I'm trying to compile why3ide (why3-0.81) with krakatoa & jessie (why-2.33) for Windows (Cygwin). Everything went fine except I can't make right bottom textbox to show notations (it is always empty), moreover I get the error (highlighted in the picture) every time when I try to select the item to proof.
Image: https://dl.dropboxusercontent.com/u/39984835/why3ide/error_capture.jpg
Here is this error:
Apply transformation introduce_premises
Why3ide callback raised an exception:
anomaly: End_of_file
Backtrace:
Raised at file "format.ml", line 197, characters 41-52
Called from file "format.ml", line 425, characters 8-33
Called from file "format.ml", line 440, characters 6-24
How can I debug this error?
(I'm newbie for OCaml)
format.ml file is here:
cygwin/lib/ocaml/format.ml
Files that refers to introduce_premises transformation are here:
why3-0.81/drivers/gappa.drv
why3-0.81/src/ide/gmain.ml
why3-0.81/src/transform/introduction.ml
why3-0.81/drivers/mathematica.drv
P.S. I tried to add why3 & why3ide tags for this post, but my reputation is not enough for that yet.
Related
I am running some code that wasn't initially mine using GPT2-XL; it was initially implemented for GPT-Neo-1.3B and T5-Large. Running an experiment using GPT2-XL, I got the following error:
File "/data/username/directory", line 631, in to_tsr_gpt_entity_inference _bleu_score = BLEU.compute(predictions=definition, File "/data/username/miniconda3/lib/python3.9/site-packages/evaluate/module.py", line 433, in compute self._finalize() File "/data/username/miniconda3/lib/python3.9/site-packages/evaluate/module.py", line 372, in _finalize self.writer.finalize() File "/data/username/miniconda3/lib/python3.9/site-packages/datasets/arrow_writer.py", line 589, in finalize self.stream.close() File "/data/username/miniconda3/lib/python3.9/site-packages/fsspec/implementations/local.py", line 358, in close return self.f.close() OSError: [Errno 28] No space left on device
The issue here is that I'm not quite sure what is running out of space; I have checked df -h and df -I for example, and I tried setting the TMPDIR to be different with export TMPDIR=/new_directory, but that didn't work, so I can only assume something else is causing this to run out of space. It appears to have something to do with BLEU from the evaluate module of hugging_face, however, the same code (including the BLEU bit) works when running GPT-Neo/T5, so I'm not quite sure what the issue is.
I'd greatly appreciate any help in answering this question.
■Error Description.
Error detected while processing function <SNR>35_debounceTimeTimerCallback[1]..
<SNR>35_tapSourceCallback[4]..<SNR>35_tapSourceCallback[1]..<lambda>30[1]..<SNR
>55_set_signs[10]..<SNR>55_place_signs:
line 5:
E716: Key not present in Dictionary: linecount + 1
■Cause of error content output
I have set up an environment for Go development using the Vim editor on VirtusalBox.
■Contents of .vimrc
call plug#begin('~/.vim/plugged')
Plug 'prabirshrestha/vim-lsp'
Plug 'mattn/vim-lsp-settings'
call plug#end()
I am unsure of the solution, can you please let me know?
It could be a bug of vim-lsp.
This pull request was merged to master 3 days ago. Removing the following lines from ~/.vim/plugged/vim-lsp/autoload/lsp/internal/diagnostics/signs.vim worked for me.
" Some language servers report an unexpected EOF one line past the end
if l:line == getbufinfo(a:bufnr)[0].linecount + 1
let l:line = l:line - 1
endif
You can see a list of the files that have been sourced by Vim with :help :scriptnames:
:scr
The XX in all the <SNR>XXs in the stack trace refers to script number XX in the output of the command above.
For example, this is the output of :scr in $ vim --clean on my machine:
1: ~/Applications/MacVim.app/Contents/Resources/vim/runtime/defaults.vim
2: ~/Applications/MacVim.app/Contents/Resources/vim/runtime/filetype.vim
3: ~/Applications/MacVim.app/Contents/Resources/vim/runtime/ftplugin.vim
4: ~/Applications/MacVim.app/Contents/Resources/vim/runtime/indent.vim
5: ~/Applications/MacVim.app/Contents/Resources/vim/runtime/syntax/syntax.vim
6: ~/Applications/MacVim.app/Contents/Resources/vim/runtime/syntax/synload.vim
7: ~/Applications/MacVim.app/Contents/Resources/vim/runtime/syntax/syncolor.vim
If I get a stack trace mentioning <SNR>4, I know the problem is in the ~/Applications/MacVim.app/Contents/Resources/vim/runtime/indent.vim file that comes with Vim. In this fictitious case, I would probably debug it a little bit further and open an issue on Vim's issue tracker.
In your case, the problem is very likely to happen in one of your plugins. Once you have identified it, you should head off to its issue tracker.
I found the script and i need run it.
I tried to run it like this (i used eval-buffer command):
(require 'subr-x)
(require 's)
(load-file "~/git-graph.el")
(require 'git-graph)
(git-graph/to-graphviz-pretty
"git"
(git-graph/git-graph-head
"E:/GitStack/repositories/gitRepo.git"
"master"))
But get an error:
Loading e:/emHome/git-graph.el (source)...done
let*: Symbol’s function definition is void: first
picture
Please tell me what is wrong. And how i can run this script?
I'm new to this.
Why are you loading library git-graph twice?
What happens if you just remove either the load-library line or the require line -- do you still get an error?
With your original code, insert this line after the load-library line:
(message "After load-library")
And insert this line after the require line:
(message "After require")
See which message(s) you get: check buffer *Messages*. That should tell you which attempt to load the library (if either) led to the error. Maybe look for the text first in the library, to see if you notice anything funny.
If it doesn't look like the problem comes from loading that library then it likely comes from the expression after your require.
Do M-x toggle-debug-on-error, then do your M-x eval-buffer, and post the *Backtrace* output here. That will show us just where the error is raised.
You can also try M-x debug-on-entry git-graph/to-graphviz-pretty and step through the debugger using d (or c to skip details of a given step). That will eventually show you which code raised the error.
TL;DR
How to find where exactly vim or nvim error started (which file?) when I'm interested in fixing the actual issue and not just removing the bad plugin? Anything better than strace and guesswork to find the error origin?
Issue
I often add a plugin to my vim or nvim config and end up getting errors on hooks (buffer open, close, write):
"test.py" [New] 0L, 0C written
Error detected while processing function 343[12]..272:
line 8:
E716: Key not present in Dictionary: _exec
E116: Invalid arguments for function get(a:args, 'exec', a:1['_exec'])
E15: Invalid expression: get(a:args, 'exec', a:1['_exec'])
The problem is, I have no idea where those come from, only get some line number of unknown file and I know it's not my vim/nvim config file.
Somewhere, you have a plugin that has defined a dictionary with anonymous-functions (check the help related to this tag).
For the curious ones, it's done this way:
let d = {}
function! d.whatever() abort
throw "blah"
endfunction
When you execute this function, you'll get the kind of error you're currently observing. That's why I stopped working this way to prefer:
let d = {}
function s:whatever() abort
throw "blah"
endfunction
let d.whatever = function('s:whatever') " a workaround is required for older versions of vim
" At least this way I'll get a `<SNR>42_whatever` in the exception throwpoint, and thus a scriptname.
That's the why. Now, back to your problem, AFAIK, the only things you'll be able to know are the two functions that have been called:
in line 12 of :function {343}, you've called
:function {272} which contains an error at line 8.
Thanks to these two commands (may be prefixed with :verbose, I don't remember exactly), you'll get the source code of the two functions, which you should be able to use in order to grep your plugins to know where it appears.
I have been stuck on a problem for three days... searched everywhere, posted on Biostar, still waiting for EMBL to respond to emails... would make a bounty if I had more rep.
After aligning sequences with EMBOSSwin needle() (pairwise global alignments) I get alignment files in pair format, with a .needle file extension. I want to use Biopython to read these alignments for later analysis.
I use AlignIO.read(open('alignment.needle'),'emboss') following the instructions in Biopython's AlignIO wiki but I keep getting an AssertionError.
My code:
>>> from Bio import AlignIO
>>> alignment = AlignIO.read(open("data/all/out/pair1_alignment.needle"), "emboss")
My error:
Traceback (most recent call last):
File "<console>", line 1, in <module>
File "C:\Python27\lib\Bio\AlignIO\__init__.py", line 423, in read
first = next(iterator)
File "C:\Python27\lib\Bio\AlignIO\__init__.py", line 370, in parse
for a in i:
File "C:\Python27\lib\Bio\AlignIO\EmbossIO.py", line 150, in __next__
assert seq.replace("-", "") != ""
AssertionError
Example Alignment File:
Download the alignment file here
Versions:
Windows 7
Python version 2.7.3
Biopython version 1.63
EMBOSS version 2.10.0-0.8
Clues:
I suspect this may be related to a warning message I kept getting when actually making the alignments, which was outputted by EMBOSS needle() function:
Warning: Sequence character string not found in ajSeqCvtKS
Duplicate post on BioStars, http://www.biostars.org/p/87226/#87399
This appears to be down to a subtle change in the EMBOSS output. You have an extremely old version, EMBOSS version 2.10.0 (February 2005), and your output file has lines like this:
gag 1288 -------------------------------------------------- 1287
Using a newer version of EMBOSS (e.g. 6.3.0), gives lines like this:
gag 1287 -------------------------------------------------- 1287
The Biopython parser is expecting the latter for alignment sections with no letters (e.g. when one sequence is much longer than the other), where the start and end coordinates agree. Please update your copy of EMBOSS, and then the parser should be happy. The current EMBOSS release is version 6.5.0.
The problem is that you're passing the wrong format file to Biopython. An explanation follows.
Formatting
The format of the file you've linked to is srspair (see the header of pair1_aligned.fasta). It's worth noting that this is not the FASTA format - that's an entirely different format.
Delving into the source of Biopython's EmbossIO, we can see that the EmbossIterator (which is called by AlignIO.read when the format is 'emboss') is only meant to handle the formats pair and simple (see Alignment formats for an explanation of the various formats).
Solution
If you export EMBOSS's output in the pair format (then call AlignIO.read as you have before), that should solve your problem.