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 $(which gcc) x86_64-conda_cos6-linux-gnu-gcc
Don't put this in a system directory or conda's bin directory, and remember to remove the link when the problem is resolved upstream. gcc --version should be version 6.
EDIT: I understand the sentiment in the comments against manipulating system paths, but maybe we can use a little critical thinking for the actual case in hand before reciting doctrine. What actually have we done with the command above? Nothing more than putting an executable (symlink) called x86_64-conda_cos6-linux-gnu-gcc in one's personal ~/bin directory.
If putting something in one's personal ~/bin directory broke future conda (after it fixes the C compiler path to point to gcc it embeds), then that would be a bug with conda. Would the existence of this verbosely named compiler mess with anything else? Unlikely either. Even if something did pick it up, it's just your system gcc after all...
I wrote application for linux which uses Qt5.
But when I am trying to launch it on the linux without Qt SDK installed, the output in console is:
Failed to load platform plugin "xcb". Available platforms are:
How can I fix this? May be I need to copy some plugin file?
When I use ubuntu with Qt5 installed, but I rename Qt directory, the same problem occurs. So, it uses some file from Qt directory...
UPDATE:
when I create in the app dir "platforms" folder with the file libqxcb.so, the app still doesnot start, but the error message changes:
Failed to load platform plugin "xcb". Available platforms are:
xcb
How can this happen? How can platform plugin be available but can't be loaded?
Use ldd (man ldd) to show shared library dependencies. Running this on libqxcb.so
.../platforms$ ldd libqxcb.so
shows that xcb depends on libQt5DBus.so.5 in addition to libQt5Core.so.5 and libQt5Gui.so.5 (and many other system libs). Add libQt5DBus.so.5 to your collection of shared libs and you should be ready to move on.
As was posted earlier, you need to make sure you install the platform plugins when you deploy your application. Depending on how you want to deploy things, there are two methods to tell your application where the platform plugins (e.g. platforms/plugins/libqxcb.so) are at runtime which may work for you.
The first is to export the path to the directory through the QT_QPA_PLATFORM_PLUGIN_PATH variable.
QT_QPA_PLATFORM_PLUGIN_PATH=path/to/plugins ./my_qt_app
or
export QT_QPA_PLATFORM_PLUGIN_PATH=path/to/plugins
./my_qt_app
The other option, which I prefer is to create a qt.conf file in the same directory as your executable. The contents of which would be:
[Paths]
Plugins=/path/to/plugins
More information regarding this can be found here and at using qt.conf
I tried to start my binary, compiled with Qt 5.7, on Ubuntu 16.04 LTS where Qt 5.5 is preinstalled. It didn't work.
At first, I inspected the binary itself with ldd as was suggested here, and satisfied all "not found" dependencies. Then this notorious This application failed to start because it could not find or load the Qt platform plugin "xcb" error was thrown.
How to resolve this in Linux
Firstly you should create platforms directory where your binary is, because it is the place where Qt looks for XCB library. Copy libqxcb.so there. I wonder why authors of other answers didn't mention this.
Then you may want to run your binary with QT_DEBUG_PLUGINS=1 environment variable set to check which dependencies of libqxcb.so are not satisfied. (You may also use ldd for this as suggested in the accepted answer).
The command output may look like this:
me#xerus:/media/sf_Qt/Package$ LD_LIBRARY_PATH=. QT_DEBUG_PLUGINS=1 ./Binary
QFactoryLoader::QFactoryLoader() checking directory path "/media/sf_Qt/Package/platforms" ...
QFactoryLoader::QFactoryLoader() looking at "/media/sf_Qt/Package/platforms/libqxcb.so"
Found metadata in lib /media/sf_Qt/Package/platforms/libqxcb.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"xcb"
]
},
"className": "QXcbIntegrationPlugin",
"debug": false,
"version": 329472
}
Got keys from plugin meta data ("xcb")
loaded library "/media/sf_Qt/Package/platforms/libqxcb.so"
QLibraryPrivate::loadPlugin failed on "/media/sf_Qt/Package/platforms/libqxcb.so" : "Cannot load library /media/sf_Qt/Package/platforms/libqxcb.so: (/usr/lib/x86_64-linux-gnu/libQt5DBus.so.5: version `Qt_5' not found (required by ./libQt5XcbQpa.so.5))"
This application failed to start because it could not find or load the Qt platform plugin "xcb"
in "".
Available platform plugins are: xcb.
Reinstalling the application may fix this problem.
Aborted (core dumped)
Note the failing libQt5DBus.so.5 library. Copy it to your libraries path, in my case it was the same directory where my binary is (hence LD_LIBRARY_PATH=.). Repeat this process until all dependencies are satisfied.
P.S. thanks to the author of this answer for QT_DEBUG_PLUGINS=1.
I tried the main parts of each answer, to no avail. What finally fixed it for me was to export the following environment variables:
LD_LIBRARY_PATH=/usr/local/lib:~/Qt/5.9.1/gcc_64/lib
QT_QPA_PLATFORM_PLUGIN_PATH=~/Qt/5.9.1/gcc_64/plugins/
Ubuntu 16.04 64bit.
I got the problem for apparently no reasons. The night before I watched a movie on my VideoLan instance, that night I would like to watch another one with VideoLan. VLC just didn't want to run because of the error into the question.
I google a bit and I found the solution it solved my problem: from now on, VLC is runnable just like before. The solution is this comand:
sudo ln -sf /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms/ /usr/bin/
I am not able to explain what are its consequencies, but I know it creates some missing symbolic link.
Since version 5, Qt uses a platform abstraction system (QPA) to abstract from the underlying platform.
The implementation for each platform is provided by plugins. For X11 it is the XCB plugin. See Qt for X11 requirements for more information about the dependencies.
There might be many causes to this problem. The key is to use
export QT_DEBUG_PLUGINS=1
before you run your Qt application. Then, inspect the output, which will point you to the direction of the error. In my case it was:
Cannot load library /opt/nao/plugins/platforms/libqxcb.so: (/opt/nao/bin/../lib/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/x86_64-linux-gnu/libpng16.so.16))
But that is solved in different threads. See for instance https://stackoverflow.com/a/50097275/2408964.
Probably this information will help. I was on Ubuntu 18.04 and when I tried to install Krita, using the ppa method, I got this error:
This application failed to start because it could not find or load the Qt platform plugin "xcb" in "".
Available platform plugins are: linuxfb, minimal, minimalegl, offscreen, wayland-egl, wayland, xcb.
Reinstalling the application may fix this problem.
Aborted
I tried all the solutions that I found in this thread and other webs without any success.
Finally, I found a post where the author mention that is possible to activate the debugging tool of qt5 using this simple command:
export QT_DEBUG_PLUGINS=1
After adding this command I run again krita I got the same error, however this time I knew the cause of that error.
libxcb-xinerama.so.0: cannot open shared object file: No such file or directory.
This error prevents to the "xcb" to load properly. So, the solution will be install the `libxcb-xinerama.so.0" right? However, when I run the command:
sudo apt install libxcb-xinerama
The lib was already installed. Now what Teo? Well, then I used an old trick :) Yeah, that one --reinstall
sudo apt install --reinstall libxcb-xinerama
TLDR: This last command solved my problem.
I ran into a very similar problem with the same error message. First, debug some by turning on the Qt Debug printer with the command line command:
export QT_DEBUG_PLUGINS=1
and rerun the application. For me this revealed the following:
"Cannot load library /home/.../miniconda3/lib/python3.7/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so: (libxkbcommon-x11.so.0: cannot open shared object file: No such file or directory)"
"Cannot load library /home/.../miniconda3/lib/python3.7/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so: (libxkbcommon-x11.so.0: cannot open shared object file: No such file or directory)"
Indeed, I was missing libxkbcommon-x11.so.0 and libxkbcommon-x11.so.0. Next, check your architecture using dpkg from the linux command line. (For me, the command "arch" gave a different and unhelpful result)
dpkg --print-architecture #result for me: amd64
I then googled "libxkbcommon-x11.so.0 ubuntu 18.04 amd64", and likewise for libxkbcommon-x11.so.0, which yields those packages on packages.ubuntu.com. That told me, in retrospect unsurprisingly, I'm missing packages called libxkbcommon-x11-0 and libxkbcommon0, and that installing those packages will include the needed files, but the dev versions will not. Then the solution:
sudo apt-get update
sudo apt-get install libxkbcommon0
sudo apt-get install libxkbcommon-x11-0
So, I spent about a day trying to figure out what was the issue; tried all the proposed solutions, but none of that worked like installing xcb libs or exporting Qt plugins folder. The solution that suggested to use QT_DEBUG_PLUGINS=1 to debug the issue didn't provide me a direct insight like in the answer - instead I was getting something about unresolved symbols within Qt5Core.
That gave me a hint, though: what if it's trying to use different files from different Qt installations? On my machine I had standard version installed in /home/username/Qt/ and some local builds within my project that I compiled by myself (I have other custom built kits as well in other locations). Whenever I tried to use any of the kits (installed by Qt maintenance tool or built by myself), I would get an "xcb error".
The solution was simple: provide the Qt path through CMAKE_PREFIX_PATH and not though Qt5_DIR as I did, and it solved the problem. Example:
cmake .. -DCMAKE_PREFIX_PATH=/home/username/Qt/5.11.1/gcc_64
I faced the same problem when after installing Viber. It had all required qt libraries in /opt/viber/plugins/.
I checked dependencies of /opt/viber/plugins/platforms/libqxcb.so and found missing dependencies. They were libxcb-render.so.0, libxcb-image.so.0, libxcb-icccm.so.4, libxcb-xkb.so.1
So I resolved my issue by installing missing packages with this libraries:
apt-get install libxcb-xkb1 libxcb-icccm4 libxcb-image0 libxcb-render-util0
I like the solution with qt.conf.
Put qt.conf near to the executable with next lines:
[Paths]
Prefix = /path/to/qtbase
And it works like a charm :^)
For a working example:
[Paths]
Prefix = /home/user/SDKS/Qt/5.6.2/5.6/gcc_64/
The documentation on this is here: https://doc.qt.io/qt-5/qt-conf.html
All you need to do is
pip uninstall PyQt5
and
conda install pyqt
Most of the problem of pyqt can be fixed by this simplest solution.
In my case, I needed to deploy two Qt apps on an Ubuntu virtualbox guest. One was command-line ("app"), the other GUI_based ("app_GUI").
I used "ldd app" to find out what the required libs are, and copied them
to the Ubuntu guest.
While the command-line executable "app" worked ok, the GUI-based executable crashed, giving
the "Failed to load platform plugin "xcb" error. I checked ldd for libxcb.so, but this too had no missing dependencies.
The problem seemed to be that while I did copy all the right libraries I accidentally had copied also libraries that were already present at the guest system.. meaning that (a) they were unnecessary to copy them in the first place and (b) worse, copying them produced incompatibilities between the install libraries.
Worse still, they were undetectable by ldd like I said..
The solution? Make sure that you copy libraries shown as missing by ldd and absolutely no extra libraries.
In my case missing header files were the reason libxcb was not built by Qt. Installing them according to https://wiki.qt.io/Building_Qt_5_from_Git#Linux.2FX11 resolved the issue:
yum install libxcb libxcb-devel xcb-util xcb-util-devel mesa-libGL-devel libxkbcommon-devel
Folks trying to get this started on Ubuntu 20.04 please try to run this and see if this solves the problem. This worked for me
sudo apt-get update -y
sudo apt-get install -y libxcb-xinerama0
I link all Qt stuff statically to the generic Linux builds of my open source projects. It makes life a bit easier. You just need to build static versions of Qt libraries first. Of course this cannot be applied to closed source software due to licensing issues. The deployment of Qt5 apps on Linux is currently a bit problematic, because Ubuntu 12.04, for example, doesn't have Qt5 libraries in the package repositories.
I had this problem, and on a hunch I removed the Qt Configs from my environment. I.e.,
rm -rf ~/.config/Qt*
Then I started qtcreator and it reconfigured itself with the existing state of the machine. It no longer remembered where my projects were, but that just meant I had to browse to them "for the first time" again.
But more importantly it built itself a coherent set of library paths, so I could rebuild and run my project executables again without the xcb or qxcb libraries going missing.
I faced the same situation, but on a Ubuntu 20.04 VM.
TL;DR: Check file permissions.
What I did:
I copied the Qt libs required to /usr/local/lib/x86_64-linux-gnu/ and added it to LD_LIBRARY_PATH
I copied the platforms folder from Qt to my application directory and added it to QT_PLUGIN_PATH
I ran ldd on the executable and in the offending libqxcb.so (ldd libqxcb.so), and it complains about some dependencies although ldconfig listed them as found.
linux-vdso.so.1 (0x00007ffee19af000)
libQt5XcbQpa.so.5 => not found
libfontconfig.so.1 => /lib/x86_64-linux-gnu/libfontconfig.so.1 (0x00007f7cb18fb000)
libfreetype.so.6 => /lib/x86_64-linux-gnu/libfreetype.so.6 (0x00007f7cb183c000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f7cb1820000)
libQt5Gui.so.5 => /usr/local/lib/x86_64-linux-gnu/libQt5Gui.so.5 (0x00007f7cb0fd4000)
libQt5DBus.so.5 => not found
I used export QT_DEBUG_PLUGINS=1 for further info. It complains about missing files, although they are there.
What I found:
For some reason, when copying to the VM through the shared folder the files permissions were not the correct ones.
Thus, I ran: sudo chmod 775 * on the libs and voilà.
I solved the issue through this https://github.com/NVlabs/instant-ngp/discussions/300
pip uninstall opencv-python
pip install opencv-python-headless
This seems to have been a problem with the cv2 Python package and how it loops in Qt
sudo ln -sf /usr/lib/...."adapt-it"..../qt5/plugins/platforms/ /usr/bin/
It creates the symbolic link it's missed. Good for QT ! Good for VLC !!
I installed the luarocks package on Linux Mint, and afterwards installed a couple of rocks such as sudo luarocks install telescope, but when running a script via lua script.lua, require cannot find the module.
Meta: Doing this Q&A style, because while questions that answer this exist, none seem to be generically titled or easily findable, and I hope that I can help someone with this.
In this specific case, the problem was simply that on my distribution, the default Lua version installed was at the time of writing this 5.2, whereas the LuaRocks package was built for 5.1, meaning that Lua 5.2 could not find the rocks due to using different paths for modules.
The solution to the problem was downloading the LuaRocks source code from its github repository, and compiling it for 5.2
./configure --lua-version=5.2
make build
sudo make install
To make sure I can also install packages for LuaJIT, which as of the moment uses 5.1 libs, I have also executed the above lines with lua-version=5.1 beforehand (if I executed them after, the default luarocks command would point at the 5.1 build.
To build LuaRocks, you need liblua5.2-dev and/or liblua5.1-dev
The solution for me is this.
I try
eval "$(luarocks path)"
and it works.
Hope it works for others.
I'm starter Z3 so my question may be too basic.
But If you let me know some information for my question, I'm very happy.
I searched before history in this site.
But I couldn't get detailed information for me. ( because maybe..my question is too basic..)
[using Visual C++]
1) First of all, I downloaded "z3 4.3.0 for window" at codePlex site.
But this file doesn't have example file(test_capi.c).
So I got "z3-89c1785b73225a1b363c0e485f854613121b70a7.zip" for example file.
( I cannot remember what I can get... :( )
I succeeded compiling python file as codeplex site quide.
But I cannot compile test_capi.c using Visual C++.
I also added "test_capi.c" at "z3 4.3.0 for window" folder but I cannot also compile.
Lastly, I just tried using "test_capi.vcxproj" of "z3-src-4.1.1" and this is succeeded.
I cannot understand.
If i want to test "my file", what file is needed at "z3 4.3.0 for window"?
Or
Do I have to use only "z3 4.1.1" for visual c++ and add "my file" at some location of "z3 4.1.1"? ( All files of Z3 4.1.1 is needed?? AND what is the Some location?)
I read other some comment - "Z3 4.3.0" is simplified.
I understood this comment that I can use only "z3 4.3.0" and test successfully.
But as i told you, I cannot compile.
Please give me some information..
[using gcc in ubuntu]
First of all, I downloaded "z3-4.3.2.07d56bdc705c-x86-ubuntu-12.04.zip" from codeplex site.
Because I tried git command for getting source code but i cannot find source code.
( I also don't know the reason..)
Anyway... "z3-4.3.2.07d56bdc705c-x86-ubuntu-12.04.zip" doesn't have any example file and only bin & include folder is existed.
So I also used "z3 4.1.1" but i cannot compile using below command.
gcc -fopenmp -o test_capi -I ../../Include -L ../../lib test_capi.c -lz3-gmp
Error is "cannot find -lz3-gmp."
In some comment, I found "use "sudo install"" but i don't know how i can install lz3.
(Of course only "sudo install" doesn't work and "sudo apt-get install z3" also doesn't work...)
For compiling "test_capi.c" using gcc, could you explain in detail..?
I'm confused many kinds of guide but i couldn't get basic information for me.
Thank you in advance and I hope to get information...even if my question is too basic..
First, you should use only one version of the source code. Version 4.1.1 is very old and newer versions do not come with test_capi.vcxproj anymore, instead everything is done via the Makefile. For the very latest version please use the unstable branch (e.g., by selecting unstable here and then clicking download.)
The examples can be compiled by calling nmake examples (on Windows) or make examples (on Linux) in the build directory. The makefile has a target called _ex_c_example which shows how to call the compiler for the C example. The various variables that this target uses are defined in build/config.mk. Note that these variables are set to different values on Windows and Linux (this file is produced by python scripts/mk_make.py).
The git command on many Linux distributions is not compatible with the codeplex git server (for a fix see here), but of course this is not necessary if you download the source code from the webpage directly.
I have been banging on this for hours now.
I am trying to push my repo changes to kiln but I get this error:
certificate checking requires Python 2.6
I have already installed a parallel install of Python 2.6 by following the instructions from this link, but the error still persists. The system is ClearOS 5.2 by the way.
My first question is, will installing/upgrading mercurial break my existing install?
I tried to re-install following these intstructions link1 and [i lost the other link], but encountered another error.
Then I found this command debuginstall and here's the result:
[root#system mercurial-1.7.5]# hg debuginstall
Checking encoding (UTF-8)...
Checking installed modules (/usr/lib/python2.4/site-packages/mercurial)...
Checking templates...
Checking patch...
Checking commit editor...
Checking username...
no username supplied (see "hg help config")
(specify a username in your configuration file)
1 problems detected, please check your install!
My another question is, can I just change the existing hg's settings to just use the python26 which is already installed?
Thanks in advance!
Install your own python (of whatever version you need) to a separate directory (e.g.: /usr/local/python-2.7.2/) and then change the invocation of hg from #!/usr/bin/python to #!/usr/local/python-2.7.2/bin/python This way you don't disturb the existing/system installation, but you can use the version you want only where you need it. The only annoying part about this is dealing with two sets of libraries, since this is really maintaining two parallel installations. So if the 'extra' python needs libraries, you must install them manually using the invocation and paths of the extra installation. Sounds complicated, but if you only need it for one program, then you set it up once and it's good to go.