I have developed a ShinyApp that is built around a C++ program. In short, what the app does is :
provides a nice interface to setup the parameters (in a text file) for the C++ app
runs the C++ compiled code using the system(...) command
displays the output of the C++ code using ggplot2
The C++ compiled code is stored into the www folder. Locally it works fine, but when I load the app to the shinyapp website (I have a free subscription), I got the following error:
sh: 1: ./a.out: Permission denied
with a.out being my compile c++ code. Any idea if
I am doing something wrong?
It is possible call a compiled c++ code within shinyapp.io?
This is a super old question, but since I stumbled on it looking for an answer for my identical problem, I would share what worked for me.
I didn't try the .bat suggestion mentioned in the comments, because that seemed to be tied to Windows OS and Shiny uses Linux.
Instead, I used R's Sys.chmod() function. In your case, if you are calling system("a.out"), before that line, put Sys.chmod("a.out", mode="777"). Note that you may want to look more into what chmod does with regards to permissions. But the code would look like:
// ...
Sys.chmod("a.out", mode="777")
system("a.out")
// ... remaining code
Related
I am trying to process a binary file generated by a PSI DRS4 for work. I tried this using a C++ code given in the src folder of the software used to run the board.
A friend of mine compiled and executed this code on his linux computer just fine. I wanted to adapt this code to windows. I went through the compilation step pretty easily but then when I try to execute it, it just crashes...
After some further investigation, what I understand is that the header(s) cannot be read properly (probably leading to the crash when they're supposed to be used later in the code)
I thus tried to read the file with HexEditor Neo and here is what I get: screenshot binary file Hexeditor
As you see the part after EHEADER becomes unreadable... Is it normal? Has anyone faced this situation before ?
I recently installed ldc through hombrew on my Mac and was testing out running a code as a script from the D wiki when I noticed that using ldmd2 to compile my program doesn't also run my program after. Whats the difference then since this is the same behavior as running ldc2.
Heres my program
import std.stdio;
void main()
{
writeln("Hello, world without explicit compilations!");
}
EDIT:
The website states "For small projects it's handy to compile and run in a single step. Most (if not all) compiler packages, contain a tool named rdmd/gdmd/ldmd or similar. For instructional purposes we'll call it rdmd." What im taking from this is it depends on which compiler your using but in the case of ldc I should be using ldmd.
ldmd2 is just a wrapper script for ldc2 which converts argument formats from dmd style over to ldc style.
So it does exactly the same thing, just some options and flags on the compile command line have different names and stuff like that.
The link is talking about rdmd which is a separate program that recursively grabs dependencies, compiles, and automatically runs. rdmd works on top of the compiler and might have been packaged with it or might need to be downloaded separately.
Its source lives here: https://github.com/D-Programming-Language/tools/blob/master/rdmd.d
and it is compatible with ldmd2's option formats.
My goal is to create a package in R with C++ code: So my questions is how?
I am following the tutorial http://www.stat.columbia.edu/~gelman/stuff_for_blog/AlanRPackageTutorial.pdf on creating an R package containing C++ code. The specific code Im trying to compile and package is exactly as described in the tutorial.
R CMD SHLIB seems to be working creating .dll file.
I can load in R using dyn.load() and test it on simulated data (as described in tutorial)
R CMD INSTALL is where the problem begins. I have done two things encountering two different errors supposedly related:
1) The tutorial says the NAMESPACE file is supposed to contain the code:
useDynLib(XDemo)
export(XDemoAutoC)
When it does R CMD INSTALL fail resulting in error:
Error in inDL(x,as.logical(local), as.logical(now),...): unable to
load shared object 'C:/.../libs/i386/XDemo.dll': Loadlibrary failure:
1% is not a valid Win32-program
2) Removing the above mentioned lines in NAMESPACE file will result in installation of package. I can succesfully load it in R but when I try to use the R function that makes a .C() call to the C++ written function I another error:
library(newpackage)
ls(package:newpackage)
[[1]] "XDemoAutoC"
Warning message:
In ls(package:newpackage) :
‘package:newpackage’ converted to character string
XDemoAutoC(c(1,2,3,4))
Error in .C("DemoAutoCor", OutVec = as.double(vector("numeric", OutLength)), :
C symbol name "DemoAutoCor" not in load table
Im running version R2.15.2 on windows 64-bit and using R64 bit.
I read the following post with a similar problem:
http://r.789695.n4.nabble.com/Include-C-DLL-error-in-C-symbol-name-not-in-load-table-td3464021.html
Except they mention nothing about the NAMESPACE-matter.
Also I read this post:
Problem with loading compiled c code in R x64 using dyn.load
So I am thinking: that based on the fact that I am able to use dyn.load() in Rx64 means that I have succesfully created x64 .dll. Assuming that the NAMESPACE file is supposed to be left as in the tutorial - hopefully fixing the >>not in load table<< error - this would mean I should focus on fixing problem one. This problem seems to be caused by something related to 32-bit. I have used Dependency Walker on the .dll file but I am not sure how to interpret the results
I really don't have any ideas on how to fix this problem so any suggestion on what to do would be welcome?
I think you are doing it wrong. Two quick suggestions:
Read the Writing R Extensions manual written to explain just this: writing R extensions including those with compiled code
Have a look at Rcpp which makes R and C++ extensions, including package building so much easier. Or so we think. Writing a package is as easy as calling Rcpp.package.skeleton(). The documentation in 1) still help.
That said, if R CMD INSTALL fails you may have some mixup in your $PATH. Never ever mix MinGW and Cygwin. Make sure no Cygwin DLLs are found when you build or call R. Path order matters greatly. See the manual for details.
I have a batch file that tries to compile a static library using Borland C++ Builder 6.0
It is called from Borland make (makefile created with bpr2mak) which is called from a .bat file (used to compile the whole project with Visual Studio and some Borland C++ Builder legacy projects), which is called from a bash shell script running inside Cygwin.
When I run the .bat file directly from a Cygwin shell, it runs OK, but when its being run from a Program calling cygwin with Boost::Process::launcher I'm getting this error:
C:\ARQUIV~1\Borland\CBUILD~1\Bin\..\BIN\TLib /u bclibs.lib #MAKE0000.###
DOS-reported error: Bad file number
TLIB 4.5 Copyright (c) 1987, 1999 Inprise Corporation
opening 'MAKE0000.###'
** error 1 ** deleting bclibs.lib
It's a complicated scenario, but this Program which calls cygwin is run whenever we need to build our software package which needs to be build for various Linux distos and Windows 32 and 64-bit.
Note: It's the only Borland Project failing, the other compile just fine (it's the only static library using borland also, so it can be some problem with the TLib tool.
The problem was that TLib does not like to have his output redirected (seen here) without having an input pipe as well. Solved by creating an input pipe to in the Boost::Process::launcher using set_stdin_behavior
I'm just guessing here, but this may have to do with long filenames and/or spaces in paths.
1) Modify your makefile so it would save current environment to a file, immediately before executing the failing command (set > d:\env.txt & echo CD=%CD% >> d:\env.txt). Then run it both ways (directly and via program) and compare the environments of good run and bad run.
2) Using filemon from Sysinternals, capture logs of disk access in both cases (these logs are going to be huge, though you can uncheck everything except Open in the filter to reduce the size). Again, compare and check for clues...
3) Try instaling everything involved to paths conforming to 8.3 scheme.
This error is not related to C++ itself. It happens when your build script opens too much files (more than defined in DOS command processor environment). To resolve this issue try to set value of files variable to 253. For Windows XP this variable defined in the file %WINDIR%\system32\config.nt.
files=253
Seems it is known bug in Borland C++ tools. Here is description and possible workaround for this issue:
Problem: Some static Lib projects will
not link correctly when compiled. You might see something
like this :
J:\Borland\CBUILD~1\bin\..\BIN\TLib /u debug\jpegD.lib #MAKE0000.###
DOS-reported error: Bad file number
TLIB 4.5 Copyright (c) 1987, 1999 Inprise Corporation
opening 'MAKE0000.###'
** error 1 ** deleting debug\jpegD.lib
MAKE failed, returned : 1
Workaround : In some cases (where the "Bad file number" error is seen) it may be possible to work around this by specifying -tDEFLIB.BMK in the BPR2MAKE Options field, and Turning off the "Capture Make Output" option.
I have not tested it, but I hope that helps.
I'm trying to profile a C++ application, that I did not write, to get a sense for where the major computation points are. I'm not a C++ expert and even less so C++ debugging/profiling expert. I believe I am running into a (common?) problem with dynamic libraries.
I compile link to Google CPU Profiler using (OS X, G++):
env LIBS=-lprofiler ./configure
make
make install
I then run profile the installed application (jags) with:
env CPUPROFILE=./jags.prof /usr/local/bin/jags regression.cmd
pprof /usr/local/bin/jags jags.prof
Unfortunately, I get the error:
pprof /usr/local/bin/jags jags.prof Can't exec "objdump":
No such file or directory at /usr/local/bin/pprof line 2833.
objdump /System/Library/Frameworks/Accelerate.framework/Versions/A/
Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib: No such file or directory
The program dynamically links to libLAPACK.dylib. So prof does not seem to understand it (?). I thought about trying to statically link, but the documents associated with the program say that it is impossible to statically link in LAPACK or BLAS (two required libraries).
Is there a way to have the profiler ignore libLAPACK? I'm okay if it doesn't sample within libLAPACK. Or how might I get profiling to work?
This error was caused by jags being a shell script, that subsequently called profilable code.
pprof /usr/local/bin/REAL_EXEC jags.prof
fixes the problem.
I don't see a clean way to do it, but maybe there's a hacky workaround -- what happens if you hack the pprof perl script (or better a copy thereof;-), line 2834, so that instead of calling error it emits the message and then does return undef;?
If you're profiling on OSX, the Shark tool is really great as well. It's very simple to use, and has worked out of the box for me when I've tried it.