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 !
Related
I am trying to install pysam.
After excecuting:
python path/to/pysam-master/setup.py build
This error is produced:
unable to execute 'x86_64-conda_cos6-linux-gnu-gcc': No such file or directory
error: command 'x86_64-conda_cos6-linux-gnu-gcc' failed with exit status 1
There are similar threads, but they all seem to address the problem assumig administriator rights, which I do not have. Is there a way around to install the needed files?
DISCLAIMER: This question derived from a previous post of mine.
manually installing pysam error: "ImportError: No module named version"
But since it might require a different approach, I made it a question of its own.
You can also receive the same error while installing some R packages if R was installed using conda (as I had).
Then just install the package by executing: conda install gxx_linux-64 to have that command available.
Source:
https://github.com/RcppCore/Rcpp/issues/770#issuecomment-346716808
It looks like Anaconda had a new release (4.3.27) that sets the C compiler path to a non-existing executable (quite an embarrassing bug; I'm sure they'll fix it soon). I had a similar issue with pip installing using the latest Miniconda, which I fixed by using the 4.3.21 version and ensuring I was not doing something like conda update conda.
See https://repo.continuum.io/miniconda/ which has release dates and versions.
It should now be safe to update conda. This is fixed in the following python packages for linux-64:
python-3.6.2-h0b30769_14.tar.bz2
python-2.7.14-h931c8b0_15.tar.bz2
python-2.7.13-hac47a24_15.tar.bz2
python-3.5.4-hc053d89_14.tar.bz2
The issue was as Jon Riehl described - we (Anaconda, formerly Continuum) build all of our packages with a new GCC package that we created using crosstool-ng. This package does not have gcc, it has a prefixed gcc - the missing command you're seeing, x86_64-conda_cos6-linux-gnu-gcc. This gets baked into python, and any extension built with that python goes looking for that compiler. We have fixed the issue using the _PYTHON_SYSCONFIGDATA_NAME variable that was added to python 3.6. We have backported that to python 2.7 and 3.5. You'll now only ever see python using default compilers (gcc), and you must set the _PYTHON_SYSCONFIGDATA_NAME to the appropriate filename to have the new compilers used. Setting this variable is something that we'll put into the activate scripts for the compiler package, so you'll never need to worry about it. It may take us a day or two to get new compiler packages out, though, so post issues on the conda-build issue tracker if you'd like to use the new compilers and need help getting started.
Relevant code changes are at:
py27: https://github.com/anacondarecipes/python-feedstock/tree/master-2.7.14
py35: https://github.com/anacondarecipes/python-feedstock/tree/master-3.5
py36: https://github.com/anacondarecipes/python-feedstock
The solution that worked for me was to use the conda to install the r packages:
conda install -c r r-tidyverse
or r-gggplot2, r-readr
Also ensure that the installation is not failing because of admin privileges.
It will save you a great deal of pain
After upgrading Golang to 1.19.1, I started to get:
# runtime/cgo
cgo: C compiler "x86_64-conda-linux-gnu-cc" not found: exec: "x86_64-conda-linux-gnu-cc": executable file not found in $PATH
Installing gcc_linux-64 from the same channel, has resolved it:
conda install -c anaconda gcc_linux-64
Somewhere in your $PATH (e.g., ~/bin), do
ln -sf $(which gcc) x86_64-conda_cos6-linux-gnu-gcc
Don't put this in a system directory or conda's bin directory, and remember to remove the link when the problem is resolved upstream. gcc --version should be version 6.
EDIT: I understand the sentiment in the comments against manipulating system paths, but maybe we can use a little critical thinking for the actual case in hand before reciting doctrine. What actually have we done with the command above? Nothing more than putting an executable (symlink) called x86_64-conda_cos6-linux-gnu-gcc in one's personal ~/bin directory.
If putting something in one's personal ~/bin directory broke future conda (after it fixes the C compiler path to point to gcc it embeds), then that would be a bug with conda. Would the existence of this verbosely named compiler mess with anything else? Unlikely either. Even if something did pick it up, it's just your system gcc after all...
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 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).
I have kept libawesomium.1.6.5.so and libawesomium.1.6.5.so.0 files in /usr/lib/awesomium.1.6.5 folder, and given the path for this .so library in ld.co.config.d, in a new .conf file, but when I run my project it gives me a
System.dll not found exception for libawesomium.1.6.5.so.0 at (wrapper managed-to-native).
How to solve this error.
when i check the existence of this library through
sudo ldconfig -p | grep libawesomium-1.6.5.so
command, it gives me the following output:
libawesomium-1.6.5.so.0 (libc6) => /usr/lib/awesomium-1.6.5/libawesomium-1.6.5.so.0
It means it exists. But still at run-time my project is giving this error :
System.dllnotfoundexception libawesomium-1.6.5.so.0
I am working on monodevelop, so can someone suggest me please what is the thing that i am missing. Is there some addon i have to install or some terminal command i have to follow. Hoping for quick responses.
Regards
Rohit
You should be able to add LIBDIR=/lib to /etc/ld.so.conf and then issue ldconfig. If not, then you might be using a VMX or other type of setup that would require to you use the linker with -W/lib for example.
i have need 2 days to find a solution for this problem!
On Linux Wheezy 32bit you need to install libjpeg62 ...
apt-get install libjpeg62
this will fix the problem! ...
I am trying to install Code::Blocks 10.05 from (non-SVN) sources (codeblocks-10.05-src.tar.bz2). My OS is Ubuntu 11.04. I needed to download and install wxWidgets first (I now have wxGTK-2.8.12), which seemed to work. I compiled it according to these instructions:
http://wiki.codeblocks.org/index.php?title=Installing_Code::Blocks_from_source_on_Linux
Then I configured C::B with
./configure --with-wx-config=/opt/wx/2.8/bin/wx-config
and ran
export LDFLAGS="-Wl,-R /opt/wx/2.8/lib"
make
sudo -i
make install
When trying to run C::B, I get the following error:
codeblocks: error while loading shared libraries: libwx_gtk2u-2.8.so.0: cannot open shared object file: No such file or directory
The same question was asked here: error while loading shared libraries, but the suggested solution (namely adding the wxWidgets config to the options passed to configure) didn't work for me.
The output of wx-config --prefix is /opt/wx/2.8,
The output of wx-config --libs is -L/opt/wx/2.8/lib -pthread -lwx_gtk2u-2.8,
and that of which wx-config is /opt/wx/2.8/bin/wx-config.
I looked for the library and found /opt/wx/lib/libwx_gtk2u-2.8.so.0 to be a link to libwx_gtk2u-2.8.so.0.8.0 in the same folder.
What might be wrong here?
The problem is that the program cannot find the WX widgets libraries at run time. You will need to set your LD_LIBRARY_PATH variable to include the location of wxWidgets like this:
LD_LIBRARY_PATH=/opt/wx/2.8/lib ./codeblocks
The reason why its failing is because you compiled codeblocks against wxWidgets found in /opt/ and not the one installed in /usr/; the program doesn't know to look in /opt for the wx libraries.
Probably the easiest way to get code::blocks up and running on Ubuntu is to just install it via the Synaptic Package Manager. Just type in codeblocks into 'Quick search'. Find codeblocks on the list and just right-click to mark for install. Any dependencies and missing libraries needed will automatically be handled and installed by Synaptic as necessary.
If you're interested in trying the C::B nightly builds on Ubuntu then you'll want to checkout Jens' unofficial debian-repository here.
You can visit Why do I have to define LD_LIBRARY_PATH with an export every time I run my application? for a more generic case. For a particular case like yours you can follow the below given steps
If you had installed wxGTK then you would see the file in /usr/local/lib. You would get this error when the the above path is not as part of the makefile. I received this error while starting wxFormBuilder after building from source on CentOS. There are 2 approaches.
Approach 1: Putting the path in .bashrc
gedit /home/{your-username}/.bashrc
Then after the line # User specific aliases and functions paste the following
export $LD_LIBRARY_PATH=/usr/local/lib.
This would work for fine but for the current login, but for other users like root you might have to do the same in the respective .bashrc files.
Approach 2: Creating your own conf files
cd /etc/ld.so.conf.d
gedit wxformbuilder.conf
Give the path /usr/local/lib and save the file.
ldconfig (To update the library path).