rpy2 printing twice the output - ipython

I upgraded to rpy2.ipython from rmagic but it seems that every statement now prints to the console. Previously, an explicit print had to be called.
Is there an option to get back the former behaviour ?

This is fixed now in version_2.4.x on bitbucket:
https://bitbucket.org/lgautier/rpy2/commits/e22cdab51c94a504c4ea9808c6fad2772a34ef5e?at=default#Lrpy/ipython/rmagic.pyT216
Basically, I had a conceptual glitch while trying to fix up that logic - R is a Lisp, and withVisible operates on the code it gets in a way that doesn't translate via rpy2's python wrapper (which will operate in pythons function execution semantics, where the innermost is evaluated, return values passed out, etc.).

Related

How to execute functions in Live editor in MATLAB

I recently started using Live editor in MATLAB and I inserted a function inside it. But, apparently, I cannot execute that particular section of code where I type function. Even the section break disappears.
Is it that using function is not suitable for live editor?
Apparently the MATLAB parser did not join the 20th century until partway through 2016, and could not interpret function definitions in scripts (live or otherwise) until R2016b. In the web-based docs, there is a notice at Add Functions to Scripts, but it took me a while to find this out because the builtin docs in R2016a or earlier do not explicitly contain this information. It is implied by the tutorials that tell you to create a new file for each function (which to me, a python programmer, sounds more like strange advice than a restriction).
Trying to define a function in a live script gives confusing errors. For example, if you create a cell with this content:
function y = myfunc(x)
y = 2*x;
end
It will underline the keyword function with a popup error that reads:
Parse error at FUNCTION: usage might be invalid MATLAB syntax.
Might be? Whom shall I ask? Upon running the cell, it prints an error after the first line:
All functions in a script must be closed with an end.
I eventually made this discovery myself thanks to a helpful message if the first thing you happen to do in a new empty live script is to start typing function on the first line; as soon as you hit the spacebar a message pops up at the top saying:
Functions and classes are not supported in the Live Editor. To continue, save the file as a plain text code file (.m).
It should work as when you add a function inside a script. For example, like this:
What function are you exactly trying to code?

Can the MATLAB editor show the file from which text is displayed? [duplicate]

In MATLAB, how do you tell where in the code a variable is getting output?
I have about 10K lines of MATLAB code with about 4 people working on it. Somewhere, someone has dumped a variable in a MATLAB script in the typical way:
foo
Unfortunately, I do not know what variable is getting output. And the output is cluttering out other more important outputs.
Any ideas?
p.s. Anyone ever try overwriting Standard.out? Since MATLAB and Java integration is so tight, would that work? A trick I've used in Java when faced with this problem is to replace Standard.out with my own version.
Ooh, I hate this too. I wish Matlab had a "dbstop if display" to stop on exactly this.
The mlint traversal from weiyin is a good idea. Mlint can't see dynamic code, though, such as arguments to eval() or string-valued figure handle callbacks. I've run in to output like this in callbacks like this, where update_table() returns something in some conditions.
uicontrol('Style','pushbutton', 'Callback','update_table')
You can "duck-punch" a method in to built-in types to give you a hook for dbstop. In a directory on your Matlab path, create a new directory named "#double", and make a #double/display.m file like this.
function display(varargin)
builtin('display', varargin{:});
Then you can do
dbstop in double/display at 2
and run your code. Now you'll be dropped in to the debugger whenever display is implicitly called by the omitted semicolon, including from dynamic code. Doing it for #double seems to cover char and cells as well. If it's a different type being displayed, you may have to experiment.
You could probably override the built-in disp() the same way. I think this would be analagous to a custom replacement for Java's System.out stream.
Needless to say, adding methods to built-in types is nonstandard, unsupported, very error-prone, and something to be very wary of outside a debugging session.
This is a typical pattern that mLint will help you find:
So, look on the right hand side of the editor for the orange lines. This will help you find not only this optimization, but many, many more. Notice also that your variable name is highlighted.
If you have a line such as:
foo = 2
and there is no ";" on the end, then the output will be dumped to the screen with the variable name appearing first:
foo =
2
In this case, you should search the file for the string "foo =" and find the line missing a ";".
If you are seeing output with no variable name appearing, then the output is probably being dumped to the screen using either the DISP or FPRINTF function. Searching the file for "disp" or "fprintf" should help you find where the data is being displayed.
If you are seeing output with the variable name "ans" appearing, this is a case when a computation is being done, not being put in a variable, and is missing a ';' at the end of the line, such as:
size(foo)
In general, this is a bad practice for displaying what's going on in the code, since (as you have found out) it can be hard to find where these have been placed in a large piece of code. In this case, the easiest way to find the offending line is to use MLINT, as other answers have suggested.
I like the idea of "dbstop if display", however this is not a dbstop option that i know of.
If all else fails, there is still hope. Mlint is a good idea, but if there are many thousands of lines and many functions, then you may never find the offender. Worse, if this code has been sloppily written, there will be zillions of mlint flags that appear. How will you narrow it down?
A solution is to display your way there. I would overload the display function. Only temporarily, but this will work. If the output is being dumped to the command line as
ans =
stuff
or as
foo =
stuff
Then it has been written out with display. If it is coming out as just
stuff
then disp is the culprit. Why does it matter? Overload the offender. Create a new directory in some directory that is on top of your MATLAB search path, called #double (assuming that the output is a double variable. If it is character, then you will need an #char directory.) Do NOT put the #double directory itself on the MATLAB search path, just put it in some directory that is on your path.
Inside this directory, put a new m-file called disp.m or display.m, depending upon your determination of what has done the command line output. The contents of the m-file will be a call to the function builtin, which will allow you to then call the builtin version of disp or display on the input.
Now, set a debugging point inside the new function. Every time output is generated to the screen, this function will be called. If there are multiple events, you may need to use the debugger to allow processing to proceed until the offender has been trapped. Eventually, this process will trap the offensive line. Remember, you are in the debugger! Use the debugger to determine which function called disp, and where. You can step out of disp or display, or just look at the contents of dbstack to see what has happened.
When all is done and the problem repaired, delete this extra directory, and the disp/display function you put in it.
You could run mlint as a function and interpret the results.
>> I = mlint('filename','-struct');
>> isErrorMessage = arrayfun(#(S)strcmp(S.message,...
'Terminate statement with semicolon to suppress output (in functions).'),I);
>>I(isErrorMessage ).line
This will only find missing semicolons in that single file. So this would have to be run on a list of files (functions) that are called from some main function.
If you wanted to find calls to disp() or fprintf() you would need to read in the text of the file and use regular expresions to find the calls.
Note: If you are using a script instead of a function you will need to change the above message to read: 'Terminate statement with semicolon to suppress output (in scripts).'
Andrew Janke's overloading is a very useful tip
the only other thing is instead of using dbstop I find the following works better, for the simple reason that putting a stop in display.m will cause execution to pause, every time display.m is called, even if nothing is written.
This way, the stop will only be triggered when display is called to write a non null string, and you won't have to step through a potentially very large number of useless display calls
function display(varargin)
builtin('display', varargin{:});
if isempty(varargin{1})==0
keyboard
end
A foolproof way of locating such things is to iteratively step through the code in the debugger observing the output. This would proceed as follows:
Add a break point at the first line of the highest level script/function which produces the undesired output. Run the function/script.
step over the lines (not stepping in) until you see the undesired output.
When you find the line/function which produces the output, either fix it, if it's in this file, or open the subfunction/script which is producing the output. Remove the break point from the higher level function, and put a break point in the first line of the lower-level function. Repeat from step 1 until the line producing the output is located.
Although a pain, you will find the line relatively quickly this way unless you have huge functions/scripts, which is bad practice anyway. If the scripts are like this you could use a sort of partitioning approach to locate the line in the function in a similar manner. This would involve putting a break point at the start, then one half way though and noting which half of the function produces the output, then halving again and so on until the line is located.
I had this problem with much smaller code and it's a bugger, so even though the OP found their solution, I'll post a small cheat I learned.
1) In the Matlab command prompt, turn on 'more'.
more on
2) Resize the prompt-y/terminal-y part of the window to a mere line of text in height.
3) Run the code. It will stop wherever it needed to print, as there isn't the space to print it ( more is blocking on a [space] or [down] press ).
4) Press [ctrl]-[C] to kill your program at the spot where it couldn't print.
5) Return your prompt-y area to normal size. Starting at the top of trace, click on the clickable bits in the red text. These are your potential culprits. (Of course, you may need to have pressed [down], etc, to pass parts where the code was actually intended to print things.)
You'll need to traverse all your m-files (probably using a recursive function, or unix('find -type f -iname *.m') ). Call mlint on each filename:
r = mlint(filename);
r will be a (possibly empty) structure with a message field. Look for the message that starts with "Terminate statement with semicolon to suppress output".

Hacklang command line program in strict mode

Is there any way to create command line programs in strict mode of Hack? As Hack's strict mode does not allow statements outside a function I can't call my main function.
(This is rather a theoretical question as it is easy to circumvent the problem by having a non-strict file to call the main function.)
It's currently not possible to write a project (command line program or otherwise) 100% in Hack strict mode due to this limitation. You will indeed need to have some bootstrap code in the toplevel ("pseudomain"), which strict currently just does not allow. The reason for this is that toplevel code is basically impossible to statically typecheck, since everything is a global and can be changed behind the scenes at any time by any code.
However the end result is silly and something we want to fix eventually -- there is, for example, no reason to prevent a single call to a function with no parameters, i.e., exactly what you need to immediately get out of pseudomain and into a function.

How do I restrict Perl debugger output to lines in my own script?

I'm running the debugger in noninteractive mode, with the output written to a file. I want to print out each line of my Perl script as it executes, but only lines in the script itself. I don't want to see the library code (File::Basename, Exporter::import, etc.) that the script calls. This seems like the sort of thing that should be easy to do, but the documentation for perldebug only discusses limiting the depth for dumping structures. Is what I want possible, and if so, how?
Note that I'm executing my program as follows:
PERLDB_OPTS="LineInfo=temp.txt NonStop=1 AutoTrace=1 frame=2" perl -dS myprog.pl arg0 arg1
By default, Devel::DumpTrace doesn't step into system modules, and you can exercise fine control over what modules the debugger will step into (it's not easy, but it's possible). Something like
DUMPTRACE_FH=temp.txt perl -d:DumpTrace=quiet myprog.pl
would be similar to what you're apparently trying to do.
Devel::DumpTrace also does a lot more processing on each line -- figuring out variable values and including them in the output -- so it may be overkill and run a lot slower than perl -dS ...
(Crikey, that's now two plugs for Devel::DumpTrace this week!)
Are you talking about not wanting to step through functions outside of your own program? For that, you want to use n instead of s.
From perldebug:
s [expr] Single step. Executes until the beginning of another
statement, descending into subroutine calls. If an
expression is supplied that includes function calls, it too
will be singleā€stepped.
n [expr] Next. Executes over subroutine calls, until the beginning
of the next statement. If an expression is supplied that
includes function calls, those functions will be executed
with stops before each statement.

io Assignment Operator not evaluating?

OperatorTable addAssignOperator(":", "myAssignMethod")
"foo" : "bar"
That gives an error that a Sequence does not respond to ":" (":" is still being treated as a message, not an operator).
I think it should get evaluated to myAssignMethod("foo", "bar") (since "foo" = "bar" becomes updateSlot("foo", "bar")), but it's not. However:
OperatorTable addAssignOperator(":", "myAssignMethod")
doString("\"foo\" : \"bar\"")
that does work properly, and myAssignMethod gets called. So how do I get whatever processing happens on the code during doString() to work in the main code of the file?
: is a valid identifier, and has special meaning. It's used to indicate number of arguments in the objective-c binding. It's highly recommended you choose another operator.
Also note, that all operator table modifications must be done prior to your file you're using them in being loaded and parsed, since operator shuffling occurs at compile time (when the file is loaded) and not at evaluation time. The REPL hides this problem as it has a new compile with each time you hit enter.
Additionally, if you want to see what something will be compiled to (useful for operators) wrap it inside a message() call. i.e., message(1 + 2) will yield 1 +(2) in the REPL.
Turns out this appears to be a bug in the Mac environment that was fixed recently; I was working off the MacPorts build of Io, and the '20090105' version of the environment has this bug. Running the same code on the Windows/Linux binaries resulted in the expected behavior.