bugGNU Octave - Bugs: bug #45338, communications package fails to...

 
 

bug #45338: communications package fails to link with libhdf5 on Windows

Submitted by:  None
Submitted on:  Wed 17 Jun 2015 07:43:11 AM UTC  
 
Category: Octave Forge PackageSeverity: 3 - Normal
Priority: 5 - NormalItem Group: Installation Failure
Status: InvalidAssigned to: Mike Miller <mtmiller>
Originator Name: MatthiasOriginator Email: -unavailable-
Open/Closed: ClosedRelease: 4.0.0
Operating System: Microsoft Windows

Add a New Comment(Rich Markup)
   

You are not logged in

Please log in, so followups can be emailed to you.

 

(Jump to the original submission Jump to the original submission)

Wed 29 Jul 2015 07:19:15 PM UTC, comment #16:

I am very happy to help you determine what the problem is, either on the help mailing list or on a bug report. If you would like it to be a bug report, I would much prefer if you opened a new bug report. You are not installing on Windows, so your installation error must be different than that reported here.

Mike Miller <mtmiller>
Project AdministratorIn charge of this item.
Wed 29 Jul 2015 06:56:56 PM UTC, comment #15:

I have a similar problem to this, however I'm on CentOS 6.6 64-bit. I've installed all dependencies (hdf5, hdf5-devel, hdf5-static, etc.) until all warning messages emitted by `configure` were resolved. I then ran through the `make; make check; sudo make install` routines. Not all tests passed, but far more did than on my other system (also CentOS 6.6 64-bit which has this problem too, but then somehow resolved itself).

I can get octave to run and install `control` and `signal` from the forge, but it cannot install the `communications` package. The installation log is listed below. I see posts for other OSs which always get chalked up to "local configuration" like this one, but it's always revolving around compiling Octave from source and the communications package.

Has anyone else come across a repeatable-working solution for this package?

octave:1> pkg install -forge -verbose communications
mkdir (/tmp/oct-oN7t9e)
untar (/tmp/communications-1.2.1.tar.gz, /tmp/oct-oN7t9e)
checking for mkoctfile... /usr/local/bin/mkoctfile-4.0.0 --verbose
checking for octave... /usr/local/bin/octave-4.0.0
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for a sed that does not truncate output... /bin/sed
checking for Octave HDF5 preprocessor flags...
checking for Octave HDF5 linker flags...
checking for Octave HDF5 libraries... -lhdf5
checking for octave_hdf5_id type... no
checking for octave_base_value::gripe_load and octave_base_value::gripe_save... no
checking whether octave_base_value::print is const-qualified... no
configure: creating ./config.status
config.status: creating Makefile
make: Entering directory `/tmp/oct-oN7t9e/communications-1.2.1/src'
/usr/local/bin/mkoctfile-4.0.0 --verbose -DGALOIS_DISP_PRIVATES _errcore_.cc -o _errcore_.oct
/usr/local/bin/mkoctfile-4.0.0 --verbose -DGALOIS_DISP_PRIVATES _gfweight_.cc -o _gfweight_.oct
/usr/local/bin/mkoctfile-4.0.0 --verbose -DGALOIS_DISP_PRIVATES cyclgen.cc -o cyclgen.oct
/usr/local/bin/mkoctfile-4.0.0 --verbose -DGALOIS_DISP_PRIVATES cyclpoly.cc -o cyclpoly.oct
g++ -c -fPIC -I/usr/local/include/octave-4.0.0/octave/.. -I/usr/local/include/octave-4.0.0/octave -I/usr/local/include -pthread -fopenmp -g -O2 -DGALOIS_DISP_PRIVATES _errcore_.cc -o _errcore_.o
g++ -c -fPIC -I/usr/local/include/octave-4.0.0/octave/.. -I/usr/local/include/octave-4.0.0/octave -I/usr/local/include -pthread -fopenmp -g -O2 -DGALOIS_DISP_PRIVATES _gfweight_.cc -o _gfweight_.o
g++ -c -fPIC -I/usr/local/include/octave-4.0.0/octave/.. -I/usr/local/include/octave-4.0.0/octave -I/usr/local/include -pthread -fopenmp -g -O2 -DGALOIS_DISP_PRIVATES cyclgen.cc -o cyclgen.o
g++ -c -fPIC -I/usr/local/include/octave-4.0.0/octave/.. -I/usr/local/include/octave-4.0.0/octave -I/usr/local/include -pthread -fopenmp -g -O2 -DGALOIS_DISP_PRIVATES cyclpoly.cc -o cyclpoly.o
g++ -shared -Wl,-Bsymbolic -o _gfweight_.oct _gfweight_.o -L/usr/local/lib/octave/4.0.0 -L/usr/local/lib -loctinterp -loctave
g++ -shared -Wl,-Bsymbolic -o _errcore_.oct _errcore_.o -L/usr/local/lib/octave/4.0.0 -L/usr/local/lib -loctinterp -loctave
/usr/local/bin/mkoctfile-4.0.0 --verbose -DGALOIS_DISP_PRIVATES genqamdemod.cc -o genqamdemod.oct
g++ -c -fPIC -I/usr/local/include/octave-4.0.0/octave/.. -I/usr/local/include/octave-4.0.0/octave -I/usr/local/include -pthread -fopenmp -g -O2 -DGALOIS_DISP_PRIVATES genqamdemod.cc -o genqamdemod.o
/usr/local/bin/mkoctfile-4.0.0 --verbose -DGALOIS_DISP_PRIVATES -c galois-def.cc -o galois-def.o
g++ -c -fPIC -I/usr/local/include/octave-4.0.0/octave/.. -I/usr/local/include/octave-4.0.0/octave -I/usr/local/include -pthread -fopenmp -g -O2 -DGALOIS_DISP_PRIVATES galois-def.cc -o galois-def.o
g++ -shared -Wl,-Bsymbolic -o cyclpoly.oct cyclpoly.o -L/usr/local/lib/octave/4.0.0 -L/usr/local/lib -loctinterp -loctave
g++ -shared -Wl,-Bsymbolic -o cyclgen.oct cyclgen.o -L/usr/local/lib/octave/4.0.0 -L/usr/local/lib -loctinterp -loctave
/usr/local/bin/mkoctfile-4.0.0 --verbose -DGALOIS_DISP_PRIVATES -c galois.cc -o galois.o
g++ -c -fPIC -I/usr/local/include/octave-4.0.0/octave/.. -I/usr/local/include/octave-4.0.0/octave -I/usr/local/include -pthread -fopenmp -g -O2 -DGALOIS_DISP_PRIVATES galois.cc -o galois.o
/usr/local/bin/mkoctfile-4.0.0 --verbose -DGALOIS_DISP_PRIVATES -c galoisfield.cc -o galoisfield.o
g++ -c -fPIC -I/usr/local/include/octave-4.0.0/octave/.. -I/usr/local/include/octave-4.0.0/octave -I/usr/local/include -pthread -fopenmp -g -O2 -DGALOIS_DISP_PRIVATES galoisfield.cc -o galoisfield.o
/usr/local/bin/mkoctfile-4.0.0 --verbose -DGALOIS_DISP_PRIVATES -c gf.cc -o gf.o
g++ -c -fPIC -I/usr/local/include/octave-4.0.0/octave/.. -I/usr/local/include/octave-4.0.0/octave -I/usr/local/include -pthread -fopenmp -g -O2 -DGALOIS_DISP_PRIVATES gf.cc -o gf.o
/usr/local/bin/mkoctfile-4.0.0 --verbose -DGALOIS_DISP_PRIVATES -c op-gm-gm.cc -o op-gm-gm.o
g++ -c -fPIC -I/usr/local/include/octave-4.0.0/octave/.. -I/usr/local/include/octave-4.0.0/octave -I/usr/local/include -pthread -fopenmp -g -O2 -DGALOIS_DISP_PRIVATES op-gm-gm.cc -o op-gm-gm.o
In file included from gf.cc:41:
ov-galois.h:41: error: ‘hid_t’ does not name a type
make: *** [gf.o] Error 1
make: *** Waiting for unfinished jobs....
g++ -shared -Wl,-Bsymbolic -o genqamdemod.oct genqamdemod.o -L/usr/local/lib/octave/4.0.0 -L/usr/local/lib -loctinterp -loctave
In file included from op-gm-gm.cc:26:
ov-galois.h:41: error: ‘hid_t’ does not name a type
make: *** [op-gm-gm.o] Error 1
make: Leaving directory `/tmp/oct-oN7t9e/communications-1.2.1/src'

Anonymous
Wed 01 Jul 2015 03:32:16 AM UTC, comment #14:

Closing as invalid since the reporter was able to get the package working and identified that the error is due to a local configuration problem.

Mike Miller <mtmiller>
Project AdministratorIn charge of this item.
Fri 19 Jun 2015 04:00:12 PM UTC, comment #13:

The shortcuts on the start menu run octave.vbs in the c:\octave\octave-4.0.0 directory.

You could try modify it:

wshSystemEnv("PATH") = OctavePath & "\bin;" & wshSystemEnv("PATH")

change to:

wshSystemEnv("PATH") = OctavePath & "\bin"

John Donoghue <lostbard>
Project Member
Fri 19 Jun 2015 03:28:55 PM UTC, comment #12:

Okay, I had a version installed from two days ago. The current version I just downloaded has all packages included (although wrong versions, but that is also already reported)
Now I understand why it works with the build_packages.m and not when I install it manually.

It seems that in my PATH variable there is another libstdc++-6.dll which octave tries to use.

Is there a way to bypass the use of my PATH and only use octave's folders?

Matthias <niowniow>
Fri 19 Jun 2015 02:04:23 PM UTC, comment #11:

There is/was already a report for signal, general and io.

Looking at a new install of octave from the official version, I have a communications package that is correct.

The issue (using the script) is that since signal fails its install, communications will fail.

If you change the versions in the build_packages.m file to be correct, it should work.

Communications should also work, but will because it is precompiled in the src folder rather than needing to be compiled in forge install.

John Donoghue <lostbard>
Project Member
Fri 19 Jun 2015 01:08:05 PM UTC, comment #10:

I did a fresh install and realized, that the C:/Octave/Octave-4.0.0/src folder does not contain the general, signal and communications packages. So they could not be installed by the build_packages.m script.

Should I create a new bug report?

Using different quotes gives the same results for me.

PATH variable, only octave-related:

It seams to be a problem with the octave-gui exe, since following works:

Matthias <niowniow>
Fri 19 Jun 2015 11:41:25 AM UTC, comment #9:

Sorry, I meant in the bin directory.

Try the system command with different quotes, as the first method doesn't produce the correct result.
On mine:

Also maybe try running in octave:
getenv('PATH')

John Donoghue <lostbard>
Project Member
Fri 19 Jun 2015 07:36:27 AM UTC, comment #8:

I tried the commands as well.

I had to be in the C:/Octave/Octave-4.0.0/bin folder to run it.

It didn't matter if I used ' or ". Both gave me the following error:

Procedure entry point "_ZSt24_throw_out_of_range_fmtPKcz" was not found in DLL "libstdc++-6.dll"

I am running Windows 7 Professional by the way.

Running the other command in octave works and returns

I used the installer from the website as well. Should I reinstall it?

Matthias <niowniow>
Fri 19 Jun 2015 12:01:56 AM UTC, comment #7:

I had to swap the ' and " to run on mine:

in octave:

system('C:/Octave/Octave-4.0.0/bin/octave-4.0.0.exe --norc --no-history --silent --eval "disp(octave_config_info.HDF5_LIBS)"');

from command line (need to be in c:\octave\octave-4.0.0 folder for it to find the octave libs to run)

C:/Octave/Octave-4.0.0/bin/octave-4.0.0.exe --norc --no-history --silent --eval "disp(octave_config_info.HDF5_LIBS)"

John Donoghue <lostbard>
Project Member
Thu 18 Jun 2015 11:00:52 PM UTC, comment #6:

So the problematic line is the following, where Matthias sees:

and John sees (and I expect):

This string comes from the following command, should be runnable from a Windows terminal, maybe needs backslashes instead of slashes:

And then, this should also be runnable from within Octave via a bash shell, so something like this should return the same string:

Mike Miller <mtmiller>
Project AdministratorIn charge of this item.
Thu 18 Jun 2015 07:53:40 PM UTC, comment #5:

For reference configure on mine installed from the official 4.0.0 installer, and run from the Start men Octave (GUI) link:

John Donoghue <lostbard>
Project Member
Thu 18 Jun 2015 05:15:09 PM UTC, comment #4:

Tell me what to do and I'll be glad to help

Matthias <niowniow>
Thu 18 Jun 2015 02:13:42 PM UTC, comment #3:

There is something wrong with the configure step in the output you pasted. I'd like to take a look at this when I have some time to set up a Windows VM again, let me know if you're willing to help test things for me.

Mike Miller <mtmiller>
Project AdministratorIn charge of this item.
Thu 18 Jun 2015 08:30:47 AM UTC, comment #2:

Hey Mike,
thanks for your support!

I started with the build_packages.m script and encountered errors. not only for the communications pkg. I couldn't figure out why some packages could be installed and some not.
Therefore I wanted to install only the ones I need.

Today, I tried build_packages.m again, and it worked for all packages. I cannot say what has changed unfortunatly. The only thing I noticed is that I still have the packages in the lib and share folder from rc-4 on my harddisk. May this affect the installation?
Nonetheless I attach the information you asked for, since I previously tried to install communications manually and still had errors

Thank you for your quick response. Now everything works fine.

Matthias <niowniow>
Wed 17 Jun 2015 03:00:36 PM UTC, comment #1:

Thanks for your bug report. Have you tried installing it via the build_packages.m script that comes with the Octave installer?

Can you run the following, more information will be printed and in the right order to be more useful to us:

and paste the output here. I'd also like to see what you have for the following values:

Mike Miller <mtmiller>
Project AdministratorIn charge of this item.
Wed 17 Jun 2015 07:43:11 AM UTC, original submission:

Hi,

I am unable to install the communications package. The make command issues an error, see below. I installed signal and control packages. With the octave-4.0.0-rc4 it worked on my machine.

I use the command

And get the following error

Anonymous

 

(Note: upload size limit is set to 16384 kB, after insertion of the required escape characters.)

Attach File(s):
   
   
Comment:
   

No files currently attached

 

Depends on the following items: None found

Items that depend on this one: None found

 

Carbon-Copy List
  • -unavailable- added by lostbard (Posted a comment)
  • -unavailable- added by niowniow (Posted a comment)
  • -unavailable- added by mtmiller (Posted a comment)
  • -unavailable- added by None (Submitted the item)
  •  

    Do you think this task is very important?
    If so, you can click here to add your encouragement to it.
    This task has 0 encouragements so far.

    Only project members can vote.

     

    Please enter the title of George Orwell's famous dystopian book (it's a date):

     

     

    Follow 5 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Wed 01 Jul 2015 03:32:16 AM UTCmtmillerOpen/ClosedOpen=>Closed
    Wed 01 Jul 2015 03:32:15 AM UTCmtmillerStatusNeed Info=>Invalid
    Thu 18 Jun 2015 02:13:42 PM UTCmtmillerSummarycommunications package fails to install=>communications package fails to link with libhdf5 on Windows
    Wed 17 Jun 2015 03:00:36 PM UTCmtmillerStatusNone=>Need Info
      Assigned toNone=>mtmiller

    Back to the top


    Powered by Savane 3.1-cleanup1