i am new to stackflow and i previously i have no background in computer system and programming. However, now i need to run analysis under cygwin for my bioinformatics project. I encounter some error when i try to compile a file name 'zone_b.linux'using cygwin, to produce an executable program. The linux file is download from web https://github.com/haddocking/HADDOCK-binding-sites-tutorial/blob/master/ana_scripts/zone_b.linux. When i try to compile using the following command under cygwin it produce the following error:
$ gcc zone_b.linux
/usr/lib/gcc/i686-pc-cygwin/6.4.0/../../../libcygwin.a(libcmain.o): In
function `main':
/usr/src/debug/cygwin-2.9.0-3/winsup/cygwin/lib/libcmain.c:37: undefined
reference to `WinMain#16'
collect2: error: ld returned 1 exit status
Error description
I search the following error under stackoverflow, and i found two post with similar problem.
First is the post from undefined reference to `WinMain#16'. It stated that the problem is due the Microsoft'linker uses a runtime library entry point(winMainCRTStartup) that calls Microsoft's non-standard WinMain instead of standard main. So, i try the post's suggestion of including the entry by following command
$ gcc zone_b.linux /entry:winMainCRTStartup
gcc: error: /entry:winMainCRTStartup: No such file or directory
However i get the error no such file or directory. I think maybe it is because i am running under cygwin not mingW.
Second post is the Undefined reference to WinMain in Cygwin. From the post, it said use -c compile flag to only produce object file. However, for my case, i am not using any -c. Therefore, i think it is not relevant to my issue.
I would appreciate if anyone could kindly explain to me since i am new to this computing area. Thank you.
zone_b.linux is the compiled and linked executable program to run on a linux machine. It is a 32-bit ELF binary file. It will not work on a Windows machine, even using cygwin or mingw32, without re-compulation.
You probably have to compile zone_b.f, a FORTRAN source file, using the gfortran compiler to create a zone_b.exe that is usable in cygwin. I saw no instructions for this, but try something like gcc zone_b.f and cross fingers. Be sure gfortran is installed using cygwin setup.
You will also need to (re-)build the other executables (cluster_struc and contact) by performing make in the ana_scripts directory. Any supplied executables (from the git clone ... or a downloaded .zip file) will not work under cygwin.
You will need to have perl and python installed. I think perl is installed by default. You can install python2 using cygwin setup. The python script looked like it will work with python2 or python3, whichever is the default. On cygwin, today, python2 is the default python. I don't do perl, so cross your fingers.
Related
If you have an answer for this, or further information, I'd welcome it. I'm following advice from here, to offer some unsolicited help by posting this question then an answer I've already found for it.
I have a bare-metal ARM board for which I'm building a cross-toolchain, from sources for GNU binutils, gcc and gdb, and for SourceWare's Newlib. I got those four working and cross-built a DoNothing.c into an ELF file - but I couldn't disassemble it with this:
$ arm-none-eabi-objdump -S DoNothing.elf
The error was:
$ arm-none-eabi-objdump: error while loading shared libraries: libdebuginfod.so.1: cannot open shared object file: No such file or directory
I'll follow up with a solution.
The error was correct - my system didn't have libdebuginfod.so.1 installed - but I have another cross-binutils, installed from binary for a different target, and its objdump -S works fine on the same host. Why would one build of objdump complain about missing that shared library, when clearly not all builds of objdump need it?
First I tried rebuilding cross binutils, specifying --without-debuginfod as a configure option. No change, which seems odd: surely that should build tools that not only don't use debuginfod but which don't depend on it in any way. (If someone can answer that, or point out what I've misunderstood, it may help people.)
Next I figured debuginfod was inescapable (for my cross-tools built from source at least), so I'd install it to get rid of the error. It's a component of the elfutils package, but installing the latest elfutils available for my Ubuntu 20.04 system didn't bring libdebuginfod.so.1 with it.
I found a later one, for Arch Linux, whose package contents suggested it would - but its package format doesn't match Ubuntu's and installing it was going to involve a lot of work. Instead I opted to build it from the Arch Linux source package. However, running ./configure on that gave a couple of infuriatingly similar errors:
configure: checking libdebuginfod dependencies, --disable-libdebuginfod or --enable-libdebuginfo=dummy to skip
...
configure: error: dependencies not found, use --disable-libdebuginfod to disable or --enable-libdebuginfod=dummy to build a (bootstrap) dummy library.
No combination of those suggestions would allow configure for elfutils-0.182 to run to completion.
The problem of course was my own lack of understanding. The solution came from the Linux From Scratch project: what worked was to issue configure with both of the suggested options, like this:
$ ./configure --prefix=/usr \
--disable-debuginfod \
--enable-libdebuginfod=dummy \
--libdir=/lib
That gave a clean configure; make worked first time, as did make check and then sudo make install which of course installed libdebuginfod.so.1 as required. I then had an arm-none-eabi-objdump which disassembles cross-compiled ELF files without complaining.
I am trying to cross-compile my Rust project on Mac OS to Linux using cargo build --target=x86_64-unknown-linux-musl.
I installed the binary for Linux + musl cross-compilation on mac using brew install FiloSottile/musl-cross/musl-cross as I would ideally want a standalone binary.
I also installed the target using rustup target add x86_64-unknown-linux-gnu
And I have the following in my .cargo/config:
[target.x86_64-unknown-linux-musl]
linker = "x86_64-linux-musl-gcc"
However, I ran into issues with 2 libraries - sqlite3 and pcap:
= note: /usr/local/Cellar/musl-cross/0.9.8/libexec/bin/../lib/gcc/x86_64-linux-musl/6.4.0/../../../../x86_64-linux-musl/bin/ld: cannot find -lsqlite3
/usr/local/Cellar/musl-cross/0.9.8/libexec/bin/../lib/gcc/x86_64-linux-musl/6.4.0/../../../../x86_64-linux-musl/bin/ld: cannot find -lpcap
collect2: error: ld returned 1 exit status
I was able to solve the sqlite3 linker issue by adding features = ["bundled"] to my Cargo.toml file (similar to what is described here - https://users.rust-lang.org/t/linker-cannot-find-lsqlite3/23230/18) as that likely built it from source (which was great) but when I tried doing the same with pcap, it gave the following error:
the package `myProject` depends on `pcap`, with features: `bundled` but `pcap` does not have these features.
After reading somewhere I also tried (with low hopes) of providing the path to the installed libpcap on mac using RUSTPATH='-L/...' cargo build ... but that resulted, of course in undefined symbol errors.
Any ideas how can I get past this issue and cross compile my Rust project into a statically linked binary on macos to run on linux?
Cross compilation does not magically take care of libraries. You cannot just say "I want musl" and have something take care of all your dependencies.
The error message you are seeing is telling you exactly this: it cannot find libsqlite3 and libpcap.
The reason the error for sqlite disappears is because your sqlite library has a bundled feature, which replaces the linking with a built-in sqlite client. This, however, also requests the pcap bundled feature, which does not exist.
You have two options:
If you do not mind the performance loss in the bundled sqlite client, change your feature definition to target the feature of the dependency requiring sqlite
If you want the raw library itself, you will have to compile it for musl
No matter what happens, you will need to cross-compile libpcap for musl with the default sysroot provided by your musl compiler. As this varies per library, you will need to consult the libpcap documentation. once you have done so, you should be able to use the -lpcap flag, and the error will resolve itself.
I am trying to cabal install a component of wxHaskell (Haskell platform 2013.2 against wxWidgets 3.0).
I was able to compile the git version with 32 bit mingw from mingw.org. But in the end, the installed wx cannot function correct, and running a minimal example gives runtime exceptions in wxc.dll. So I try to compile the same thing under TDM-GCC 4.8.1 64bit, since the wxWidgets people provide their binary in the form of TDM-GCC compiled binaries.
But I immediately run into compilation errors with TDM-GCC, telling me
error: 'strnlen' was not declared in this scope
What surprises me is that even though both mingw32 and TDM-gcc uses the same external gcc from Haskell Platform c:\HaskellPlatform\2013.2.0.0\mingw\bin\gcc.exe, one would give an error while the other compiles fine.
The first file causing problem is src\cpp\eljaccelerator.cpp. It compiles OK under mingw32:
...
c:\HaskellPlatform\2013.2.0.0\mingw\bin\gcc.exe -Wl,--hash-size=31 -Wl,--reduce-
memory-overheads -Isrc/include -IC:/MinGW/msys/1.0/local/include/wx-3.0 -IC:/Min
GW/msys/1.0/local/lib/wx/include/msw-unicode-3.0 -D__WXMSW__ -DWXUSINGDLL -D_LAR
GEFILE_SOURCE=unknown -DwxcREFUSE_MEDIACTRL -DBUILD_DLL -c src\cpp\eljaccelerato
r.cpp -o dist\build\src/cpp/eljaccelerator.o
but gives an error under TDM-gcc:
Building wxc
c:\HaskellPlatform\2013.2.0.0\mingw\bin\gcc.exe -Wl,--hash-size=31 -Wl,--reduce-
memory-overheads -Isrc/include -IC:/mingw/msys/1.0/local/include/wx-3.0 -IC:/min
gw/msys/1.0/local/lib/wx/include/msw-unicode-3.0 -D__WXMSW__ -DWXUSINGDLL -D_FIL
E_OFFSET_BITS=64 -DwxcREFUSE_MEDIACTRL -DBUILD_DLL -c src\cpp\eljaccelerator.cpp
-o dist\build\src/cpp/eljaccelerator.o
In file included from C:/mingw/msys/1.0/local/include/wx-3.0/wx/crt.h:19:0,
from C:/mingw/msys/1.0/local/include/wx-3.0/wx/string.h:4305,
from C:/mingw/msys/1.0/local/include/wx-3.0/wx/memory.h:15,
from C:/mingw/msys/1.0/local/include/wx-3.0/wx/object.h:19,
from C:/mingw/msys/1.0/local/include/wx-3.0/wx/wx.h:15,
from src/include/wrapper.h:20,
from src\cpp\eljaccelerator.cpp:1:
C:/mingw/msys/1.0/local/include/wx-3.0/wx/wxcrt.h: In function 'size_t wxStrnlen
(const char*, size_t)':
C:/mingw/msys/1.0/local/include/wx-3.0/wx/wxcrt.h:173:92: error: 'strnlen' was n
ot declared in this scope
C:/mingw/msys/1.0/local/include/wx-3.0/wx/wxcrt.h: In function 'size_t wxStrnlen
(const wchar_t*, size_t)':
C:/mingw/msys/1.0/local/include/wx-3.0/wx/wxcrt.h:187:95: error: 'wcsnlen' was n
ot declared in this scope
Failed to install wxc-0.90.1.1
I was wondering if anyone has any similar experience. Any idea what went wrong and how to fix compilation for TDM-GCC? I tried adding #include <cstring> to wxcrt.h but it doesn't change anything.
FYI, I have compiled wxWidgets 3.0.0 from source in mingw and tdm-gcc versions respectively, using
./configure --enable-stl && make && make install
I can provide more details if needed.
First of all, wxWidgets certainly does work with MinGW, the fact that only TDM binaries are provided simply means that someone volunteered to provide the latter but not the former. But all three popular versions of MinGW (the two already mentioned and MinGW-w64) do work, so there must be something wrong with the build...
However while they all work, they are certainly different compilers, so what do you mean that they both use the same gcc binary? It must be either a MinGW one or a TDM one, but it can't be both at once.
It's also very suspicious that the configure detects different flags to use for the large file support. Look at config.log, something must have gone wrong and there must be some errors in the initial stage in it.
I'm attempting to compile a relatively simple Fortran executable so that it can be passed around to other Windows users that don't have Cygwin (or something of the sort) installed, however, I'm unable to get the executable to operate as a standalone. I've tried gfortran -static file.f and gfortran -static-libgfortran file.f, however other users always encounter this error:
The program can’t start because cygwin1.dll is missing from your computer. Try reinstalling the program to fix this problem.
From what I've read online (e.g. here), the -static option should be sufficient. I have verified that running the executable from my machine (DOS prompt) does work.
I have gcc (gfortran) version 4.7.3. I should also point out this is my first attempt at compiling portable Fortran.
Update
After realizing that this isn't a gfortran-specific issue (thanks to replies here), searches led me to related posts here and here
This is partially explained in the Cygwin FAQ. The solution is to install the mingw64-i686-gcc-fortran package with its dependencies, and cross-compile your code with i686-w64-mingw32-gfortran -static.
Just package the cygwin1.dll along with your binary file (both in the same folder) then it will run just fine.
I am trying to compile a simple hello world program in Haskell, with Haskell Platform 2011.2.0.1. If I load the code in WinGHCi, and use the GUI to compile, the .exe is created. Then I can run the .exe from Cygwin.
But if I try to compile the code in Cygwin (using ghc --make), linker fails. But again, if I compile from the Windows cmd prompt, then the compile+linker works fine.
Are there any other environment variables I need to import into Cygwin, to make the compile+linker work in it? I have put the following dirs in my Cygwin PATH: 2011.2.0.1/lib/extralibs/bin, 2011.2.0.1/bin (these are the only two valid Haskell related entries that I could see in the Windows environment variables).
I also noticed a couple of invalid items in the Windows environment variables (this looks like a bug in the Haskell installation):
(system var) C/ProgramFiles/Haskell/bin - this dir does not exist because I have installed Haskell in D disk.
(user var) userxxx/ApplicationData/cabal/bin - this dir does not exist.
I tried to file a bug report in HaskellPlatform, but I dont have permission to do it.
Without access to your development environment or a listing of the errors that you're getting, I can only assume that the issue is related to the way that you've set up your PATH.
GHC on Windows comes bundled with its own gcc compiler (for C code) and ld linker. If you've installed Cygwin, you've probably also installed the MinGW toolchain, which comes with its own version of gcc and ld. Then, you've probably made your PATH variable list /usr/bin before the path to the Haskell Platform binary directories, which makes ghc find the MinGW linker and C compiler before it finds the versions that were bundled with GHC.
You need to make sure that the HP directories are listed before the Cygwin directories. It should not be like this:
$ echo $PATH
/bin:/usr/bin:.../2011.2.0.1/bin
Instead, it should be like this:
$ echo $PATH
.../2011.2.0.1/bin:/bin:/usr/bin
This is only a guess at what the issue might be, and you should provide more details for a better diagnosis.