I am calling an R function from the R package e1071 which is interfaced with libsvm (a C program). This function is passing C (printf) warning messages to the R console. I know this because the warning messages are of the form (warning:...) whereas R warning messages are capitalized (i.e. Warning:...).
I've tried everything to get rid of these messages in R (sink, suppressWarnings, invisible) but nothing seems to work.
Any ideas?
Thanks!
The function uses stdio instead of Rprintf/REprintf or warning which is why re-direction of the R output won't work. The proper solution is to fix the calls in libsvm to use R output instead.
Hacking the stdio output is possible - you can re-direct the output to your own pipe and do what you want with it, but a) it's a bit of work in C and b) it's dangerous because you need to restore the standard behavior after you're done with the function - even if it errors out and c) in may interact with R output if used on a shell.
If you want a really whacky, dirty yet quick solution, run your function in collect(parallel(..., silent=TRUE))[[1]] from multicore - it suppresses stdout (you can add multicore:::closeStderr() if you want to suppress stderr as well).
Related
I have a function that pretty prints a data structure, its function prototype is:
void print_mode(FILE *fp, Mode *mode);
the FILE* allows you to redirect the output to anywhere you want, e.g. stdout, stderr, a file etc. Mode is the data structure
I am trying to call this function from within gdb and want the output to be directed to the gdb console window, stdout?
I have tried:
(gdb) p print_mode(STDOUT,fragment_mode)
No symbol "STDOUT" in current context.
(gdb) p print_mode(stdout,fragment_mode)
$17 = void
neither of which work
any ideas how i can get the output of the function to display in the gdb console?
should add - I am using gdb within emacs 24.2.1 under linux
STDOUT seems to be macro, which is not know to GDB, as handled prior to compilation by the pre-preprocessor.
Using stdout should do the job.
However the function print_mode() simply does not seem to print out anything.
In terms what's being printed to the console by the program being debugged, GDB's commands printand call should not make a difference.
For details on this you might like to read here: https://sourceware.org/gdb/onlinedocs/gdb/Calling.html
An issue might be that stdout by default is line buffered, so output would not occur before detecting a linefeed and print_mode() perhaps does not send a linefeed (\n).
To test this just use stderr as output file, as the latter isn't buffered:
p print_mode(stderr, fragment_mode)
Oh dear - silly mistake. You're right, stdout does do the job.
I forgot that having upgraded from emacs 23 to 24, the way gdb works has changed in as much as it now opens a separate buffer *input/output of program-name* to which it redirects the output of the program being debugged. In the prior version of emacs it was all displayed in the same, single gdb buffer.
So my second attempt was actually working, I was just looking in the wrong place so didn't see the output
I am running a Ruby gem which relies on a C extension (not a call to system).
The C code makes several calls to printf.
I want to silence the output of these calls.
Changing Ruby's STDOUT (example) or STDERR does not prevent the text from being output.
Is it possible to do this without modifying the C code? If so, how?
Someone originally commented on my post suggesting to use IO.reopen. This worked for me. The person has unfortunately since deleted his/her comment, so I'm posting the more detailed function I used in the end:
def silence_stdout(log = '/dev/null')
old = $stdout.dup
$stdout.reopen(File.new(log, 'w'))
yield
$stdout = old
end
Usage:
silence_stdout { foo } # Won't be displayed, won't be logged.
silence_stdout('log.txt') { bar } # Won't be displayed, logged in log.txt.
It is possible that Ruby is printing to stderr instead of stdout, which is why changing Ruby's stdout doesn't fix your problem.
(Both stderr and stdout typically go to the console.)
Try redirecting stderr. As I recall it'd be: myprogram 2> /dev/null
If you have access to the C source code:
#define printf(...)
This macro form is a C99 variadic macro.
[This question is not about fixing the error. But about redirecting it]
I have a program (C/linux) which displays error on the console due to missing shared library. It says "can't load library ...." . How can I redirect this output into a file ?
I tried this inside my program:
close(2);
open("/home/user/test.txt", O_CREAT|O_RDWR);
It correctly redirects the output generated from the program printfs. But the "can't load library ...." still comes on console!
I don't want to use the > operator for this purpose. I want to do it from inside my program. Any suggestions?
Thanks
The error message is generated by the loader, which happens before the program even starts. So there's nothing you can do from within a program that doesn't even get to run to influence the behaviour of the loader.
If you really need to fiddle with the file descriptors used by the shell, check out the exec shell command to close and redirect file descriptors permanently. That way you can get around using the redirection operator >, although that's arguably a far less tidy approach.
You will need a wrapper program. It could be a shell script. Do the redirection then try to run the original program.
A program cannot catch errors that happen to it before it even starts running. Library link happens before any other code runs.
Seems like the message is generated before your program starts - so to redirect it, you'll have to use the 2> operator. Otherwise you'll have to use the dlopen... etc. calls to do the linking on runtime.
try making sure that the environment variable LD_LIBRARY_PATH is correct.
that warnings & error mesages comes befor your program starts to work so only option is > operator
use this way
./a.out >& filename
I'm running Mathematica 8 on a MacOSX, trying to compile even the simplest program to C. Anything having to do with C simply doesn't work in Mathematica. I have GCC 4.2 installed; I've even reinstalled it multiple times with XCode. Here's what I'm doing and the errors I'm getting:
First, I always evaluate the command
Needs["CCompilerDriver`"]
If I set the compilation target to C,
c = Compile[ {{x}}, x^2 + Sin[x^2], CompilationTarget -> "C"];
I get an error that reads: Compile::nogen : A library could not be created from the compiled function.
If I try to create a library,
demoFile = FileNameJoin[{$CCompilerDirectory,"SystemFiles","CSource","createDLL_demo.c"}];
lib = CreateLibrary[{demoFile},"testLibrary"]
I get an message $Failed. Wolfram says that this is because I don't have a C compiler installed. I find that hard to believe because when I run
CCompilers[]
It tells me that I've got GCC installed: {{"Name" -> "GCC",
"Compiler" -> CCompilerDriver'GCCCompiler`GCCCompiler,
"CompilerInstallation" -> "/usr/bin", "CompilerName" -> Automatic}}
What's more, terminal says I have GCC installed too!! Any help would be appreciated. I'd really like to compile Mathematica to C.
In this answer I'll collect some debugging steps for similar problems, for future reference. Feel free to edit/improve them.
If compiling to C code does not work from Mathematica 8,
Check that you have a supported C compiler installed and it works (the obvious).
Note that the compiler does not necessarily have to be in the PATH, at least on Windows/Visual Studio it doesn't.
Check that Mathematica recognizes the compiler
<< CCompilerDriver`
CCompilers[]
will list the compilers known to Mathematica.
Check what commands Mathematica executes to compile the generated C code:
Compiler`$CCompilerOptions = {"ShellCommandFunction" -> Print};
Compile[{{x}}, x^2, CompilationTarget -> "C"];
Note that with "ShellCommandFunction" -> Print the commands will not be executed, so you'll need to re-set Compiler`$CCompilerOptions to {} after this step is complete to allow command execution again.
Check the output/errors from the compiler:
Compiler`$CCompilerOptions = {"ShellOutputFunction" -> Print};
Compile[{{x}}, x^2, CompilationTarget -> "C"];
These last two steps will hopefully give you enough clues to proceed. With this information you can check if the correct library / include paths are passed to the compiler (in the case of gcc/icc, look at the -L option which specifies library paths and the -I option which specifies include paths). Then check if the required include and library files are present at those paths.
If you get Compile::nogen, you can see the compiler output by setting ShellOutputFunction->Print right in the Compile expression:
c = Compile[ {{x}}, x^2 + Sin[x^2],
CompilationTarget -> {"C", "ShellOutputFunction"->Print}];
In general, this is how you can pass options to the underlying CreateLibrary call, by changing CompilationTarget->"C" to CompilationTarget->{"C", options}. Setting Compiler`$CCompilerOptions works too, but this technique has the advantage of not setting a global variable.
It is a shame that the only error you are seeing is $Failed, that's not terribly helpful; I wonder if perhaps there are some file or directory permissions problems?
I'm running on linux not Mac so I am not sure if my setup is "close enough" or not. On my machine your Compile command succeeds and generates a file .Mathematica/ApplicationData/CCompilerDriver/BuildFolder/blackie-desktop-5077/compiledFunction1.so in my home directory. Is there any way you can find a .Mathematica directory associated with your userid, and see if it exists and is writeable by mathematica?
Also, you could check to see if "gcc" is or is not being accessed by checking the file access time of /usr/bin/gcc before and after your call to Compile. From an operating system shell you can do ls -lu /usr/bin/gcc or from Mathematica perhaps Import["!ls -lu /usr/bin/gcc", "Text"]
Sorry if the question is worded wrong - I don't know the right word for what I'm asking for! :)
Say, you have some simple C program like:
#include <stdio.h>
int main()
{
int a=2;
printf("Hello World %d\n", a);
return 0;
}
Typically, this would have to be saved in a file (say, hello.c); then we run gcc on the source file and obtain executable file - and if we compiled in debug information, then we can use gdb on the executable, to step through lines of code, and inspect variables.
What I would like to have, is basically some sort of a "C" shell - similar to the Python shell; in the sense that I can have a sequence of Python commands in a file (a script) - or I can just paste the same commands in the shell, and they will execute the same. In respect to the simple program above, this is what I'd like to be able to do (where C> represents the imagined prompt):
C> #include <stdio.h>
(stdio.h included)
C> int a=2;
C> printf("Hello World %d\n", a);
Hello World 2
C>
In other words, I'd like to be able to execute individual C commands interactively (I'm guessing this would represent on-the-fly compilation of sorts?). Initially I was misled by the name of the C shell (csh) - but I don't think it will be able to execute C commands on the fly.
So, first and foremost, I'd like to know if it is possible somehow to persuade, say, gdb to perform in this manner? If not, is there anything else that would allow me to do something similar (some special shell, maybe)?
As for the context - I have some code where I have problems troubleshooting pointers between structs and such; here the way gdb can printout structs works very well - however, to isolate the problem, I have to make new source files, paste in data, compile and debug all over again. In this case, I'd much rather have the possibility to paste several structs (and their initialization commands) in some sort of a shell - and then, inspect using printf (or even better, something akin to gdb's print) typed directly on the shell.
Just for the record - I'm not really persuaded something like this really exists; but I thought I'd ask anyways :)
Thanks in advance for any answers,
Cheers!
EDIT: I was a bit busy, so haven't had time to review all answers yet for accept (sorry :) ); just wanted to add a little comment re:"interpreted vs. machine code"; or as mentioned by #doron:
The problem with running C /C++ source interactively is that
the compiler is not able to perform line by line interpretation of the code.
I am fully aware of this - but let's imagine a command line application (could even be an interpreted one), that gives you a prompt with a command line interface. At start, let's assume this application generates this simple "text file" in memory:
##HEADER##
int main()
{
##MAIN##
return 0;
}
Then, the application simply waits for a text to be entered at the prompt, and ENTER to be pressed; and upon a new line:
The application checks:
if the line starts with #define or #include, then it is added below the ##HEADER## - but above the int main() line - in the temp file
anything else, goes below ##MAIN## line - but above return 0; line - in the temp file
the temp file is stripped of ##HEADER## and ##MAIN## lines, and saved to disk as temp.c
gcc is called to compile temp.c and generate temp.out executable
if fail, notify user, exit
gdb is called to run the temp.out executable, with a breakpoint set at the return 0; line
if fail, notify user, exit
execution is returned to the prompt; the next commands the user enters, are in fact passed to gdb (so the user can use commands like p variable to inspect) - until the user presses, say, Ctrl+1 to exit gdb
Ctrl+1 - gdb exits, control is returned to our application - which waits for the next code line all over again.. etc
(subsequent code line entries are kept in the temp file - placed below the last entry from the same category)
Obviously, I wouldn't expect to be able to paste the entire linux kernel code into an application like this, and expect it to work :) However, I would expect to be able to paste in a couple of structs, and to inspect the results of statements like, say:
char dat = (char) (*(int16_t*)(my->structure->pdata) >> 32 & 0xFF) ^ 0x88;
... so I'm sure in what is the proper syntax to use (which is usually what I mess up with) - without the overhead of rebuilding and debugging the entire software, just to figure out whether I should have moved a right parenthesis before or after the asterisk sign (in the cases when such an action doesn't raise a compilation error, of course).
Now, I'm not sure of the entire scope of problems that can arise from a simplistic application architecture as above. But, it's an example, that simply points that something like a "C shell" (for relatively simple sessions/programs) would be conceptually doable, by also using gcc and gdb - without any serious clashes with the, otherwise, strict distinction between 'machine code' and 'interpreted' languages.
There are C interpreters.
Look for Ch or CINT.
Edit: found a new (untested) thing that appears to be what the OP wants
c-repl
Or just use it [...] like driving a Ferarri on city streets.
Tiny C Compiler
[... many features, including]
C script supported : just add '#!/usr/local/bin/tcc -run' at the first line of your C source, and execute it directly from the command line.
When your CPU runs a computer program, it runs something called machine code. This is a series of binary instructions that are specific to the CPU that you are using. Since machine code is quite hard to hand code, people invented higher level languages like C and C++. Unfortunately the CPU only understands machine code. So what happens is that we run a compiler that converts the high-level source language into machine code. Computer languages in this class are compiled language like C and C++. These languages are said to run natively since the generated machine code is run by the CPU without any further interpretation.
Now certain languages like Python, Bash and Perl do not need to be compiled beforehand and are rather interpreted. This means that the source file is read line by line by the interpreter and the correct task for the line is performed. This gives you the ability run stuff in an interactive shell as we see in Python.
The problem with running C /C++ source interactively is that the compiler is not able to perform line by line interpretation of the code. It is designed solely to generate corresponding machine code and therefore cannot run your C / C++ source interactively.
#buddhabrot and #pmg - thank you for your answers!
For the benefit of n00bery, here is a summary of the answers (as I couldn't immediately grasp what is going on): what I needed (in OP) is handled by what is called a "C Interpreter" (not a 'C shell'), of which the following were suggested:
CINT | ROOT - Ubuntu: install as sudo apt-get install root-system-bin (5.18.00-2.3ubuntu4 + 115MB of additional disk space)
c-repl (c-repl README)- Ubuntu: install as sudo apt-get install c-repl (c-repl_0.0.20071223-1_i386.deb + 106kB of additional disk space)
Ch standard edition - standard edition is freeware for windows/Unix
For c-repl - there is a quick tutorial on c-repl homepage as an example session; but here is how the same commands behave on my Ubuntu Lucid system, with the repository version (edit: see Where can I find c-repl documentation? for a better example):
$ c-repl
> int x = 3
> ++x
> .p x
unknown command: p
> printf("%d %p\n", x, &x)
4 0xbbd014
> .t fprintf
repl is ok
> #include <unistd.h>
<stdin>:1:22: warning: extra tokens at end of #include directive
> getp
p getp
No symbol "getp" in current context.
> printf("%d\n", getpid())
10284
> [Ctrl+C]
/usr/bin/c-repl:185:in `readline': Interrupt
from /usr/bin/c-repl:185:in `input_loop'
from /usr/bin/c-repl:184:in `loop'
from /usr/bin/c-repl:184:in `input_loop'
from /usr/bin/c-repl:203
Apparently, it would be best to build c-repl from latest source.
For cint it was a bit difficult to find something relateed to it directly (the webpage refers to ROOT Tutorials instead), but then I found "Le Huy: Using CINT - C/C++ Interpreter - Basic Commands"; and here is an example session from my system:
(Note: if cint is not available on your distribution's package root-system-bin, try root instead.)
$ cint
cint : C/C++ interpreter (mailing list 'cint#root.cern.ch')
Copyright(c) : 1995~2005 Masaharu Goto (gotom#hanno.jp)
revision : 5.16.29, Jan 08, 2008 by M.Goto
No main() function found in given source file. Interactive interface started.
'?':help, '.q':quit, 'statement','{statements;}' or '.p [expr]' to evaluate
cint> L iostream
Error: Symbol Liostream is not defined in current scope (tmpfile):1:
*** Interpreter error recovered ***
cint> {#include <iostream>}
cint> files
Error: Symbol files is not defined in current scope (tmpfile):1:
*** Interpreter error recovered ***
cint> {int x=3;}
cint> {++x}
Syntax Error: ++x Maybe missing ';' (tmpfile):2:
*** Interpreter error recovered ***
cint> {++x;}
(int)4
cint> .p x
(int)4
cint> printf("%d %p\n", x, &x)
4 0x8d57720
(const int)12
cint> printf("%d\n", getpid())
Error: Function getpid() is not defined in current scope (tmpfile):1:
*** Interpreter error recovered ***
cint> {#include <unistd.h>}
cint> printf("%d\n", getpid())
10535
(const int)6
cint> .q
Bye... (try 'qqq' if still running)
In any case, that is exactly what I needed: ability to load headers, add variables, and inspect the memory they will take! Thanks again, everyone - Cheers!
Python and c belongs to different kinds of language. Python is interpreted line by line when running, but c should compile, link and generate code to run.