PCRE issue when setting up WSGI application - linux

I am working with Ubuntu 16.04.2 LTS.
I have been following a guide
How To Set Up uWSGI and Nginx to Serve Python Apps on Ubuntu 14.04. Once I have set up the virtualenv I follow the instructions:
pip install uwsgi
You can verify that it is now available by typing:
uwsgi --version
If it returns a version number, the uWSGI server is available for use.
However when I do this I get:
uwsgi: error while loading shared libraries: libpcre.so.1: cannot open
shared object file: No such file or directory
If I push on and work further through the guide things fall over when I try use uwsgi.
My research tells me that PCRE is Perl Compatible Regular Expressions and several people have asked questions online with libpcre.so.1 issues with other applications.
For example a response to a similar issue relating to nginx:
The message means what it says. The nginx executable was compiled to
expect the PCRE (Perl-compatible Regular Expression) shared library to
be available somewhere on LD_LIBRARY_PATH or specified in
/etc/ld.so.conf or whatever equivalent library-locating mechanisms
apply to your operating system, and it cannot find the library.
You will need to install PCRE - or configure your environment so that
nginx will look for the PCRE library where it is installed.
But I can't find much relevant to installing PCRE or configuring it. Most install instructions use: apt-get install libpcre3 libpcre3-dev and then reinstalling uwsgi pip install uwsgi -I. As in this example. Where I have tried everything posted and got nowhere.
I think my principle issue is that I don't understand the problem very well or how to do the things mentioned in the nginx example above.
Any insight or guidance would be much appreciated.

Even though my context may be different, the following steps should help you as well.
I did pip install uwsgi into my environment created by conda create -yn <env_name> python. Note, that one wouldn't even need to install PCRE into the environment, because it is included with Anaconda. We can see this issue in the environment, after source activate <env_name>:
# uwsgi --version
uwsgi: error while loading shared libraries: libpcre.so.1: cannot open...
With root/sudo access you can find where libpcre.so.1 is/will be:
# find / -name libpcre.so.1
/opt/anaconda3/lib/libpcre.so.1
Now let Linux know how to access it:
# ldconfig /opt/anaconda3/lib/
That's all you need to make it work. You can see the change you are making:
# find / -name uwsgi
/opt/anaconda3/envs/<env_name>/bin/uwsgi
# ldd -d /opt/anaconda3/envs/<env_name>/bin/uwsgi
linux-vdso.so.1 => (0x00007fff2d1ba000)
...
/lib64/ld-linux-x86-64.so.2 (0x00007ff98dbc5000)
undefined symbol: pcre_free (/opt/anaconda3/envs/cts/bin/uwsgi)
PS Turned out ldconfig above populates global cache /etc/ld.so.cache, which, in my case, clashed with system library (/lib/x86_64-linux-gnu/libdbus-1.so.3). So I had to revert the change by running ldconfig without parameters and resort to runtime linking = starting uwsgi as
# LD_LIBRARY_PATH=/opt/anaconda3/lib uwsgi --version

Related

OSError: cannot load library 'gobject-2.0-0': Additionally, ctypes.util.find_library() did not manage to locate a library called 'gobject-2.0-0'

While installing saleor, I have encountered with the below issue.
OSError: cannot load library 'gobject-2.0-0': error 0x7e. Additionally, ctypes.util.find_library() did not manage to locate a library called 'gobject-2.0-0'
I have tried all the solutions given in stack overflow as well as git. Nothing seems to be working.
Can someone please help me out.
Tools installed:
python: 3.8 / 3.9
GTK3
I have also updated the GTK3\bin in the top of the environment variables as said in the other solutions.
Download the https://www.msys2.org/ and install it.
a) install gtk package and python bundles from MSYS2 terminal. We can start this with command shell. and pacman -S mingw-w64-x86_64-gtk3
b) pacman -S mingw-w64-x86_64-python-gobject
Update your $XDG_DATA_HOME and XDG_DATA_DIRS to the installed path for example :
'C:/msys64/mingw64/share'
Reboot your system and check, it will work.
Another option that worked for me is :
Install MSYS2 from https://www.msys2.org.
Install GTK3 DLL Dependencies from here : https://github.com/tschoonj/GTK-for-Windows-Runtime-Environment-Installer/releases
And then set environment path variables to your windows variable path file.
WEASYPRINT_DLL_DIRECTORIES=C:\GTK3\bin

AWS EC2 Linux: Cannot open shared object file

I am trying to get (specific versions of) Chrome and Chromedriver (and ultimately Selenium) running on an AWS EC2 Linux instance that was handed over to me for testing. Following the first four steps of this guide, I
navigated into my /tmp directory,
ran sudo wget https://chromedriver.storage.googleapis.com/102.0.5005.61/chromedriver_linux64.zip,
unzipped chromedriver,
and moved chromedriver into my /usr/bin.
However, when I go to inspect chromedriver - version for a sanity check, I get the following error:
chromedriver: error while loading shared libraries: libxcb.so.1: cannot open shared object file: No such file or directory
Several posts on this and other sites documenting similar quandaries (error while loading shared libraries: <...>) suggest that maybe this error is due to the absence of libxcb from my instance, but I am such a novice that I'm just not sure (I don't even know what libxcb is for). Hoping to get some feedback on how to proceed. If any other info about my instance would be helpful, feel free to let me know. Thanks!
If you type yum whatprovides libxcb.so.1 you will see the name and version of the library that provides the file you are missing.
Generally, I found out that libX11 provides most libraries needed for chrome and chromedriver. So try:
sudo yum install -y libX11
and then repeat the above steps.

unable to execute 'x86_64-conda_cos6-linux-gnu-gcc': No such file or directory (pysam installation)

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...

Deployement Qt error [duplicate]

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 voilĂ .
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 !!

Error while install gcc49 in Ubuntu by using linuxbrew

I want to install the latest gcc49 in a Ubuntu Linux, and I am familiar with Homebrew in Mac, so I would like to use the Linux version of it, i.e., Linuxbrew. So I installed Linuxbrew and typed
$ brew install gcc49
The dependencies gmp4, mpfr2 and etc. will be installed first. I have added a if OS.mac? condition in gmp4 so it can be installed successfully, but when installing mpfr2 (also added the condition), the make check failed with the error:
...
/tmp/mpfr2-i5YD/mpfr-2.4.2/tests/.libs/lt-tpow_all: error while loading shared libraries: libgmp.so.3: cannot open shared object file: No such file or directory
FAIL: tpow_all
=======================
148 of 148 tests failed
=======================
As you can see, the tests can not find libgmp.so.3 which is just installed. But gmp4 is keg only since it will conflict with gmp in main repository.
But the configure options are set with the correct location of gmp4:
./configure --disable-dependency-tracking --prefix=/home/dongli/.linuxbrew/Cellar/mpfr2/2.4.2 --with-gmp=/home/dongli/.linuxbrew/opt/gmp4
How to solve this problem? Thanks!
You think you are doing it wrong by insisting on a third-party scripting solution that is not native to the OS.
There are prebuilt versions of gcc et al provided by the same maintainers in this PPA on Launchpad. These are previews / testreleases of what will be in the next Ubuntu releases.
I found the problem, that is the environment has been reset after each system call in Ruby formula. So we need to set the correct LD_LIBRARY_PATH as
if OS.linux?
ENV["LD_LIBRARY_PATH"] = "#{Formula["..."].opt_prefix}/lib:...:$LD_LIBRARY_PATH"
end
so that LD_LIBRARY_PATH persists during the build processes.

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