I am trying to build NetCDF4 from source on MacOSX. When I run ./configure I get the error:
checking for library containing H5Fflush... no
configure: error: Can't find or link to the hdf5 library. Use --disable-netcdf-4, or see config.log for errors.
I installed hdf5 before, and set the environment variables as:
LDFLAGS=-L/opt/local/lib
CPPFLAGS=-I/opt/local/include
In /opt/local/lib I have these files:
libhdf5.8.dylib
libhdf5.a
libhdf5.dylib
libhdf5.settings
libhdf5_cpp.8.dylib
libhdf5_cpp.a
libhdf5_cpp.dylib
libhdf5_hl.8.dylib
libhdf5_hl.a
libhdf5_hl.dylib
libhdf5_hl_cpp.8.dylib
libhdf5_hl_cpp.a
libhdf5_hl_cpp.dylib
And in /opt/local/include I have:
hdf5.h hdf5_hl.h
Why doesn't the configure script find the hdf5 library? I am happy to provide more information if needed!
EDIT:
My ultimate goal is to install netcdf4 for use as a Fortran module. I have tried installing everything through MacPorts, and it seemed to work, but when I tried to use it, the compiler told me that there was no netcdf.mod file, and sure enough there wasn't one to be found anywhere.
It turns out that just typing:
sudo port install netcdf-fortran
only installs the library files, but doesn't create a .mod file, which I guess is needed. So I found out that other people had the same problem, and the advice given was to install it with gcc44, which did create a .mod file, but then my compiler told me that the .mod file was built with a different version of gfortran and it couldn't be used, so that's why I am trying to build it from scratch, but if someone has a faster option, I would be more than happy to try it!
Ok, I finally figured it out.
I reinstalled netcdf-fortran with macports, then the .mod file suddenly appeared, I then had the problem, however, that when running gfortran, it would tell me that netcdf.mod was compiled with a different version of fortran than the one I am using. (Macports uses 4.8), so got gcc48 from macports and am using gfortran-mp-4.8 to compile now and it works.
Still don't know how to build all these things from scratch, but it works now at least!!!
Typically, I see this when there is a downstream dependency that cannot be fulfilled. The test program created by configure is finding libhdf5, but compilation is still failing because it cannot find something like libz or libszip, depending on how your libhdf5 was compiled.
If you check your config.log file and look for the error, it will probably tell you something along the lines of 'unresolved symbol'. This will give a clue as to which library is missing. If it is linking against the statically-built libhdf5, you may need to add the appropriate library usingLDFLAGS.
If you post the relevant portion of your config.log file, we may be able to help sort out what exactly is going wrong.
Sometimes it doesn't work in the configure parameters like
./configure --enable-shared --enable-fortran --enable-netcdf-4
CPPFLAGS=-I$home/apps2/include LDFALGS=-L$home/apps2/lib --prefix=$home/apps2
or doesn't work when export CPPFLAGS=-I$home/apps2/include in the open SHELL.
Maybe you can set the env vars CPPFLAGS and LDFLAGS in the .bashrc file (prior to the first two ways).
Related
I'm trying to compile geany-plugins-1.28. The debugger plugin (the only one I need) gives the error:
debug.c:53:21: fatal error: vte/vte.h: No such file or directory
#include <vte/vte.h>
Clearly it needs to know where this file is located to compile. I found the vte.h file in the src directory of the main program geany-1.28. When running
sudo ./configure cflags=-I/home/pi/Desktop/geany-1.28/src
I get the same error about the missing header later trying to compile the debugger plugin.
I ran
./configure --help
to get all the flag options. The output is here
How do I get this to configure correctly so that it compiles. I need to compile the debugger version 1.28 myself because apt only installs 1.24 which I think has a bug because it crashes when I run my code with the error:
close failed in file object destructor:
sys.execpthook is missing
lost sys.stderr
CFLAGS is case-sensitive environment variable, so you should set it before running configure, not try to pass it as a command line argument. This variant:
$ export CFLAGS=-I/home/pi/Desktop/geany-1.28/src
$ ./configure
leaves CFLAGS set for current shell until you leave it. While this:
$ CFLAGS=-I/home/pi/Desktop/geany-1.28/src ./configure
sets variable only for current command, i.e. configure.
Some other issues:
You do not need sudo to configure and make. It is also unnecessary for make install if you set PREFIX to a path you have privileges to write to.
Does plugin's build system also builds all it's dependencies? If not, you may face linker errors a bit later.
Update:
I have tried to build debugger plugin and got rid of your error. It seems that vte.h coming with Geany is it's intrinsic, while the plugin requires full-featured file from the library. So I just installed vte and vte-devel from repos. Nevertheless, I got some other unrelated errors coming from Glib. I will not continue my attempts to build all this right now. Hope my effort will be helpful at least a little.
As in this answer stated, vte.h is not the file you are looking for. Install libvte(-dev) package on your system and rerun configure.
Just for the record: vte.h on Geany is a dummy to allow Geany to kind of dynamical enable vte or disable it depending on vte is installed on the system or not.
I'm trying to install Python 3.5.2 on CentOS 7. The build appears to succeed, but executing python3 elicits
python3: error while loading shared libraries: libpython3.5m.so.1.0: cannot open shared object file: No such file or directory
I checked this question as the only link that appeared to help. ldd does show the file as missing, and it does not seem to exist anywhere, although /usr/lib/libpython3.5m.so exists.
By any chance, is /usr/lib/libpython3.5m.so the correct file? I have no problem making a link, but I don't want to shoot myself in the foot if it's wrong. I also wonder whether there are related layers of yak fur waiting for me. Perhaps I need to make clean and rebuild with other options?
Much along the same lines as the quoted question, I still need to repair LD_LIBRARY_PATH. The global solution is at least a workaround:
export LD_LIBRARY_PATH=/usr/lib/
The problem was mostly in locating the wayward file.
You should make it by ./configure --enable-shared
then
make && make install
after that,
vim /etc/ld.so.conf.d/python3.conf && and add a new line
/usr/local/lib
try /sbin/ldconfig
hope it works !
I have instaled Cygwin after running MinGW for a while now. But when I try to compile the console gives me:
/usr/lib/gcc/x86_64-pc-cygwin/4.9.2/cc1.exe: error while loading shared libraries: ?: cannot open shared object file: No such file or directory
What does this mean?
I have the same problem and I found the solution.
According to the FAQ of Cygwin
Q: Why is C:\cygwin\usr\bin invisible from windows?
A: Because it does not really exist. In cygwin, /usr/bin is just a link to /bin.
So trying to add "C:\cygwin\usr\bin" to PATH will be in vain.
Add "C:\cygwin64\bin" to PATH instead. Hope this helps :)
You are missing a library, please run cygcheck /usr/lib/gcc/x86_64-pc-cygwin/4.9.2/cc1.exe or ldd /usr/lib/gcc/x86_64-pc-cygwin/4.9.2/cc1.exe to see what is the missing library.
(I'd rather ask a question in the comments first, but I don't have enough reputation yet.)
Your cc1 is unable to load some DLLs it needs to start. Looking at the Cygwin source code, this can be either a library specified in LD_PRELOAD, or -- more probably -- a library the executable depends on. The ? in the error message seems to be the default return value of find_first_notloaded_dll (hookapi.cc), in case the function can't determine what library is missing.
To diagnose the issue, I suggest checking your PATH variable (or even clearing it of any non-Cygwin paths and trying the compilation again) and/or using Dependency Walker to find the missing DLLs (start it from a Cygwin shell, so it can see the same PATH). ldd (included with Cygwin) may also give some clues, but I wouldn't bet on it.
It's possible a clean re-install of Cygwin will be necessary to solve the issue.
Most likely, you are simply missing /usr/bin in the PATH variable.
Adding 'export PATH=/usr/bin:$PATH' to your .bashrc file will solve the issue.
Adding some background info. I had the same problem when building my own program and linking it against graphviz cgraph.dll. Turns out this is related to where windows searches for DLLs (see here: https://msdn.microsoft.com/en-us/library/7d83bc18.aspx) So adding the path of your missing library to PATH should fix the problem.
It is unfortunate that the message doesn't include the name of the library. Luckily cmd.exe DOES give you this name (so it's good for something after all;)
Are you including the path to your lib directory?
Looks like you are not
I'm not very familiar with Cygwin, I mainly use MinGW, but I think the error message speaks for itself
I also came this error on windows machine while executing .exe file generated by scilab2C i.e toolbox for Scilab
For Windows 32 bit Add the environment variable path as follow :
C:\cygwin\usr\i686-pc-cygwin\bin
Hope so this will solve your issue.
Just had this problem trying to compile a package with make and it wanted some cygguile dll file that was just installed along with make.
My solution was I had not only migrated my cygwin64 directory across drives because the sector sizes were mismatched for some reason even though the drivers were both under 2TB and should have been using 512 byte sector sizes.. So I had to install a new system and move files over there, might have had weird permissions on them.
Also had to patch cygwin1.dll end of Jan 2020 because of a recent input problem in ConEmu with Windows 10 1903 build, but just did it again with this working so that doesn't seem to be the issue.
Reinstalling cygwin by deleting that entire directory, taking ownership of it first.., seemed to work now...
I am trying to install octave on my machine (Scientific Linux 6.4 based on red hat) without having root access. After running the following:
./configure CPPFLAGS="-I/some_stuff/user_name/bin/pcre-8.32/include" LDFLAGS="-L/some_stuff/user_name/bin/pcre-8.32/lib"
(I had to install pcre apriori; before I got errors re: pcre), I get a message along the lines:
configure: error: You are required to have BLAS and LAPACK libraries
Now LAPACK has just been made in $HOME/bin/lapack-3.4.2 yet the same error is still there. Also $HOME/bin is part of the path.
Any way to tell the configure tool for octave about this? (the obvious thing of adding another CPPFLAG/LDFLAG does not work). I'm assuming I'll encounter more such issues along the way, so any generic help/hint is greatly appreciated.
My level of linux is rudimentary to say the least, but I'm willing to work through it.
Thanks,
Dan
Does this site shed any light on the problem? It describes the configuration options.
http://www.gnu.org/software/octave/doc/interpreter/Installation.html
First, you should rather ./configure all your software with some common prefix, such as --prefix=$HOME/soft/
Unless you know well what you are doing, I recommend against having different prefix for each installed software. You could add $HOME/soft/bin to your $PATH
And you should configure and build all the dependencies before configuring octave (and that includes BLAS, LAPACK and their dependencies).
Then, you want to pass specific configuration options, perhaps like --with-blas=$HOME/soft
I think you should pass the prefix used when configuring BLAS; you may want to run ./configure --help first.
Read carefully each package's installation instructions. For Octave, they are here. Each package has their own.
Some software may require you to configure and build outside of their source tree!
I'm trying to modify GTK2 on Ubuntu Oneiric.
I download the source:
apt-get source libgtk2.0-0
cd gtk+2.0-2.24.6/
I try to compile and overwrite the current GTK2:
./configure --prefix=/usr
sudo make
Soemhow I get an error (I have all the necessary libraries and the build-essential package etc):
In file included from gtkquery.c:26:0:
gtkquery.h:31:2: error: #error "gtkfilechooserprivate.h is not supported API for general use"
By the way, I am able to modify and recompile GTK3 with no problems with the same steps.
If use debuild, I get thousands of
dpkg-source: error: cannot represent change to gtk+2.3.0-2.24.6/gtk+2.0-2.24.6/something: binary file contents changed
You won't get anything near the Ubuntu-provided build if you try building it by hand that way -- you'll miss all the ./configure options and other settings. (Look into debian/rules for the full details of what they're setting.)
Instead, try debian/rules build.
For reasons I haven't investigated yet (possibly including me not understanding how it should work), that didn't work on the first package I tried, but setting up pbuilder let me build the package I wanted.
It might feel like overkill to get a clean chroot as a build environment, but it is way too easy to build yourself problems that no one else in the world can replicate because you've got something funny on your local system.