Re: [Ifeffit] problems installing athena et al under ubuntu 16.04 LTS

[Juan de la figuera]

Just tested it. Great!

Juan

El jue., 1 dic. 2016 a las 22:58, Bruce Ravel () escribió:

> I just checked a fix into github that addresses the problem Juan
> identified.  Matt's assessment at
> https://github.com/bruceravel/demeter/issues/42 was exactly right.  I
> adopted his second solution.
>
> Thanks to all of you for this discussion.
> B
>
>
>
> On 11/25/2016 05:23 AM, Juan de la figuera wrote:
> > Hi,
> >
> > I send one of the data files we are currently acquiring (SPLINE beamline
> > at ESRF).
> >
> > I have checked that my compiled 0.9.24 version works with the examples
> > cu10k.dat file, but it is true, as Robert confirmed, that strange things
> > happen if you mark ev instead of kev.
> >
> > With our data files like the one enclosed, dathena chokes on the scale.
> > Actually it opens the window but it has x10^9 scale. On the other hand,
> > the 0.9.24 for Windows opens the files ok. Now, the files are
> > MSDOS-ended files, I tried converting them to Linux-ending, but same
> > result. I also tried putting a # comment on the first line.
> >
> > I stress that Athena 0.8.061 (included in the horae package in ubuntu)
> > opens the file like a charm.
> >
> > One additional detail (just in case), I have Ubuntu 16.04 LTS 64-bit.
> >
> > Best,
> > Juan
> >
> >
> > ___
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>
>
> --
>   Bruce Ravel   bra...@bnl.gov
>
>   National Institute of Standards and Technology
>   Synchrotron Science Group at NSLS-II
>   Building 743, Room 114
>   Upton NY, 11973
>
>   Homepage:http://bruceravel.github.io/home/
>   Software:https://github.com/bruceravel
>   Demeter: http://bruceravel.github.io/demeter/
> ___
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Re: [Ifeffit] problems installing athena et al under ubuntu 16.04 LTS

[Bruce Ravel]

I just checked a fix into github that addresses the problem Juan 
identified.  Matt's assessment at 
https://github.com/bruceravel/demeter/issues/42 was exactly right.  I 
adopted his second solution.


Thanks to all of you for this discussion.
B



On 11/25/2016 05:23 AM, Juan de la figuera wrote:

Hi,

I send one of the data files we are currently acquiring (SPLINE beamline
at ESRF).

I have checked that my compiled 0.9.24 version works with the examples
cu10k.dat file, but it is true, as Robert confirmed, that strange things
happen if you mark ev instead of kev.

With our data files like the one enclosed, dathena chokes on the scale.
Actually it opens the window but it has x10^9 scale. On the other hand,
the 0.9.24 for Windows opens the files ok. Now, the files are
MSDOS-ended files, I tried converting them to Linux-ending, but same
result. I also tried putting a # comment on the first line.

I stress that Athena 0.8.061 (included in the horae package in ubuntu)
opens the file like a charm.

One additional detail (just in case), I have Ubuntu 16.04 LTS 64-bit.

Best,
Juan


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--
 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Building 743, Room 114
 Upton NY, 11973

 Homepage:http://bruceravel.github.io/home/
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
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Re: [Ifeffit] problems installing athena et al under ubuntu 16.04 LTS

[Matt Newville]

Hi Juan, Robert,

OK, I was able to reproduce the problem on a Fedora 23 Linux system with
the latest versions of Demeter and Larch.

I can see that the conversion of energy from eV to keV. Clicking different
combinations of the Numerator/Denominator buttons can alter the energy by
factors of 1000, and is not completely reversible.  I see a factor of 1000
as a multiplicative factor in the Energy Text Control window when "keV" is
selected, but this appears to not be editable.

I also see that this only happens when using the Larch backend and not the
Ifeffit backend.  And, I can also see that the energy is being set to the
very large value in Larch.  So that's a good set of clues to work with.

--Matt


On Fri, Nov 25, 2016 at 12:03 PM, Robert Gordon 
wrote:

> Hi Juan,
>
> I can open your file. It displays without issue.
> My system is amd64 with ubuntu 16.04 LTS.
> The version of Demeter I cloned from git is 0.9.26 (using the git clone
> instruction), mostly following the 'David Hughes' guide" from here
> https://bruceravel.github.io/demeter/documents/SinglePage/
> demeter_nonroot.html
> which seems to be what you found elsewhere.
> There were a couple of differences I had to work around:
> libpng3-dev had libpng12-dev substituted for it by apt
> libgif4 and libwxgtk2.8-dev were not found. I manually installed
> giflib-5.1.4 and apt installed gtk2.0
>
> I had to ctrl-c out of a loop regarding "can't find apache" when doing
> ./Build installdeps
> (Googling suggests this might be due to perl/build/cpan trying to use
> mod_perl-1.31 instead of -2.0.4
> since 1.31 is slightly newer).
>
> I am still tweaking my system, so this is a fresh install of demeter this
> morning - no larch yet,
> so I get a 'no larch_server' message, but your file displays without issue.
>
> You indicated you have version 0.9.24. What other differences did you
> encounter?
>
> -R.
>
>
> On 11/25/2016 2:23 AM, Juan de la figuera wrote:
>
> Hi,
>
> I send one of the data files we are currently acquiring (SPLINE beamline
> at ESRF).
>
> I have checked that my compiled 0.9.24 version works with the examples
> cu10k.dat file, but it is true, as Robert confirmed, that strange things
> happen if you mark ev instead of kev.
>
> With our data files like the one enclosed, dathena chokes on the scale.
> Actually it opens the window but it has x10^9 scale. On the other hand, the
> 0.9.24 for Windows opens the files ok. Now, the files are MSDOS-ended
> files, I tried converting them to Linux-ending, but same result. I also
> tried putting a # comment on the first line.
>
> I stress that Athena 0.8.061 (included in the horae package in ubuntu)
> opens the file like a charm.
>
> One additional detail (just in case), I have Ubuntu 16.04 LTS 64-bit.
>
> Best,
> Juan
>
>
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Re: [Ifeffit] problems installing athena et al under ubuntu 16.04 LTS

[Robert Gordon]

Hi Juan,

I can open your file. It displays without issue.
My system is amd64 with ubuntu 16.04 LTS.
The version of Demeter I cloned from git is 0.9.26 (using the git clone
instruction), mostly following the 'David Hughes' guide" from here
https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.html
which seems to be what you found elsewhere.
There were a couple of differences I had to work around:
libpng3-dev had libpng12-dev substituted for it by apt
libgif4 and libwxgtk2.8-dev were not found. I manually installed 
giflib-5.1.4 and apt installed gtk2.0


I had to ctrl-c out of a loop regarding "can't find apache" when doing 
./Build installdeps
(Googling suggests this might be due to perl/build/cpan trying to use 
mod_perl-1.31 instead of -2.0.4

since 1.31 is slightly newer).

I am still tweaking my system, so this is a fresh install of demeter 
this morning - no larch yet,

so I get a 'no larch_server' message, but your file displays without issue.

You indicated you have version 0.9.24. What other differences did you 
encounter?


-R.

On 11/25/2016 2:23 AM, Juan de la figuera wrote:

Hi,

I send one of the data files we are currently acquiring (SPLINE 
beamline at ESRF).


I have checked that my compiled 0.9.24 version works with the examples 
cu10k.dat file, but it is true, as Robert confirmed, that strange 
things happen if you mark ev instead of kev.


With our data files like the one enclosed, dathena chokes on the 
scale. Actually it opens the window but it has x10^9 scale. On the 
other hand, the 0.9.24 for Windows opens the files ok. Now, the files 
are MSDOS-ended files, I tried converting them to Linux-ending, but 
same result. I also tried putting a # comment on the first line.


I stress that Athena 0.8.061 (included in the horae package in ubuntu) 
opens the file like a charm.


One additional detail (just in case), I have Ubuntu 16.04 LTS 64-bit.

Best,
Juan


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Re: [Ifeffit] problems installing athena et al under ubuntu 16.04 LTS

[Juan de la figuera]

Hi,

I send one of the data files we are currently acquiring (SPLINE beamline at
ESRF).

I have checked that my compiled 0.9.24 version works with the examples
cu10k.dat file, but it is true, as Robert confirmed, that strange things
happen if you mark ev instead of kev.

With our data files like the one enclosed, dathena chokes on the scale.
Actually it opens the window but it has x10^9 scale. On the other hand, the
0.9.24 for Windows opens the files ok. Now, the files are MSDOS-ended
files, I tried converting them to Linux-ending, but same result. I also
tried putting a # comment on the first line.

I stress that Athena 0.8.061 (included in the horae package in ubuntu)
opens the file like a charm.

One additional detail (just in case), I have Ubuntu 16.04 LTS 64-bit.

Best,
Juan


016_Co_foil16.dat
Description: Binary data
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Re: [Ifeffit] problems installing athena et al under ubuntu 16.04 LTS

[Robert Gordon]

Hi Juan,

I just installed demeter and larch on an Ubuntu 16.04lts system today.
I can reproduce something like your error. I use the 10K Cu data in the 
examples

folder.

If I import it and don't select the numerator on import, the plot window 
has issues

(~10^307 axis limit), but the file gets listed in the data list.

I can get 10^9 for the energy axis by specifying keV instead of eV for 
the import energy.


i.e. Matt's question: Did you import the data correctly?
(and why 10^9 if it is supposedly multiplying by 1000?...would have 
thought 10^6...)


Did you import a number of datasets with mixed keV and eV energy scales? 
I did that once
where the first file was in keV and subsequent ones in eV and the energy 
scale was decidedly

off for the subsequent ones.

cheers,
Robert

On 11/23/2016 7:45 PM, Matt Newville wrote:

Hi Juan,

On Wed, Nov 23, 2016 at 12:43 PM, Juan de la figuera 
> wrote:


Dear all,

I have been installing demeter from git under ubuntu 16.04 LTS,
following the non-root instructions from:
https://gist.github.com/waveform80/3959252


I also installed xraylarch from git. Xaylarch is only missing:
#=== Warning: Some recommended Python Packages are missing:
epics:  needed for using the EPICS control system
pyFAI:  needed for xrd modules

It seems to work, but when I try to open a file that can be open
properly from Athena installed on Windows, I get:

Trying Larch server:

/home/juan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/share/ini/larch_server.in
i
Trying Larch server:  larch_server -p 4968 start
larch_server port=4968: started

gnuplot> set xrange [ 690013 : 795561 ]
 ^
line 0: warning: integer overflow; changing to floating point

gnuplot> set xrange [ 690013 : 795561 ]
^
line 0: warning: integer overflow; changing to floating point


and although it opens the data in a gnuplot window, the scale is
off (7x10^9 instead of 7x10^3). I am assuming once it is confused
about the scale, it makes a mess with the data.



Did you import the data correctly?

Did you try this with more than one data file?

Why did you not include that data file in your request for help?

If you had included the (or a) file giving you trouble, it would allow 
someone else to try to reproduce the problem, which might actually 
lead to an answer.


--Matt

PS:  Athena version 0.8.061 is more than 5 years old and is not supported.



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Re: [Ifeffit] problems installing athena et al under ubuntu 16.04 LTS

[Matt Newville]

Hi Juan,

On Wed, Nov 23, 2016 at 12:43 PM, Juan de la figuera <
juan.delafigu...@gmail.com> wrote:

> Dear all,
>
> I have been installing demeter from git under ubuntu 16.04 LTS, following
> the non-root instructions from:
> https://gist.github.com/waveform80/3959252
>
> I also installed xraylarch from git. Xaylarch is only missing:
> #=== Warning: Some recommended Python Packages are missing:
> epics:  needed for using the EPICS control system
> pyFAI:  needed for xrd modules
>
> It seems to work, but when I try to open a file that can be open properly
> from Athena installed on Windows, I get:
>
> Trying Larch server: /home/juan/perl5/lib/perl5/x86
> _64-linux-gnu-thread-multi/Demeter/share/ini/larch_server.ini
> Trying Larch server:  larch_server -p 4968 start
> larch_server port=4968: started
>
> gnuplot> set xrange [ 690013 : 795561 ]
>  ^
> line 0: warning: integer overflow; changing to floating point
>
> gnuplot> set xrange [ 690013 : 795561 ]
>   ^
> line 0: warning: integer overflow; changing to floating point
>
>
> and although it opens the data in a gnuplot window, the scale is off
> (7x10^9 instead of 7x10^3). I am assuming once it is confused about the
> scale, it makes a mess with the data.
>


Did you import the data correctly?

Did you try this with more than one data file?

Why did you not include that data file in your request for help?

If you had included the (or a) file giving you trouble, it would allow
someone else to try to reproduce the problem, which might actually lead to
an answer.

--Matt

PS:  Athena version 0.8.061 is more than 5 years old and is not supported.
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Re: [Ifeffit] problems installing athena et al under ubuntu 16.04 LTS

[Juan de la figuera]

Hi to all,

I found that there is actually an "horae" package in ubuntu. It is a bit
old (0.8.061 for athena) but it takes care of all the installing. Ifeffit
is also packaged, both by Carlo Segre .

Juan

El mié., 23 nov. 2016 a las 21:56, Juan de la figuera (<
juan.delafigu...@gmail.com>) escribió:

> BTW, it does not seem to be a problem with locale, I set it to "C"
> beforehand:
>
> juan@maghemite:xraylarch$ locale
> LANG=C
> LANGUAGE=C
> LC_CTYPE="C"
> LC_NUMERIC="C"
> LC_TIME="C"
> LC_COLLATE="C"
> LC_MONETARY="C"
> LC_MESSAGES="C"
> LC_PAPER="C"
> LC_NAME="C"
> LC_ADDRESS="C"
> LC_TELEPHONE="C"
> LC_MEASUREMENT="C"
> LC_IDENTIFICATION="C"
> LC_ALL=C
>
>
> El mié., 23 nov. 2016 a las 19:43, Juan de la figuera (<
> juan.delafigu...@gmail.com>) escribió:
>
> Dear all,
>
> I have been installing demeter from git under ubuntu 16.04 LTS, following
> the non-root instructions from:
> https://gist.github.com/waveform80/3959252
>
> I also installed xraylarch from git. Xaylarch is only missing:
> #=== Warning: Some recommended Python Packages are missing:
> epics:  needed for using the EPICS control system
> pyFAI:  needed for xrd modules
>
> It seems to work, but when I try to open a file that can be open properly
> from Athena installed on Windows, I get:
>
> Trying Larch server:
> /home/juan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/share/ini/larch_server.ini
>
> Trying Larch server:  larch_server -p 4968 start
> larch_server port=4968: started
>
> gnuplot> set xrange [ 690013 : 795561 ]
>  ^
> line 0: warning: integer overflow; changing to floating point
>
> gnuplot> set xrange [ 690013 : 795561 ]
>   ^
> line 0: warning: integer overflow; changing to floating point
>
>
> and although it opens the data in a gnuplot window, the scale is off
> (7x10^9 instead of 7x10^3). I am assuming once it is confused about the
> scale, it makes a mess with the data.
> The output of probe -bv is:
> t/000_ifeffit.t .
> 1..6
> ok 1 - show
> ok 2 - show arrays:
> ok 3 - get_scalar 1.2345
> ok 4 - put scalar
> ok 5 - put/get_string: my.xmu
> ok 6 - put/get_array:
> ok
> t/001_base.t 
> 1..24
> Trying Larch server:
> /home/juan/soft/demeter/blib/lib/Demeter/share/ini/larch_server.ini
> Trying Larch server:  larch_server -p 4969 start
> larch_server port=4969: started
> ok 1 - new() works
> ok 2 - group is set: orihs
> ok 3 - unique group names: orihs & bcxkm
> ok 4 - installation location identified
> ok 5 - identity string
> ok 6 - generic object is not plottable
> ok 7 - generic object has no data
> ok 8 - Project role works
> ok 9 - demeter can do introspection
> ok 10 - ifeffit disposal mode flag: 1
> ok 11 - handle unknown mode gracefully
> ok 12 - other disposal modes all false
> ok 13 - turn on screen disposal mode flag
> ok 14 - turn on file disposal mode flag
> ok 15 - turn on buffer disposal mode flag
> ok 16 - unknown window not recognized
> ok 17 - known element (Cu) is recognized
> ok 18 - unknown element (Ci) not recognized
> ok 19 - simple template works
> not ok 20 - simple disposal to Ifeffit: string
>
> #   Failed test 'simple disposal to Ifeffit: string'
> #   at t/001_base.t line 69.
> not ok 21 - simple disposal to Ifeffit: scalar
>
> #   Failed test 'simple disposal to Ifeffit: scalar'
> #   at t/001_base.t line 70.
> Use of uninitialized value in numeric eq (==) at t/001_base.t line 71.
> not ok 22 - simple disposal to Ifeffit: array
>
> #   Failed test 'simple disposal to Ifeffit: array'
> #   at t/001_base.t line 71.
> ok 23 - simple disposal wrapper works
> ok 24 - plot_with works
> # Looks like you failed 3 tests of 24.
>
> Any help would be appreciated.
>
>
> Juan
>
>
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Re: [Ifeffit] problems installing athena et al under ubuntu 16.04 LTS

[Juan de la figuera]

BTW, it does not seem to be a problem with locale, I set it to "C"
beforehand:

juan@maghemite:xraylarch$ locale
LANG=C
LANGUAGE=C
LC_CTYPE="C"
LC_NUMERIC="C"
LC_TIME="C"
LC_COLLATE="C"
LC_MONETARY="C"
LC_MESSAGES="C"
LC_PAPER="C"
LC_NAME="C"
LC_ADDRESS="C"
LC_TELEPHONE="C"
LC_MEASUREMENT="C"
LC_IDENTIFICATION="C"
LC_ALL=C


El mié., 23 nov. 2016 a las 19:43, Juan de la figuera (<
juan.delafigu...@gmail.com>) escribió:

> Dear all,
>
> I have been installing demeter from git under ubuntu 16.04 LTS, following
> the non-root instructions from:
> https://gist.github.com/waveform80/3959252
>
> I also installed xraylarch from git. Xaylarch is only missing:
> #=== Warning: Some recommended Python Packages are missing:
> epics:  needed for using the EPICS control system
> pyFAI:  needed for xrd modules
>
> It seems to work, but when I try to open a file that can be open properly
> from Athena installed on Windows, I get:
>
> Trying Larch server:
> /home/juan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/share/ini/larch_server.ini
>
> Trying Larch server:  larch_server -p 4968 start
> larch_server port=4968: started
>
> gnuplot> set xrange [ 690013 : 795561 ]
>  ^
> line 0: warning: integer overflow; changing to floating point
>
> gnuplot> set xrange [ 690013 : 795561 ]
>   ^
> line 0: warning: integer overflow; changing to floating point
>
>
> and although it opens the data in a gnuplot window, the scale is off
> (7x10^9 instead of 7x10^3). I am assuming once it is confused about the
> scale, it makes a mess with the data.
> The output of probe -bv is:
> t/000_ifeffit.t .
> 1..6
> ok 1 - show
> ok 2 - show arrays:
> ok 3 - get_scalar 1.2345
> ok 4 - put scalar
> ok 5 - put/get_string: my.xmu
> ok 6 - put/get_array:
> ok
> t/001_base.t 
> 1..24
> Trying Larch server:
> /home/juan/soft/demeter/blib/lib/Demeter/share/ini/larch_server.ini
> Trying Larch server:  larch_server -p 4969 start
> larch_server port=4969: started
> ok 1 - new() works
> ok 2 - group is set: orihs
> ok 3 - unique group names: orihs & bcxkm
> ok 4 - installation location identified
> ok 5 - identity string
> ok 6 - generic object is not plottable
> ok 7 - generic object has no data
> ok 8 - Project role works
> ok 9 - demeter can do introspection
> ok 10 - ifeffit disposal mode flag: 1
> ok 11 - handle unknown mode gracefully
> ok 12 - other disposal modes all false
> ok 13 - turn on screen disposal mode flag
> ok 14 - turn on file disposal mode flag
> ok 15 - turn on buffer disposal mode flag
> ok 16 - unknown window not recognized
> ok 17 - known element (Cu) is recognized
> ok 18 - unknown element (Ci) not recognized
> ok 19 - simple template works
> not ok 20 - simple disposal to Ifeffit: string
>
> #   Failed test 'simple disposal to Ifeffit: string'
> #   at t/001_base.t line 69.
> not ok 21 - simple disposal to Ifeffit: scalar
>
> #   Failed test 'simple disposal to Ifeffit: scalar'
> #   at t/001_base.t line 70.
> Use of uninitialized value in numeric eq (==) at t/001_base.t line 71.
> not ok 22 - simple disposal to Ifeffit: array
>
> #   Failed test 'simple disposal to Ifeffit: array'
> #   at t/001_base.t line 71.
> ok 23 - simple disposal wrapper works
> ok 24 - plot_with works
> # Looks like you failed 3 tests of 24.
>
> Any help would be appreciated.
>
>
> Juan
>
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[Ifeffit] problems installing athena et al under ubuntu 16.04 LTS

[Juan de la figuera]

Dear all,

I have been installing demeter from git under ubuntu 16.04 LTS, following
the non-root instructions from:
https://gist.github.com/waveform80/3959252

I also installed xraylarch from git. Xaylarch is only missing:
#=== Warning: Some recommended Python Packages are missing:
epics:  needed for using the EPICS control system
pyFAI:  needed for xrd modules

It seems to work, but when I try to open a file that can be open properly
from Athena installed on Windows, I get:

Trying Larch server:
/home/juan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/share/ini/larch_server.ini

Trying Larch server:  larch_server -p 4968 start
larch_server port=4968: started

gnuplot> set xrange [ 690013 : 795561 ]
 ^
line 0: warning: integer overflow; changing to floating point

gnuplot> set xrange [ 690013 : 795561 ]
  ^
line 0: warning: integer overflow; changing to floating point


and although it opens the data in a gnuplot window, the scale is off
(7x10^9 instead of 7x10^3). I am assuming once it is confused about the
scale, it makes a mess with the data.
The output of probe -bv is:
t/000_ifeffit.t .
1..6
ok 1 - show
ok 2 - show arrays:
ok 3 - get_scalar 1.2345
ok 4 - put scalar
ok 5 - put/get_string: my.xmu
ok 6 - put/get_array:
ok
t/001_base.t 
1..24
Trying Larch server:
/home/juan/soft/demeter/blib/lib/Demeter/share/ini/larch_server.ini
Trying Larch server:  larch_server -p 4969 start
larch_server port=4969: started
ok 1 - new() works
ok 2 - group is set: orihs
ok 3 - unique group names: orihs & bcxkm
ok 4 - installation location identified
ok 5 - identity string
ok 6 - generic object is not plottable
ok 7 - generic object has no data
ok 8 - Project role works
ok 9 - demeter can do introspection
ok 10 - ifeffit disposal mode flag: 1
ok 11 - handle unknown mode gracefully
ok 12 - other disposal modes all false
ok 13 - turn on screen disposal mode flag
ok 14 - turn on file disposal mode flag
ok 15 - turn on buffer disposal mode flag
ok 16 - unknown window not recognized
ok 17 - known element (Cu) is recognized
ok 18 - unknown element (Ci) not recognized
ok 19 - simple template works
not ok 20 - simple disposal to Ifeffit: string

#   Failed test 'simple disposal to Ifeffit: string'
#   at t/001_base.t line 69.
not ok 21 - simple disposal to Ifeffit: scalar

#   Failed test 'simple disposal to Ifeffit: scalar'
#   at t/001_base.t line 70.
Use of uninitialized value in numeric eq (==) at t/001_base.t line 71.
not ok 22 - simple disposal to Ifeffit: array

#   Failed test 'simple disposal to Ifeffit: array'
#   at t/001_base.t line 71.
ok 23 - simple disposal wrapper works
ok 24 - plot_with works
# Looks like you failed 3 tests of 24.

Any help would be appreciated.

Juan
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