I've been following the link (Guidelines for including TMB c++ code in an R package) to include a .cpp TMB model into my R package (fishmethods).
I got it to work on Windows using a Makefile.win file with the code:
all: EP_likelihood.dll
# Comment here preserves the prior tab
EP_likelihood.dll: EP_likelihood.cpp
Rscript --vanilla -e "TMB::compile('EP_likelihood.cpp','-O0 -g',DLLFLAGS='')"
clean:
rm -rf *.dll
and, in the Description file, setting
LinkingTo: TMB
and adding "TMB" to the *Imports:" line. Also, I added to the "Namespace" file
importFrom("TMB","MakeADFun","sdreport")
and
useDynLib(EP_likelihood).
I am able to build and install the package on Windows. I want to make the .cpp model portable across platforms because the updated package will be put on CRAN. I've been reading the "Writing R Extensions" manual particularly under "Writing Portable Packages" but I don't understand fully what I have to do (I am not a professional programmer). Would anyone have any suggestions or have an example that I could examine?
Thanks in advance.
Related
I want to run serial commands from a Bealgebone to a 4Dsystems display. Therefore I copied the c library found here into a directory and created a test program main.c:
#include "Picaso_const4D.h"
#include "Picaso_Serial_4DLibrary.h"
int main(int argc,char *argv[])
{
OpenComm("/dev/ttyUSB0", B115200); // Matches with the display "Comms" rate
gfx_BGcolour(0xFFFF);
gfx_Cls();
gfx_CircleFilled(120,160,80,BLUE);
while (1) {}
}
Now when I do gcc -o main main.c its says
main.c:2:37: fatal error: Picaso_Serial_4DLibrary.h: No such file or
directory
So I try linking it:
gcc main.c -L. -lPICASO_SERIAL_4DLIBRARY
which gives me the same error. Then I tried to create a static library:
gcc -Wall -g -c -o PICASO_SERIAL_4DLIBRARY PICASO_SERIAL_4DLIBRARY.C
which gives me this:
PICASO_SERIAL_4DLIBRARY.C:1:21: fatal error: windows.h: No such file
or directory compilation terminated.
What am I doing wrong? the git page clearly says this library is created for people who do not run windows.
Thanks in advance!
You're not getting a linker error; you're getting a preprocessor error. Specifically, your preprocessor can't find Picaso_Serial_4DLibrary.h. Make sure that it's in your include path; you can add directories to your include path using the -I argument to gcc.
You've had two problems. First was the picaso_whatever.h file that couldn't be found. You fixed that with the -I you added. But, now, the picaso.h wants windows.h
What are you building on? WinX or BSD/Linux?
If you're compiling on WinX, you need to install the "platform sdk" for visual studio.
If you're using mingw or cygwin, you need to do something else.
If on WinX, cd to the C: directory. Do find . -type f -name windows.h and add a -I for the containing directory.
If under Linux, repeat the find at the source tree top level. Otherwise, there is probably some compatibility cross-build library that you need to install.
Or, you'll have to find WinX that has it as Picaso clearly includes it. You could try commenting out one or more of the #include's for it and see if things are better or worse.
If you can't find a real one, create an empty windows.h and add -I to it and see how bad [or good] things are.
You may need the mingw cross-compiler. See https://forums.wxwidgets.org/viewtopic.php?t=7729
UPDATE:
Okay ... Wow ... You are on the right track and close, but this is, IMO, ugly WinX stuff.
The primary need of Picaso is getting a serial comm port connection, so the need from within windows.h is [thankfully] minimal. It needs basic boilerplate definitions for WORD, DWORD, etc.
mingw or cygwin will provide their own copies of windows.h. These are "clean room" reimplementations, so no copyright issues.
mingw is a collection of compile/build tools that let you use gcc/ld/make build utilities.
cygwin is more like: I'd like a complete shell-like environment similar to BSD/Linux. You get bash, ls, gcc, tar, and just about any GNU utility you want.
Caveat: I use cygwin, but have never used mingw. The mingw version of windows.h [and a suite of .h files that it includes underneath], being open source, can be reused by other projects (e.g. cygwin, wine).
Under Linux, wine (windows emulator) is a program/suite that attempts to allow you to run WinX binaries under Linux (e.g. wine mywinpgm).
I git cloned the Picaso library and after some fiddling, I was able to get it to compile after pointing it to wine's version of windows.h
Picaso's OpenComm is doing CreateFile [a win32 API call]. So, you'll probably need cygwin. You're opening /dev/ttyUSB0. /dev/* implies cygwin. But, /dev/ttyUSB0 is a Linux-like name. You may need some WinX-style name like "COM:" or whatever. Under the cygwin terminal [which gives you a bash prompt], do ls /dev and see what's available.
You can get cygwin from: http://cygwin.com/ If you have a 64 bit system, be sure to use the 64 bit version of the installer: setup-x86_64.exe It's semi-graphical and will want two directories, one for the "root" FS and one to store packages. On my system, I use C:\cygwin64 and C:\cygwin64_packages--YMMV.
Note that the installer won't install gcc by default. You can [graphically] select which packages to install. You may also need some "devel" packages. They have libraries and .h files that a non-developer wouldn't need. As, docs mention, you can rerun the installer as often as you need. You can add packages that you forgot to specify or even remove ones that you installed that you don't need anymore.
Remember that you'll need to adjust makefile -I and/or -L option appropriately. Also, when building the picaso library, gcc generated a ton of warnings about overflow of a "large integer". The code was doing:
#define control_code -279
unsigned char buf[2];
buf[0] = control_code >> 8;
buf[1] = control_code;
The code is okay, and the warning is correct [because the code is sloppy]. If the code had done:
#define control_code -279
unsigned char buf[2];
buf[0] = (unsigned) control_code >> 8;
buf[1] = (unsigned) control_code;
it probably would have been silent. Use -Wno-overflow in your Makefile to get rid of the warnings rather that edit 50 or so lines
I'm trying to use YCM for the first time so in order to make it work I decided to give a chance for the YCM-Generator, which generates the .ycm_extra_conf.py file automatically based on the makefile.
So far my program is just a simple hello world.
#include <stdio.h>
int main()
{
printf("Hello World!");
return 0;
}
I'm using the CMakeLists.txt trick to generate the makefile.
file(GLOB sources *.h *.c)
add_executable(Foo ${sources})
then after executing the YCM-Generator script, I get this output
Running cmake in '/tmp/tmp_YknVy'... $ cmake
/home/pedro/Desktop/Projetos/teste
Running make... $ make -i -j4
Cleaning up...
Build completed in 1.5 sec
Collected 2 relevant entries for C compilation (0 discarded).
Collected 0 relevant entries for C++ compilation (0 discarded).
Created YCM config file with 0 C flags
YCM plugin does find the .ycm_extra_conf.py file, but the auto-completion doesn't work right, for example, if I type "floa", it doesn't suggests "float", but It only suggests things that I used before like "int" or "printf".
Am I missing something or this is working as intended?
So I fixed it.
For c it does require a .ycm_extra_conf.py , while a friend of mine could make it work without one in c++.
The auto complete only suggest automatically functions that were previously used, if you don't remember a function name you have to press <Ctrl-Space>
YCM-Generator didn't do the job, so I modified the example file myself following the comments.
If you are used to Visual Assist, the auto complete works but it's really weak if compared to VA, which is a shame... I really hope someone port that plugin to Linux.
I've already got Vim with YouCompleteMe plugin (compiled with semantic support for C-family languages), which I use for Python etc. Now I'd like to try it with C (I've never developed with C before, so I've got a slightly fuzzy idea about some details, like the necessary flags.)
To use YCM's semantic completion features with C, I need to provide it a .ycm_extra_conf.py file; the YCM user guide points to YCM's own .ycm_extra_conf.py as a reference (link).
Would the following (based on the aforesaid .ycm_extra_conf.py) produce "a minimal working setup" for C (to which I could then point g:ycm_global_ycm_extra_conf):
The flags:
flags = [
'-Wall', '-Wextra', '-Werror',
'-std=c11',
'-x', 'c'
]
and FlagsForFile function without the final_flags.remove( '-stdlib=libc++' ) line.
Otherwise the example file would remain as-it-is. I believe that -isystem flags are strictly YCM-related, is that correct?
I was searching for this too and seems here we haven't get a good solution. Even this is a very old question I hope this might help someone. The following works for me,
import os
import ycm_core
flags = [
'-Wall',
'-Wextra',
'-Werror',
'-Wno-long-long',
'-Wno-variadic-macros',
'-fexceptions',
'-ferror-limit=10000',
'-DNDEBUG',
'-std=c99',
'-xc',
'-isystem/usr/include/',
]
SOURCE_EXTENSIONS = [ '.cpp', '.cxx', '.cc', '.c', ]
def FlagsForFile( filename, **kwargs ):
return {
'flags': flags,
'do_cache': True
}
By the way, that long config file by the default bothers me so much. I should give credit for this post, http://cocoaspice.logdown.com/posts/302432-youcompleteme-toss-notes
Nothing at all is perfectly valid as long as the sources can be compiled by simply clang++ -c source (c vs. c++ is decided from extension). YCM happily completes in scratch tests created in random directories for me.
The -x c is not needed. If the source has extension .c or .h, it is assumed to be C and if it has extension .C, .cc, .cpp, .cxx, .H, .hh, .hpp or .hxx it is assumed C++. Only if you have C++ headers with just .h you need -x c++-header.
Newest clang (4.9) already defaults to c11 and c++11, so you shouldn't need those either.
So you only need any -I flags and the warnings are useful.
To give you a working example, here is the configuration I'm using for Arduino projects.
https://github.com/WeAreLeka/Bare-Arduino-Project/blob/master/.ycm_extra_conf.py
In the flags I've put all the Arduino libraries provided by the IDE and needed to compile my code.
I've also written a little function to find the other libraries in my /lib dir that I'm using in my project and to add them automatically to flags. It's line 57.
It's helpful if you use a lot of libs and don't want to modify your conf file each time.
Without the -I /path/to/lib/folder you won't get autocompletion.
Hope this helps :)
I have an open source project that relies on another open source project (let's call that other project X). Both are written in C. I've had to hack pieces of X to get multi-threading to work. This causes some issues when trying to package up the code for distribution. To make things easier, I've just included the entirety of X within mine along with the few little hacks I've made.
I'd like to do something more sophisticated now in order to keep the improved functionality of X (it has frequent releases and mine does not) without having to repackage the whole project (with my hacks) within my project again each time that X has a release.
There are only 3 or 4 functions in that need to override. I can follow what is going on in this IBM Tutorial, but how can I modify my Makefile.am to generate the Makefile changes suggested in that article? To summarize, the article suggests writing my own functions with the same signatures as the ones I want to override (in a file called libfuncs.c) and then add the following 'libs' target to the makefile:
all: libs setresgid-tester
libs: libfuncs.c
gcc -shared -Wl,-soname,libfuncs.so.1 -o libfuncs.so.1.0 libfuncs.c
ln -s libfuncs.so.1.0 libfuncs.so.1
ln -s libfuncs.so.1 libfuncs.so
setresgid-tester: setresgid-tester.c
gcc -o setresgid-tester setresgid-tester.c
All of that makes sense to me. What I need to do, however, is to have this 'libs' target created for me with the autotools. I have a Makefile.am works well right now. How do I modify it to produce the desired results above? It was difficult to find in the autotools documentation, but I may just not have known exactly what to look for.
I'm happy to provide more details if helpful. Thanks in advance.
I'm trying to accelerate a key function in a c project (not c++) using CUDA.
For some reason, i can't get the Makefile's to recognise the .cu extension when I change the name of one of the files to .cu.
It's using a configure script and .am/.in/.deps files, which I don't really understand all that well, but basically I grepped references to file.c and changed them all to file.cu, but it produces a file.o: File Not Found error.
Top level make file
https://www.dropbox.com/s/g282qvbdu8pdas0/Makefile
Src folder makefile
https://www.dropbox.com/s/b4pq026od8gauqi/Makefile
The search command I used was
grep -R -i "file.c"
and I simply changed them all to file.cu, then re-ran configure, make clean, make all - result is File Not Found.
I suppose it must be something to do with extensions being ignored/accepted by the Makefile, but as it's been a long time since I've programmed in C and I've never used such complex Makefiles I don't know how to fix it.
Any ideas?
*PS Also, file.cu has compile errors at the moment, but the error message I'm getting is File Not Found, so I think that's not the problem.
You need to have a rule to build o file from a cu file:
cudafile.o: cudafile.cu
nvcc $(NVCC_FLAGS) -c %< -o $#
So you also need to specify the rule for the cu file, and use nvcc for compilation.
The following guide seems to cover it...
http://mcclanahoochie.com/blog/2011/02/automake-and-cuda/
Actually, most of the advice given in the link seems unnecessary for basic compilation, but for some reason I found that when I re-created the config file using autoconf it worked. No explanation comes to mind.