]
> ./process_values.c: In function ‘read_aggregate’:
> ./process_values.c:394:7: warning: ignoring return value of ‘fgets’,
> declared with attribute warn_unused_result [-Wunused-result]
> ./process_values.c: In function ‘do_array’:
> ./process_values.c:691:8: warning: ignoring return value of ‘fread’,
> declared with attribute warn_unused_result [-Wunused-result]
> ./process_values.c: In function ‘read_vec_descript’:
> ./process_values.c:310:7: warning: ignoring return value of ‘fgets’,
> declared with attribute warn_unused_result [-Wunused-result]
> ./process_values.c: In function ‘read_array_dims’:
> ./process_values.c:341:7: warning: ignoring return value of ‘fgets’,
> declared with attribute warn_unused_result [-Wunused-result]
> ./process_values.c: In function ‘read_string_value’:
> ./process_values.c:556:7: warning: ignoring return value of ‘fgets’,
> declared with attribute warn_unused_result [-Wunused-result]
> ./process_values.c:571:8: warning: ignoring return value of ‘fgets’,
> declared with attribute warn_unused_result [-Wunused-result]
> ./process_values.c: In function ‘do_float’:
> ./process_values.c:479:8: warning: ignoring return value of ‘fread’,
> declared with attribute warn_unused_result [-Wunused-result]
> ./process_values.c:499:8: warning: ignoring return value of ‘fread’,
> declared with attribute warn_unused_result [-Wunused-result]
> ./process_values.c: In function ‘do_error’:
> ./process_values.c:440:7: warning: ignoring return value of ‘fgets’,
> declared with attribute warn_unused_result [-Wunused-result]
> ./process_values.c:443:8: warning: ignoring return value of ‘fgets’,
> declared with attribute warn_unused_result [-Wunused-result]
> make check-DEJAGNU
> make[1]: Entering directory `/home/magaldi/Softwares/Loaddap/tmp/loaddap-3.7.1'
> srcdir=`CDPATH="${ZSH_VERSION+.}:" && cd . && pwd`; export srcdir; \
> EXPECT=expect; export EXPECT; \
> runtest=runtest; \
> if /bin/bash -c "$runtest --version" > /dev/null 2>&1; then \
> exit_status=0; l='writedap'; for tool in $l; do \
> if $runtest --tool $tool --srcdir testsuite ; \
> then :; else exit_status=1; fi; \
> done; \
> else echo "WARNING: could not find \`runtest'" 1>&2; :;\
> fi; \
> exit $exit_status
> WARNING: Couldn't find tool init file
> Test Run By root on Wed Nov 16 17:34:18 2011
> Native configuration is x86_64-unknown-linux-gnu
>
> === writedap tests ===
>
> Schedule of variations:
> unix
>
> Running target unix
> Using /usr/share/dejagnu/baseboards/unix.exp as board description file
> for target.
> Using /usr/share/dejagnu/config/unix.exp as generic interface file for target.
> Using testsuite/config/unix.exp as tool-and-target-specific interface file.
> Running testsuite/writedap.1/data.1.exp ...
> FAIL: data: : fnoc1
> FAIL: data: : fnoc1 & fnoc2
> FAIL: data: : fnoc1 & fnoc2 (using -c)
> FAIL: data: : fnoc3 (two variables)
> FAIL: data: : fnoc3 & fnoc2
> Running testsuite/writedap.1/options.1.exp ...
> FAIL: option: -d: coads
> XFAIL: option: -d: dsp 2
> Running testsuite/writedap.1/options.2.exp ...
> FAIL: option: -f: coads
> XFAIL: option: -f: dsp 2
> Running testsuite/writedap.1/options.3.exp ...
> FAIL: option: (none): coads
> XFAIL: option: (none): dsp 2
> Running testsuite/writedap.1/options.4.exp ...
> FAIL: option: -v: coads
> XFAIL: option: -v: dsp 2
>
> === writedap Summary ===
>
> # of unexpected failures 9
> # of expected failures 4
> writedap test suite 1.0
> make[1]: *** [check-DEJAGNU] Error 1
> make[1]: Leaving directory `/home/magaldi/Softwares/Loaddap/tmp/loaddap-3.7.1'
> make: *** [check-am] Error 2

Yup, these all fail, but install the executable anyway - the tests themselves are broken. Of course, this is hardly confidence inspiringm I know, but we're working to get this client back into decent shape.

Let me know how it goes.

James
>
>
> Any help will be appreciated,
> Marcello

>> Please let me know.
>>
>> James
>>>
>>> Thanks in advance,
>>> Marcello
>>
>> --
>> James Gallagher
>> jgallagher at opendap.org
>> 406.723.8663
>>
>>
>>
>
>
>
> --
> ----
> Marcello G. Magaldi
> ---------------------------------------------------------------------------------------
> Consiglio Nazionale delle Ricerche (CNR)
> Istituto di Scienze Marine (ISMAR)
> U.O.S. di Pozzuolo di Lerici (SP)
> Forte Santa Teresa, 19032 Lerici (SP), Italy
>
> e-mail: marcello...@sp.ismar.cnr.it
> phone: +39 (0187) 978-306
> fax: +39 (0187) 970-585
> webpage: http://magaldi.sp.ismar.cnr.it
> ---------------------------------------------------------------------------------------

--
James Gallagher
jgallagher at opendap.org
406.723.8663

[Marcello Magaldi]

Hi James,

first of all thank you for your help. The make install runs thru
without errors. Anyway when I am testing in matlab with a simple
command like

x = loaddap('-A', 'http://test.opendap.org/opendap/data/nc/
coads_climatology.nc')

I am getting

Error: Communication with the loaddap helper application writedap:
No such file or directory
This may be due to an earlier error. However, if there was no previous
error message, please report this to support at opendap.org.

x =

1x1 struct array with no fields.

And also in terminal something like

/home/magaldi/Softwares/Loaddap/loaddap_3_7_1/bin/writedap: /usr/local/
MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11'
not found (required by /home/magaldi/Softwares/Loaddap/loaddap_3_7_1/
bin/writedap)
/home/magaldi/Softwares/Loaddap/loaddap_3_7_1/bin/writedap: /usr/local/
MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11'
not found (required by /home/magaldi/Softwares/Libdap/libdap_3_11_1/
lib/libdapclient.so.3)
/home/magaldi/Softwares/Loaddap/loaddap_3_7_1/bin/writedap: /usr/local/
MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11'
not found (required by /home/magaldi/Softwares/Libdap/libdap_3_11_1/
lib/libdap.so.11)
/home/magaldi/Softwares/Loaddap/loaddap_3_7_1/bin/writedap: /usr/local/
MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.15'
not found (required by /home/magaldi/Softwares/Libdap/libdap_3_11_1/
lib/libdap.so.11)

> > e-mail: marcello.maga...@sp.ismar.cnr.it

[Marcello Magaldi]

Ok... I got it to work... The libstdc++.so.6 in the Matlab dir did not
contain the newer versions GLIBCXX_3.4.11 and 15.

I copied the more recent /usr/lib/x86_64-linux-gnu/libstdc++.so.6 and
everything looks fine so far.

Thanks again,
Marcello

[Gallagher James]

On Nov 17, 2011, at 3:24 AM, Marcello Magaldi wrote:

> Ok... I got it to work... The libstdc++.so.6 in the Matlab dir did not
> contain the newer versions GLIBCXX_3.4.11 and 15.
>
> I copied the more recent /usr/lib/x86_64-linux-gnu/libstdc++.so.6 and
> everything looks fine so far.

Great!

James

[surm...@gmail.com]

Hi , I have installed libDAP and loadDAP in my laptop with out error. My matlab version is R2011b.
 When I am testing in matlab with a simple

command like

 x = loaddap('-A', 'http://test.opendap.org/opendap/data/nc/
coads_climatology.nc')

I am getting

Error: Communication with the loaddap helper application writedap:
No such file or directory
This may be due to an earlier error. However, if there was no previous
error message, please report this to support at opendap.org.

x =

1x1 struct array with no fields.

And also in terminal something like

usr/local/bin/writedap: /usr/local/MATLAB/R2011b/sys/os/glnx86/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/local/bin/writedap)
/usr/local/bin/writedap: /usr/local/MATLAB/R2011b/sys/os/glnx86/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/local/lib/libdapclient.so.3)
/usr/local/bin/writedap: /usr/local/MATLAB/R2011b/sys/os/glnx86/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/local/lib/libdap.so.10)

Please help me to overcome this problem.
Thank you in advance.