bugGNU Octave - Bugs: bug #59164, [octave forge] (stk) install error...

 
 

bug #59164: [octave forge] (stk) install error about rmdir

Submitter:  None
Submitted:  Tue 22 Sep 2020 07:13:32 PM UTC
   
 
Category:  Octave Package Severity:  3 - Normal
Priority:  5 - Normal Item Group:  Installation Failure
Status:  Fixed Assigned to:  None
Originator Name:  Originator Email:  -email is unavailable-
Open/Closed:  * Closed Release:  * 7.0.90
Operating System:  * GNU/Linux Fixed Release:  None
Planned Release:  None
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Thu 24 Feb 2022 03:55:33 AM UTC, comment #16: 

Thank you for solving this problem @jbect.

I can confirm for Octave 7 (hg_id: https://hg.savannah.gnu.org/hgweb/octave/rev/2aff9dda08f1) that the recently released stk-2.7.0 fixes this issue.

Kai Torben Ohlhus <siko1056>
Group Member
Thu 27 Jan 2022 08:15:48 AM UTC, comment #15: 

The problem has been solved upstream (I think):

https://github.com/stk-kriging/stk/commit/b852e9fcd2117f0d77176863fb7543cd3d5777b2

If somebody wants to test on Octave 7: a build of STK from the tip of master is available here:

https://github.com/stk-kriging/stk/suites/5078867948/artifacts/151283492

(file stk-2.7.0tar.gz inside the octaveforge directory).

Julien Bect <jbect>
Mon 24 Jan 2022 09:28:35 PM UTC, comment #14: 

Thank you Kai for identifying the problem so precisely.

I will fix it asap.

(I was in the process of preparing a new release anyway.)

Julien Bect <jbect>
Mon 24 Jan 2022 05:43:11 PM UTC, comment #13: 

Your question brings my understanding in doubt as well.  I will reach out to Rik in discourse https://octave.discourse.group/t/function-form-vs-command-form/2137, who fixed the behavior in bug #57830.

Kai Torben Ohlhus <siko1056>
Group Member
Mon 24 Jan 2022 05:41:49 PM UTC, comment #12: 

It might make sense to update the language in the NEWS file. "Command form" is pretty close to "command syntax" where the latter is well defined in the manual and the former seems to mean something different.
I can see where the confusion came from.
IIUC the distinction is between the functions being called with or without output arguments. Why not write that directly?

Markus Mützel <mmuetzel>
Group administrator
Mon 24 Jan 2022 05:27:10 PM UTC, comment #11: 

Oh, now I understand. The distinction between command and function is not only whether it uses parentheses but also whether there is an output variable. So even if it uses parentheses without an output variable, it will trigger an error for non-ecisting directories. Is my understanding correct?

Arun Giridhar <arungiridhar>
Group Member
Mon 24 Jan 2022 05:20:57 PM UTC, comment #10: 

Regarding the stk development I cannot say much and we have to wait for the maintainers to take action.

To narrow down the error, I set a breakpoint in pkg case "install" and stepped all the way through until the real error showed up.  "line 296" does not make much sense to me (probably a wrongly calculated line offset?).

The NEWS is correct, see:


# Command Form
>> rmdir non-existing
error: rmdir: operation failed: No such file or directory
>> rmdir ("non-exising", "s")
remove entire contents of non-exising? (yes or no) yes
error: rmdir: operation failed: No such file or directory

# Function Form (return value)
>> bool = rmdir ("non-exising", "s")
remove entire contents of non-exising? (yes or no) yes
bool = 0


Kai Torben Ohlhus <siko1056>
Group Member
Mon 24 Jan 2022 04:42:18 PM UTC, comment #9: 

@Kai: your analysis makes sense but there are two things I don't understand:

  • The error given is line 296 and the line you highlight as the error is line 580. Why are they so different? Was there a major change to the stk package that has not been released yet?


  • The News item says it will throw an error for the command form but not the function form of rmdir and similar functions. Since it is being called in the package with the function form, why is an error thrown? Does the News file need editing?
Arun Giridhar <arungiridhar>
Group Member
Mon 24 Jan 2022 03:55:57 PM UTC, comment #8: 

Adding the package maintainers.

The problem is that Octave 7 and newer are no longer graceful with deleting non-existing files.


rmdir ("non-exising", "s");


throws an error instead of returning false.

https://hg.savannah.gnu.org/hgweb/octave/file/8c6486ffc1d9/etc/NEWS.7.md#l18

This happens here:

https://sourceforge.net/p/octave/stk/ci/default/tree/stk_init.m#l580


rmdir (fullfile (mole_dir, 'matlab'), 's');


The "matlab" folder is not packaged:


rmdir (fullfile (mole_dir, 'matlab'), 's');


See https://sourceforge.net/p/octave/stk/ci/default/tree/admin/build_tools/build_octpkg.m#l69


ignore_list = {'.hg', '.pc', 'admin', 'misc/mole/matlab', 'build', 'sandbox'};


Removing those lines in "stk_init.m" should do the trick with another small bug fix package release.

Kai Torben Ohlhus <siko1056>
Group Member
Thu 20 Jan 2022 04:21:11 PM UTC, comment #7: 

I too am now getting this error on current dev source of Octave (Octave 8, hg id b15e026c5a31.


octave:4> pkg install -forge stk
error: rmdir: operation failed: No such file or directory
error: called from
    stk_init>stk_init__config_mole at line 296 column 5
    stk_init at line 57 column 9
    post_install at line 37 column 5
    install>finish_installation at line 820 column 7
    install at line 240 column 7
    pkg at line 603 column 9


Not sure what the error source is yet. My available compilers are gcc 11.1 and clang 13.0 on Linux.

I looked at the source for stk_init.m here: https://sourceforge.net/p/octave/stk/ci/default/tree/stk_init.m

It is even more confusing because line 296 in that file is completely blank, and it is not even inside the stk_init__config_mole subfunction!

I take it there was some change to the package source that is not pushed to a release version?

I see multiple occurrences of rmpath and rmdir in that function, but so far I cannot see which one of them is triggering the error I see.

Arun Giridhar <arungiridhar>
Group Member
Wed 23 Sep 2020 01:08:21 PM UTC, comment #6: 

Please delete or disregard comment #5. Meant for a different bug, not this one. Sorry for posting in the wrong tab.

Anonymous
Wed 23 Sep 2020 01:05:03 PM UTC, comment #5: 

Those extra dots would definitely account for the peaks showing at odd locations.

Running ldd on the .oct files inside the signal package, most of the linked libraries are very standard. One thing to try is that since it links to libgomp, it is worth ruling out multi-thread behavior as a potential cause. Could you run "export OMP_NUM_THREADS=1" before running Octave, and see if it changes the output? If the problem persists at least we will know that it's not because of threading.

Anonymous
Wed 23 Sep 2020 12:46:40 PM UTC, comment #4: 

@Kai: Yes, it's Octave 7.0.0 built from the dev source. GCC version is 10.2.0 and Clang version is 10.0.1. Output of ver is this:


octave:1> ver
----------------------------------------------------------------------
GNU Octave Version: 7.0.0 (hg id: 903fe321649b)
GNU Octave License: GNU General Public License
Operating System: Linux 5.8.6-1-MANJARO #1 SMP PREEMPT Thu Sep 3 14:19:36 UTC 2020 x86_64
----------------------------------------------------------------------
Package Name        | Version | Installation directory
--------------------+---------+-----------------------
           arduino  |   0.6.0 | /home/def/packagesoctave/arduino-0.6.0
               cgi  |   0.1.2 | /home/def/packagesoctave/cgi-0.1.2
           control  |   3.2.0 | /home/def/packagesoctave/control-3.2.0
    data-smoothing  |   1.3.0 | /home/def/packagesoctave/data-smoothing-1.3.0
         dataframe  |   1.2.0 | /home/def/packagesoctave/dataframe-1.2.0
      econometrics  |   1.1.2 | /home/def/packagesoctave/econometrics-1.1.2
         financial  |   0.5.3 | /home/def/packagesoctave/financial-0.5.3
                ga  |  0.10.1 | /home/def/packagesoctave/ga-0.10.1
           general  |   2.1.1 | /home/def/packagesoctave/general-2.1.1
          geometry  |   4.0.0 | /home/def/packagesoctave/geometry-4.0.0
               gsl  |   2.1.1 | /home/def/packagesoctave/gsl-2.1.1
             image  |  2.12.0 | /home/def/packagesoctave/image-2.12.0
 image-acquisition  |   0.2.2 | /home/def/packagesoctave/image-acquisition-0.2.2
instrument-control  |   0.5.0 | /home/def/packagesoctave/instrument-control-0.5.0
          interval  |   3.2.0 | /home/def/packagesoctave/interval-3.2.0
                io  |   2.6.1 | /home/def/packagesoctave/io-2.6.1
    linear-algebra  |   2.2.3 | /home/def/packagesoctave/linear-algebra-2.2.3
              lssa  |   0.1.3 | /home/def/packagesoctave/lssa-0.1.3
           mapping  |   1.4.0 | /home/def/packagesoctave/mapping-1.4.0
           matgeom  |   1.2.2 | /home/def/packagesoctave/matgeom-1.2.2
     miscellaneous  |   1.3.0 | /home/def/packagesoctave/miscellaneous-1.3.0
               mvn  |   1.1.0 | /home/def/packagesoctave/mvn-1.1.0
               nan  |   3.5.0 | /home/def/packagesoctave/nan-3.5.0
               ocl  |   1.1.1 | /home/def/packagesoctave/ocl-1.1.1
           octproj  |   2.0.1 | /home/def/packagesoctave/octproj-2.0.1
             optim  |   1.6.0 | /home/def/packagesoctave/optim-1.6.0
          parallel  |   4.0.0 | /home/def/packagesoctave/parallel-4.0.0
          queueing  |   1.2.7 | /home/def/packagesoctave/queueing-1.2.7
            signal  |   1.4.1 | /home/def/packagesoctave/signal-1.4.1
           splines  |   1.3.3 | /home/def/packagesoctave/splines-1.3.3
        statistics  |   1.4.2 | /home/def/packagesoctave/statistics-1.4.2
            struct  |  1.0.16 | /home/def/packagesoctave/struct-1.0.16
          symbolic  |   2.9.0 | /home/def/packagesoctave/symbolic-2.9.0
             video  |   2.0.0 | /home/def/packagesoctave/video-2.0.0
              vrml  |  1.0.13 | /home/def/packagesoctave/vrml-1.0.13


Anonymous
Wed 23 Sep 2020 12:24:00 AM UTC, comment #3: 

@OP: Can you be more precise about you system (which version of gcc, clang).  From you hg id https://hg.savannah.gnu.org/hgweb/octave/graph/903fe321649b I conclude you are working on Octave 7?

Kai Torben Ohlhus <siko1056>
Group Member
Tue 22 Sep 2020 08:09:36 PM UTC, comment #2: 

Problem persists after switching from Clang to GCC. Octave dev version, hg id 903fe321649b.

Anonymous
Tue 22 Sep 2020 07:36:59 PM UTC, comment #1: 

worked for me in octave 6.0.91

John Donoghue <lostbard>
Group Member
Tue 22 Sep 2020 07:13:32 PM UTC, original submission:  

This is all the error there is for hg id 903fe321649b:


octave:1> pkg install -forge stk
error: rmdir: operation failed: No such file or directory
error: called from
    stk_init>stk_init__config_mole at line 296 column 5
    stk_init at line 57 column 9
    post_install at line 37 column 5
    install>finish_installation at line 800 column 7
    install at line 234 column 7
    pkg at line 568 column 9


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    Follow 9 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2022-02-24 siko1056 StatusConfirmed Fixed
        Open/ClosedOpen Closed
    2022-01-24 siko1056 Item GroupUnexpected Error or Warning Installation Failure
    2022-01-24 siko1056 StatusNeed Info Confirmed
        Releasedev 7.0.90
    2022-01-24 siko1056 Carbon-Copy- Added -email is unavailable-
    2022-01-24 siko1056 Carbon-Copy- Added -email is unavailable-
    2020-09-23 siko1056 StatusNone Need Info
        Summary[Forge] Error installing stk, blank error about rmdir [octave forge] (stk) install error about rmdir

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