Pkg install struct - octave 5.1 from flatpak, mint 18/ubuntu

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Pkg install struct - octave 5.1 from flatpak, mint 18/ubuntu

phofman
Hi,

upon installing octave 5.1 from flatpak I wanted to recompile the
packages needed for my project for new octave. Previously I was using
octave 4.2.2, all packages compiled in home/octave. OS Mint 18 = Ubuntu
16.04. I uninstalled all packages (pkg uninstall) and started installing
again one by one.

When installing struct I get the following error:

octave:13> pkg install -forge struct
In file included from error-helpers.cc:22:
error-helpers.h:31:22: error: ‘octave_execution_exception’ does not name
a type; did you mean ‘make_execution_exception’?
  void c_verror (const octave_execution_exception&, const char *, ...);
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~
                       make_execution_exception
error-helpers.cc:36:17: error: ‘octave_execution_exception’ does not
name a type; did you mean ‘make_execution_exception’?
  c_verror (const octave_execution_exception&, const char *fmt, ...)
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~
                  make_execution_exception
error-helpers.cc: In function ‘void _p_error(const char*, ...)’:
error-helpers.cc:60:8: error: ‘cerr’ is not a member of ‘std’
    std::cerr << msg;
         ^~~~
error-helpers.cc:60:8: note: ‘std::cerr’ is defined in header
‘<iostream>’; did you forget to ‘#include <iostream>’?
error-helpers.cc:23:1:
+#include <iostream>

error-helpers.cc:60:8:
    std::cerr << msg;
         ^~~~
make: *** [Makefile:40: error-helpers.o] Error 1
make: Entering directory „/tmp/oct-BOaV4z/struct-1.0.15/src“
CXXFLAGS="-O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector-strong -grecord-gcc-switches
-Wno-deprecated-declarations" /app/bin/mkoctfile-5.1.0 -c error-helpers.cc
make: Leaving directory „/tmp/oct-BOaV4z/struct-1.0.15/src“

pkg: error running `make' for the struct package.
error: called from
     configure_make at line 99 column 9
     install at line 184 column 7
     pkg at line 441 column 9

Thanks a lot for any hints.

Best regards,

Pavel.


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Re: Pkg install struct - octave 5.1 from flatpak, mint 18/ubuntu

Mike Miller-4
On Tue, Mar 05, 2019 at 21:35:11 +0100, pavel wrote:
> When installing struct I get the following error:
[…]
> pkg: error running `make' for the struct package.
> error: called from
>     configure_make at line 99 column 9
>     install at line 184 column 7
>     pkg at line 441 column 9

Hi Pavel,

The current release of the struct package (1.0.15) isn't compatible with
Octave 5 yet.

If you need the struct package you can go back to using Octave 4.2 as
provided by your OS, or you can try to install a development snapshot of
the struct package from the repository [1] into Octave 5.1.

This is a known issue, you don't need to report anything, just be
patient until the package maintainers make a new release for Octave 5.

HTH,

--
mike



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Re: Pkg install struct - octave 5.1 from flatpak, mint 18/ubuntu

phofman
Hi Mike,


> If you need the struct package you can go back to using Octave 4.2 as
> provided by your OS, or you can try to install a development snapshot of
> the struct package from the repository [1] into Octave 5.1.
>
> This is a known issue, you don't need to report anything, just be
> patient until the package maintainers make a new release for Octave 5.

Thanks for the info. All the packages I use are included in the
pre-compiled build of windows64 octave 5.1. From that I concluded those
packages are already compatible with octave 5.1 and I went ahead with
octave upgrade in linux. Or perhaps are (some of) those packages
included in the windows build their devel snapshots?

Thanks a lot,

Pavel.


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Re: Pkg install struct - octave 5.1 from flatpak, mint 18/ubuntu

mmuetzel
phofman wrote
> Thanks for the info. All the packages I use are included in the
> pre-compiled build of windows64 octave 5.1. From that I concluded those
> packages are already compatible with octave 5.1 and I went ahead with
> octave upgrade in linux. Or perhaps are (some of) those packages
> included in the windows build their devel snapshots?

Some of the Octave Forge packages are patched for the Windows installer.
Either to make them cross-compile or to fix compatibility issues with
Octave. "of-signal" is one of them:
https://hg.octave.org/mxe-octave/file/tip/src

Markus



--
Sent from: http://octave.1599824.n4.nabble.com/Octave-General-f1599825.html


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Re: Pkg install struct - octave 5.1 from flatpak, mint 18/ubuntu

phofman
Hi Markus,

>
> Some of the Octave Forge packages are patched for the Windows installer.
> Either to make them cross-compile or to fix compatibility issues with
> Octave. "of-signal" is one of them:
> https://hg.octave.org/mxe-octave/file/tip/src

Are the windows-installer patches part of the packages upstream repos?
How is the windows installer built? Any extra patches somewhere outside
the main repos?

Fortunately the struct package seems to have the patches placed into the
main branch - the commit
https://sourceforge.net/p/octave/struct/ci/320e8484cd10b73cef40c9b51d99ebbb0c7b8360/ 
(dated after the stable release) will probably fix my problem. I will
try the HEAD/devel version then.

Best regards,

Pavel.






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Re: Pkg install struct - octave 5.1 from flatpak, mint 18/ubuntu

mmuetzel
Am 06. März 2019 um 11:09 Uhr schrieb "Pavel Hofman"

> Hi Markus,
>
> >
> > Some of the Octave Forge packages are patched for the Windows installer.
> > Either to make them cross-compile or to fix compatibility issues with
> > Octave. "of-signal" is one of them:
> > https://hg.octave.org/mxe-octave/file/tip/src
>
> Are the windows-installer patches part of the packages upstream repos?
> How is the windows installer built? Any extra patches somewhere outside
> the main repos?
>
> Fortunately the struct package seems to have the patches placed into the
> main branch - the commit
> https://sourceforge.net/p/octave/struct/ci/320e8484cd10b73cef40c9b51d99ebbb0c7b8360/ 
> (dated after the stable release) will probably fix my problem. I will
> try the HEAD/devel version then.

The packages in the Windows installer are built from the released package versions with the additional patches from the source I pointed to in the previous mail.
Some (but afaik not all) of these patches are taken from the development version of the respective packages.
In general, we don't care much about compatibility with previous Octave versions for the bundled packages. This is probably more important for the package developers.

Markus


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Re: Pkg install struct - octave 5.1 from flatpak, mint 18/ubuntu

phofman
> Am 06. März 2019 um 11:09 Uhr schrieb "Pavel Hofman"
>
> The packages in the Windows installer are built from the released package versions with the additional patches from the source I pointed to in the previous mail.
> Some (but afaik not all) of these patches are taken from the development version of the respective packages.

I see, now I understand. Do you think the section
https://wiki.octave.org/MXE "Compiling for your Linux system" will work
for octave 5.1? I would like to use the patched packages in octave-mxe
for the 5.1, instead of fighting each package individually.

I wonder why linux octave 5.1 from flatpak did not use these
pre-compiled packages right away, perhaps they are not included in the
flatpak or must be "linked" somehow?

> In general, we don't care much about compatibility with previous Octave versions for the bundled packages. This is probably more important for the package developers.
That is fine for me, I need just working octave with working set of
default packages on linux. My project will take a few months to complete
and I do not want to code for an outdated octave version.

Thanks a lot,

Pavel.


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Re: Pkg install struct - octave 5.1 from flatpak, mint 18/ubuntu

mmuetzel
Am 06. März 2019 um 13:28 Uhr schrieb "Pavel Hofman":
> Do you think the section
> https://wiki.octave.org/MXE "Compiling for your Linux system" will work
> for octave 5.1? I would like to use the patched packages in octave-mxe
> for the 5.1, instead of fighting each package individually.
I think that should be working.
Or you could try with the development versions of the respective packages.

>
> I wonder why linux octave 5.1 from flatpak did not use these
> pre-compiled packages right away, perhaps they are not included in the
> flatpak or must be "linked" somehow?
I am not a flatpak expert. But afaik all dependencies have to be part of the flatpak container. That might make Octave with all packages quite a large container.

Markus


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Re: Pkg install struct - octave 5.1 from flatpak, mint 18/ubuntu

phofman
Dne 06. 03. 19 v 20:33 "Markus Mützel" napsal(a):
> Am 06. März 2019 um 13:28 Uhr schrieb "Pavel Hofman":
>> Do you think the section
>> https://wiki.octave.org/MXE "Compiling for your Linux system" will work
>> for octave 5.1? I would like to use the patched packages in octave-mxe
>> for the 5.1, instead of fighting each package individually.
> I think that should be working.
Unfortunately I got stuck at the dreaded problem with libreadline.
Several targets fail with error:

gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP

There are several patches to libreadline in src, IMO some of them
ifdef'd only for windows. But they seem ok with this respect. The actual
build of readline 6.2 (download log, build log) seems perfectly OK.


> Or you could try with the development versions of the respective packages.

The devel packages will very likely work, just compiling octave 5.1
first :-)

>
>>
>> I wonder why linux octave 5.1 from flatpak did not use these
>> pre-compiled packages right away, perhaps they are not included in the
>> flatpak or must be "linked" somehow?
> I am not a flatpak expert. But afaik all dependencies have to be part of the flatpak container. That might make Octave with all packages quite a large container.

You are right. Octave from flatpak does not have e.g. units (for package
miscellaneous), pg_config (for database) etc in the layer
/app/octave/bin/. I am not sure it is possible to pkg install these
packages on octave running in flatpak. I tried to include these missing
requirements to the flatpak dir in /var/lib/flatpak/...., to no avail. I
would prefer compiling octave from sources (MXE) without flatpak.

Thanks a lot for any suggestion with the readline problem. Apart of that
I think the build will go OK.

Best regards,

Pavel.


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Re: Pkg install struct - octave 5.1 from flatpak, mint 18/ubuntu

phofman

Dne 06. 03. 19 v 23:07 pavel napsal(a):
> Dne 06. 03. 19 v 20:33 "Markus Mützel" napsal(a):

> Unfortunately I got stuck at the dreaded problem with libreadline.
> Several targets fail with error:
>
> gawk: symbol lookup error:
> /home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
> symbol: UP
>
> There are several patches to libreadline in src, IMO some of them
> ifdef'd only for windows. But they seem ok with this respect. The actual
> build of readline 6.2 (download log, build log) seems perfectly OK.
>
>

The fact is that for all packages which have the readline UP string
error in compile logs there is no binary in
mxe-octave-4c5a70572b2b/usr/bin (dbus, flac, tiff, etc.)

pavel@precision ~/mxe-octave-4c5a70572b2b/log $ rgrep -w UP *
20190306_210023/build-perl:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/perl5/5.26.1/unicore/lib/SB/UP.pl
20190306_210023/build-perl:smazáno
'/home/pavel/mxe-octave-4c5a70572b2b/tmp-build-perl-install/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/perl5/5.26.1/unicore/lib/SB/UP.pl'
20190306_210023/build-perl:smazáno
'/home/pavel/mxe-octave-4c5a70572b2b/tmp-build-perl/perl-5.26.1/lib/unicore/lib/SB/UP.pl'
20190306_210803/build-autoconf:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190306_210803/flac:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190306_210803/flac:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190306_210803/libpng:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190306_210803/libpng:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190306_210803/jasper:checking dynamic linker characteristics... awk:
symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190306_210803/jasper:awk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190306_210803/jasper:awk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190306_210803/jasper:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190306_210803/libunistring:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190306_210803/libunistring:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190306_210803/dbus:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190306_210803/dbus:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190306_210803/dbus:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190306_210803/dbus:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190306_210803/dbus:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190306_210803/dbus:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190306_210803/dbus:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190306_210803/tiff:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190306_212947/build-autoconf:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190307_190038/build-autoconf:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190307_190134/build-autoconf:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
20190307_190231/build-autoconf:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
build-autoconf:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
dbus:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
dbus:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
dbus:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
dbus:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
dbus:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
dbus:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
dbus:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
flac:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
flac:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
jasper:checking dynamic linker characteristics... awk: symbol lookup
error: /home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6:
undefined symbol: UP
jasper:awk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
jasper:awk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
jasper:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
libpng:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
libpng:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
libunistring:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
libunistring:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP
tiff:gawk: symbol lookup error:
/home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
symbol: UP



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Re: Pkg install struct - octave 5.1 from flatpak, mint 18/ubuntu

phofman

Dne 07. 03. 19 v 19:22 Pavel Hofman napsal(a):

>
> Dne 06. 03. 19 v 23:07 pavel napsal(a):
>> Dne 06. 03. 19 v 20:33 "Markus Mützel" napsal(a):
>
>>
>
> The fact is that for all packages which have the readline UP string
> error in compile logs there is no binary in
> mxe-octave-4c5a70572b2b/usr/bin (dbus, flac, tiff, etc.)
>

The procedure described in
https://wiki.octave.org/Octave_for_Debian_systems#The_right_way works
perfectly, incl. the list of package prerequisites for Ubuntu 16.04. All
octave packages from hg repo were compilable via pkg install too. Also
playrec is compilable and  works. Solved for now.

Thanks,

Pavel.



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Re: Pkg install struct - octave 5.1 from flatpak, mint 18/ubuntu

mmuetzel
In reply to this post by phofman
Am 06. März 2019 um 23:07 Uhr schrieb "pavel":

> Dne 06. 03. 19 v 20:33 "Markus Mützel" napsal(a):
> > Am 06. März 2019 um 13:28 Uhr schrieb "Pavel Hofman":
> >> Do you think the section
> >> https://wiki.octave.org/MXE "Compiling for your Linux system" will work
> >> for octave 5.1? I would like to use the patched packages in octave-mxe
> >> for the 5.1, instead of fighting each package individually.
> > I think that should be working.
> Unfortunately I got stuck at the dreaded problem with libreadline.
> Several targets fail with error:
>
> gawk: symbol lookup error:
> /home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
> symbol: UP
>
> There are several patches to libreadline in src, IMO some of them
> ifdef'd only for windows. But they seem ok with this respect. The actual
> build of readline 6.2 (download log, build log) seems perfectly OK.

MXE Octave now builds readline 8.0. Do you still see this error when compiling the newer version?

Markus


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Re: Pkg install struct - octave 5.1 from flatpak, mint 18/ubuntu

phofman
Hi Markus,

Dne 10. 03. 19 v 18:50 "Markus Mützel" napsal(a):

>>
>> gawk: symbol lookup error:
>> /home/pavel/mxe-octave-4c5a70572b2b/usr/lib/libreadline.so.6: undefined
>> symbol: UP
>>
>> There are several patches to libreadline in src, IMO some of them
>> ifdef'd only for windows. But they seem ok with this respect. The actual
>> build of readline 6.2 (download log, build log) seems perfectly OK.
>
> MXE Octave now builds readline 8.0. Do you still see this error when compiling the newer version?

clean build from hg tip:

mkdir
'/home/pavel/mxe-octave-fd5e5727326c/tmp-build-pkg-config/pkg-config-0.29.2.build'
cd
'/home/pavel/mxe-octave-fd5e5727326c/tmp-build-pkg-config/pkg-config-0.29.2'
&& autoreconf
m4macros/glib-gettext.m4:39: error: m4_copy: won't overwrite defined
macro: glib_DEFUN
m4macros/glib-gettext.m4:39: the top level
autom4te: /usr/bin/m4 failed with exit status: 1
aclocal: error: echo failed with exit status: 1
autoreconf: aclocal failed with exit status: 1
/home/pavel/mxe-octave-fd5e5727326c/Makefile:935: target
„build-only-build-pkg-config“ failed

Best regards,

Pavel.