I want to use R's mathematical functions as provided in libRmath from Ocaml. I successfully installed the library via brew tap homebrew science && brew install --with-librmath-only r. I end up with a .dylib in /usr/local/lib and a .h in /usr/local/include. Following the Ocaml ctypes tutorial, i do this in utop
#require "ctypes.foreign";;
open Ctypes;;
open Foreign;;
let test_pow = foreign "pow_di" (float #-> int #-> returning float);;
this complains that it can't find the symbol. What am I doing wrong? Do I need to open the dynamic library first? Set some environment variables? After googling, I also did this:
nm -gU /usr/local/lib/libRmath.dylib
which gives a bunch of symbols all with a leading underscore including 00000000000013ff T _R_pow_di. In the header file, pow_di is defined via some #define directive from _R_pow_di. I did try variations of the name like "R_pow_di" etc.
Edit: I tried compiling a simple C program using Rmath using Xcode. After setting the include path manually to include /usr/local/include, Xcode can find the header file Rmath.h. However, inside the header file, there is an include of R_ext/Boolean.h which does not seem to exist. This error is flagged by Xcode and compilation stops.
Noob alert: this may be totally obvious to a C programmer...
In order to use external library you still need to link. There're at least two different ways, either link using compiler, or link even more dynamically using dlopen.
For the first method use the following command (as an initial approximation):
ocamlbuild -pkg ctypes.foreign -lflags -cclib,-lRmath yourapp.native
under premise that your code is put into yourapp.ml file.
The second method is to use ctypes interface to dlopen to open the library. Using the correct types and name for the C function call, this goes like this:
let library = Dl.dlopen ~filename:"libRmath.dylib" ~flags:[]
let test_pow = foreign ~from:library "R_pow_di" (double #-> int #-> returning double)
Related
I am very new to Frama-c and I got an issue when I am trying to open a C source file.
The error shows as
"fatal error: event.h: No such file or directory. Compilation terminated".
[kernel] Parsing FRAMAC_SHARE/libc/__fc_builtin_for_normalization.i (no preprocessing)
[kernel] Parsing WorkSpace/bipbuffer.c (with preprocessing)
[kernel] user error: failed to run: gcc -E -C -I. -dD -D__FRAMAC__ -nostdinc -D__FC_MACHDEP_X86_32 -I/usr/share/frama-c/libc -o '/tmp/bipbuffer.ce6d077.i' '/home/xxx/WorkSpace/bipbuffer.c' you may set the CPP environment variable to select the proper preprocessor command or use the option "-cpp-command".
[kernel] user error: stopping on file "/home/xxx/WorkSpace/bipbuffer.c" that has errors. Add'-kernel-msg-key pp' for preprocessing command.
So bascially I am trying to open a C source file but it returns an error like this. I aslo tried other very simple C files like hello world and other slicing functions, it works well.
I thought it was because I didn't have the dependencies of 'event.h' but it still return these errors after I installed the libevent dependencies. I am not sure if I need to manually set some path of the dependencies for frama-c
Here is part of the C file (Source link: https://memcached.org/) that I would like to open:
#include "stdio.h"
#include <stdlib.h>
/* for memcpy */
#include <string.h>
#include "bipbuffer.h"
static size_t bipbuf_sizeof(const unsigned int size)
{
return sizeof(bipbuf_t) + size;
}
int bipbuf_unused(const bipbuf_t* me)
{
if (1 == me->b_inuse)
/* distance between region B and region A */
return me->a_start - me->b_end;
else
return me->size - me->a_end;
}
......
Thanks,
Compilers and other tools working with C source code need to know where to find header files. There are some standard places where they look automatically, but Frama-C has fewer of those than (and different ones from) a normal compiler.
You need to find out where event.h is installed, then pass something like -cpp-extra-args "-I /path/to/directory/" to Frama-C. Pass the directory name only, not including the name event.h itself.
In addition to Isabelle Newbie's answer, I'd like to point out that the Chlorine version of Frama-C, whose beta has been recently announced, features a new option -json-compilation-database that attempts to read the arguments to be passed to the pre-processor from a compilation database.
Such database can be generated directly by cmake, but there are solutions for make-based project such as the one you refer to, in particular bear, which intercepts the commands launched by make to build the database.
Here's a detailed summary of how you could proceed, using the new -json-compilation-database option from Frama-C 17 Chlorine, plus an extra script list_files.py (which is not in the beta, but will be available in the final 17 release, and can be downloaded here):
Get the source files you want to analyze with Frama-C, run ./configure, and if possible try to disable optional dependencies from external libraries; for instance, some code bases include optional dependencies based on availability of libraries/system features, but have fallback options (resorting to standard C library or POSIX functions). The more you give Frama-C, the better the chances of analyzing it well, so if such external libraries are not essential, excluding them might help get a more "POSIXy" code, which should help. This is typically visible in config.h files, in macros commonly named HAVE_*.
Compile and install Build EAR or some equivalent tool to obtain a compile_commands.json file.
Run bear make (or cmake with flag CMAKE_EXPORT_COMPILE_COMMANDS) to get the compile_commands.json file.
Run the aforementioned list_files.py in the directory containing compile_commands.json to obtain the list of C sources used during compilation.
Run Frama-C (17 Chlorine or newer), giving it the list of sources found in the previous step, plus option -json-compilation-database . to parse the compile_commands.json and, hopefully, get the appropriate preprocessing flags.
Ideally, this should suffice, but in practice, this is rarely enough. In particular due to the presence of external libraries and non-C99, non-POSIX functions, the following steps are always needed.
6. Inclusion of external libraries
At this step, Frama-C will complain about the lack of event.h. You'll have to include the headers of this library yourself. Note: copying headers directly from your /usr/include is not likely to work, due to several architecture-specific definitions, especially files such as bits/*.h..
Instead, consider downloading the external libraries and preparing them (e.g. running ./configure at least). Then manually add the extra include directory via -cpp-extra-args="-I <path/to/your/sources/for/libevent.h>/include".
7. Inclusion of missing non-POSIX headers
Some other headers may be missing, in particular GNU- or BSD-specific sources (e.g. sysexits.h). Get these headers and add them when necessary. The error message in this case comes from the preprocessor (gcc) and is similar to this:
memcached.c:51:10: fatal error: sysexits.h: No such file or directory
#include <sysexits.h>
^~~~~~~~~~~~
compilation terminated.
8. Definition of missing non-POSIX types and constants
At this point, all necessary headers should be available, but parsing with Frama-C may still fail. This is due to usage of non-POSIX type definitions (e.g. caddr_t, struct ling), non-POSIX constants (e.g. MAXPATHLEN, SOCK_NONBLOCK, NI_MAXSERV). Error messages typically resemble the following:
[kernel] memcached.c:3261: Failure: Cannot resolve variable MAXPATHLEN
Constants are often easy to provide manually, by grepping what's available in your /usr/include.
Type definitions, on the other hand, may require some copy-pasting at the right places, especially if they depend on other types which are also missing. This step is hardly automatizable, but relatively straightforward once you get used to some specific error messages.
For instance, the following error message is related to a missing type definition (caddr_t):
[kernel] Parsing memcached.c (with preprocessing)
[kernel] memcached.c:1074:
syntax error:
Location: line 1074, between columns 38 and 47, before or at token: c
1072 *hdr++ = 0;
1073 *hdr++ = 0;
1074 assert((void *) hdr == (caddr_t)c->msglist[i].msg_iov[0].iov_base + UDP_HEADER_SIZE);
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
1075 }
1076
Note that the token just before c is (caddr_t), which has never been defined (it is often defined as either void * or char *).
The following error message is related to an incomplete type, i.e., a struct used somewhere but never defined:
[kernel] memcached.c:5811: User Error:
variable `ling' has initializer but incomplete type
It means that variable ling's type, which is struct linger (non-POSIX), has never been defined. In this case, we can copy it from our /usr/include/bits/socket.h:
struct linger
{
int l_onoff; /* Nonzero to linger on close. */
int l_linger; /* Time to linger. */
};
Note: if there are POSIX constants/definitions missing from Frama-C's libc, consider notifying its developers, or proposing pull requests in Frama-C's Github.
9. Fixing incompatible and missing function prototypes
Parsing is likely to succeed after the previous step, but it may still fail due to incompatible function prototypes. For instance, you may get:
[kernel] User Error: Incompatible declaration for usleep:
different integer types int and unsigned int
First declaration was at assoc.c:238
Current declaration is at items.c:1573
This is the consequence of a warning emitted earlier:
[kernel:typing:implicit-function-declaration] slabs.c:1150: Warning:
Calling undeclared function usleep. Old style K&R code?
It means that function usleep is called, but it does not have a prototype, therefore Frama-C uses the pre-C99 convention of "implicit int": it generates such a prototype, but later in the code, an actual declaration of usleep is found, and its type is not int. Hence the error.
To prevent this, you need to ensure usleep's prototype is properly included. Since it is not POSIX.1-2008, you need to either define/undefine the appropriate macros (see unistd.h), or add your own prototype.
At the end, this should allow Frama-C to parse the files and build an AST.
However, there are several missing prototypes yet; we were just lucky that none conflicted with actual declarations. Ideally, you'll consider the parsing stage done when there are no more messages such as implicit-function-declaration and similar warnings.
Some of the missing prototypes in memcached, such as getsubopt, are POSIX and should be integrated into Frama-C's standard library. Others might make part of a small library of non-standard stubs, to be reused for other software.
Contributing with results for future reuse
Successful conclusion of the parsing stage for such open source libraries is enough to consider them for integration into this repository of open source case studies, so that future users can start their analyses without having to redo all of these steps. (The repository is oriented towards Eva, but not exclusively: parsing is useful for all of Frama-C plug-ins.)
I would like to know how in the Julia language, I can determine if a file.jl is run as script, such as in the call:
bash$ julia file.jl
It must only in this case start a function main, for example. Thus I could use include('file.jl'), without actually executing the function.
To be specific, I am looking for something similar answered already in a python question:
def main():
# does something
if __name__ == '__main__':
main()
Edit:
To be more specific, the method Base.isinteractive (see here) is not solving the problem, when using include('file.jl') from within a non-interactive (e.g. script) environment.
The global constant PROGRAM_FILE contains the script name passed to Julia from the command line (it does not change when include is called).
On the other hand #__FILE__ macro gives you a name of the file where it is present.
For instance if you have a files:
a.jl
println(PROGRAM_FILE)
println(#__FILE__)
include("b.jl")
b.jl
println(PROGRAM_FILE)
println(#__FILE__)
You have the following behavior:
$ julia a.jl
a.jl
D:\a.jl
a.jl
D:\b.jl
$ julia b.jl
b.jl
D:\b.jl
In summary:
PROGRAM_FILE tells you what is the file name that Julia was started with;
#__FILE__ tells you in what file actually the macro was called.
tl;dr version:
if !isdefined(:__init__) || Base.function_module(__init__) != MyModule
main()
end
Explanation:
There seems to be some confusion. Python and Julia work very differently in terms of their "modules" (even though the two use the same term, in principle they are different).
In python, a source file is either a module or a script, depending on how you chose to "load" / "run" it: the boilerplate exists to detect the environment in which the source code was run, by querying the __name__ of the embedding module at the time of execution. E.g. if you have a file called mymodule.py, it you import it normally, then within the module definition the variable __name__ automatically gets set to the value mymodule; but if you ran it as a standalone script (effectively "dumping" the code into the "main" module), the __name__ variable is that of the global scope, namely __main__. This difference gives you the ability to detect how a python file was ran, so you could act slightly differently in each case, and this is exactly what the boilerplate does.
In julia, however, a module is defined explicitly as code. Running a file that contains a module declaration will load that module regardless of whether you did using or include; however in the former case, the module will not be reloaded if it's already on the workspace, whereas in the latter case it's as if you "redefined" it.
Modules can have initialisation code via the special __init__() function, whose job is to only run the first time a module is loaded (e.g. when imported via a using statement). So one thing you could do is have a standalone script, which you could either include directly to run as a standalone script, or include it within the scope of a module definition, and have it detect the presence of module-specific variables such that it behaves differently in each case. But it would still have to be a standalone file, separate from the main module definition.
If you want the module to do stuff, that the standalone script shouldn't, this is easy: you just have something like this:
module MyModule
__init__() = # do module specific initialisation stuff here
include("MyModule_Implementation.jl")
end
If you want the reverse situation, you need a way to detect whether you're running inside the module or not. You could do this, e.g. by detecting the presence of a suitable __init__() function, belonging to that particular module. For example:
### in file "MyModule.jl"
module MyModule
export fun1, fun2;
__init__() = print("Initialising module ...");
include("MyModuleImplementation.jl");
end
### in file "MyModuleImplementation.jl"
fun1(a,b) = a + b;
fun2(a,b) = a * b;
main() = print("Demo of fun1 and fun2. \n" *
" fun1(1,2) = $(fun1(1,2)) \n" *
" fun2(1,2) = $(fun2(1,2)) \n");
if !isdefined(:__init__) || Base.function_module(__init__) != MyModule
main()
end
If MyModule is loaded as a module, the main function in MyModuleImplementation.jl will not run.
If you run MyModuleImplementation.jl as a standalone script, the main function will run.
So this is a way to achieve something close to the effect you want; but it's very different to saying running a module-defining file as either a module or a standalone script; I don't think you can simply "strip" the module instruction from the code and run the module's "contents" in such a manner in julia.
The answer is available at the official Julia docs FAQ. I am copy/pasting it here because this question comes up as the first hit on some search engines. It would be nice if people found the answer on the first-hit site.
How do I check if the current file is being run as the main script?
When a file is run as the main script using julia file.jl one might want to activate extra functionality like command line argument handling. A way to determine that a file is run in this fashion is to check if abspath(PROGRAM_FILE) == #__FILE__ is true.
I have got a 16-bit MPU which is different from x86_16 in size of size_t, ptrdiff_t etc. Can anybody give me details and clear instructions about how to customize machine dependency in Frama-C for my MPU?
There is currently no way to do that directly from the command line: you have to write a small OCaml script that will essentially define a new Cil_types.mach (a record containing the necessary information about your architecture) and register it through File.new_machdep. Assuming you have a file my_machdep.ml looking like that:
let my_machdep = {
Cil_types.sizeof_short = 2;
sizeof_int = 2;
sizeof_long = 4;
(* ... See `cil_types.mli` for the complete list of fields to define *)
}
let () = File.new_machdep "my_machdep" my_machdep
You will then be able to launch Frama-C that way to use the new machdep:
frama-c -load-script my_machdep.ml -machdep my_machdep [normal options]
If you want to have the new machdep permanently available, you can make it a Frama-C plugin. For that, you need a Makefile of the following form:
FRAMAC_SHARE:=$(shell frama-c -print-share-path)
PLUGIN_NAME=Custom_machdep
PLUGIN_CMO=my_machdep
include $(FRAMAC_SHARE)/Makefile.dynamic
my_machdep must be the name of your .ml file. Be sure to choose a different name for PLUGIN_NAME. Then, create an empty Custom_machdep.mli file (touch Custom_machdep.mli should do the trick). Afterwards, make && make install should compile and install the plug-in so that it will be automatically loaded by Frama-C. You can verify this by launching frama-c -machdep help that should output my_machdep among the list of known machdeps.
UPDATE
If you are using some headers from Frama-C's standard library, you will also have to update $(frama-c -print-share-path)/libc/__fc_machdep.h in order to define appropriate macros (related to limits.h and stdint.h mostly).
I wrote
let fact x =
let result = ref 1 in
for i = 1 to x do
result := !result * i;
Printf.printf "%d %d %d\n" x i !result;
done;
!result;;
in a file named "Moduletest.ml", and
val fact : int -> int
in a file named "Moduletest.mli".
But, why don't they work?
When I tried to use in ocaml,
Moduletest.fact 3
it told me:
Error: Reference to undefined global `Moduletest'
What's happening?
Thanks.
OCaml toplevel is linked only with a standard library. There're several options on how to make other code visible to it:
copy-pasting
evaluating from the editor
loading files #use directive
making custom toplevel
loading with ocamlfind
Copy-pasting
This self-describing, you just copy code from some source and paste it into toplevel. Don't forget that toplevel won't evaluate your code until you add ;;
Evaluating from the editor
Where the editor is of course Emacs... Well, indeed it can be any other capable editor, like vim for example. This method is an elaboration of the previous, where the editor is actually responsible for copying and pasting the code for you. In Emacs you can evaluate the whole file with C-c C-b command, or you can narrow it to a selected area with C-c C-r, and the most granular is to use C-c C-e, i.e., evaluate an expression. Although it is slightly buggy.
Loading with #use directive.
This directive accepts a filename, and it will essentially copy and paste the code from the file. Notice, that it won't create a file-module for you/ For example, if you have file test.ml with this contents:
(* file test.ml *)
let sum x y = x + y
then loading it with the #use directive, will actually bring to your scope, sum value:
# #use "test.ml";;
# let z = sum 2 2
You mustn't to qualify sum with Test., because no Test module is actually created. #use directive merely copies the contents of the file to the toplevel. Nothing more.
Making custom toplevels
You can create your own toplevel with your code compiled in. It is an advanced theme, so I will skip it.
Loading libraries with ocamlfind
ocamlfind is a tool that allows you to find and load libraries, installed on your system, into your toplevel. By default, toplevel is not linked with any code except standard library. Even, not all parts of the library are actually linked, e.g., Unix module is not available, and needed to be loaded explicitly. There're primitive directives that can load any library, like #load and #include, but they are not for a casual user, especially if you have excellent ocamlfind at your disposal. Before using it, you need to load it, since it is also not available by default. The following command, will load ocamlfind and add few new directives:
# #use "topfind";;
In a process of loading it will show you a little hint on how to use it. The most interesting directive, that is added is #require. It accepts a library name, and loads (i.e., links) its code into toplevel:
# #require "unix";;
This will load a unix library. If you're not sure, about the name of the library you can always view all libraries with a #list command. The #require directive is clever and it will automatically load all dependencies of the library.
If you do not want to type all this directives every time you start OCaml top-level, then you cam create .ocamlinit file in your home directory, and put them there. This file will be loaded automatically on a top-level startup.
I have tested your code and it looks fine. You should "load" it from the OCaml toplevel (launched from the same directory as your .ml and .mli files) in the following way:
# #use "Moduletest.ml";;
val fact : int -> int = <fun>
# fact 4;;
4 1 1
4 2 2
4 3 6
4 4 24
- : int = 24
Is there a way to set the compiler warnings to be interpreted as an error in the Arduino IDE?
Or any generic way to set GCC compiler options?
I have looked at the ~/.arduino/preferences.txt file, but I found nothing that indicates fine-tuned control. I also looked if I could set GCC options via environment variables, but I did not find anything.
I don't want to have verbose compiler output (which you can specify using the IDE) that is way too much distracting non-essential information, and I don't want to waste my time on reading through it.
I want for a compilation to stop on a warning, so code can be cleaned up. My preference would be to be able to set -Werror= options, but a generic -Werror will do for the small code size of .ino projects.
Addendum:
Based on the suggestion in the selected answer, I implemented an avr-g++ script and put that in the path before the normal avr-g++. For that I changed the Arduino command as follows:
-export PATH="${APPDIR}/java/bin:${PATH}"
+export ORGPATH="${APPDIR}/java/bin:${PATH}"
+export PATH="${APPDIR}/extra:${ORGPATH}"
And in the new directory extra in the APPSDIR (where the Arduino command is located), I have
an avr-g++ which is a Python script:
#!/usr/bin/env python
import os
import sys
import subprocess
werr = '-Werror'
wall = '-Wall'
cmd = ['avr-g++'] + sys.argv[1:]
os.environ['PATH'] = os.environ['ORGPATH']
fname = sys.argv[-2][:]
if cmd[-2].startswith('/tmp'):
#print fname, list(fname) # this looks strange
for i, c in enumerate(cmd):
if c == '-w':
cmd[i] = wall
break
cmd.insert(1, werr)
subprocess.call(cmd)
So you replace the first command with the original compiler name and reset the environment used to exclude the extra directory.
The fname is actually strange. If you print it, it is only abc.cpp, but its length is much larger and it actually starts with /tmp. So I check for that to decide whether to add/update the compile options.
It looks like you are on Linux. Arduino is a script, so you can set PATH in the script to include a directory at the beginning to a directory containing a program, avr-g++. Then the Java stuff should take the compiler from there, should it not?
That program then calls the normal /usr/bin/avr-g++ with the extra options.
One option you have is to compile your sketches from the command line. Take a look at this makefile.