I am trying to get PL/R running on a linux server where I do not have root access. The installation itself works fine using the command below:
LD_INCLUDE_PATH="$HOME/pgsql/include" LD_LIBRARY_PATH="$HOME/pgsql/lib:$HOME/lib/R/lib" PGDATA="$HOME/usr/pgsql/data" PG_LIB_DIR="$HOME/pgsql/lib" R_HOME="$HOME/lib/R" USE_PGXS=1 make
When I try to add the plr extension to a database with CREATE EXTENSION plr; however, I get the following error:
ERROR: could not load library "~/lib/postgresql/plr.so": libR.so: cannot open shared object file: No such file or directory
I read on the bottom of the install documentation page that I should add the library path to the LD config file /etc/ld.so.conf, but I do not have root access and I can not change this file.
Is there a workaround for this?
thanks in advance
You need to set LD_LIBRARY_PATH="$HOME/pgsql/lib:$HOME/lib/R/lib" at run-time in the PostgreSQL server's environment. Since you appear to be running PostgreSQL out of your home directory under your own user ID that should be as easy as exporting the environment variable before running pg_ctl, eg:
LD_LIBRARY_PATH="$HOME/pgsql/lib:$HOME/lib/R/lib" pg_ctl -D the_datadir start
Alternately you could see if you can re-compile PL/R with rpath linking enabled, so plr.so has a path to libR.so embedded in it by the linker at compile time. Pass the -rpath option in LDFLAGS or pass -Wl,-rpath in CFLAGS. See -rpath in man ld and -Wl in man gcc.
Related
I installed OpenFOAM on Ubuntu (which is itself on WSL Windows Subsystem for Linux).
I have a problem when trying to launch paraFoam and I have this error :
Invalid $PV_PLUGIN_PATH and -plugin-path= not defined
No supplementary ParaView/OpenFOAM reader modules
Using builtin reader: paraFoam -vtk
paraview: error while loading shared libraries: libQt5Core.so.5: cannot open shared object file: No such file or directory
It seems that it comes from paraview or Qt but I don't know what to do.
The file libQt5Core.so.5 does exist in the computer
When I type qmake --version I have
QMake version 3.1
Using Qt version 5.12.8 in /usr/lib/x86_64-linux-gnu
Since you are using WSL1, this issue is common. you can solve it by running the following command:
sudo strip --remove-section=.note.ABI-tag /usr/lib/x86_64-linux-gnu/libQt5Core.so.5
To solve the issue related to the GLIBCXX, try:
sudo cp /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /opt/OpenFOAM/ThirdParty-v2006/platforms/linux64/gcc-6.3.0/lib64/libstdc++.so.6
I'm trying (for hours now) to install the cargo crate diesel_cli for postgres. However, every time I run the recommended cargo command:
cargo install diesel_cli --no-default-features --features postgres
I wait a few minutes just to see the same build fail with this message:
note: LINK : fatal error LNK1181: cannot open input file 'libpq.lib'
error: aborting due to previous error
error: failed to compile `diesel_cli v1.4.1`, intermediate artifacts can be found at `C:\Users\<user name here>\AppData\Local\Temp\cargo-installUU2DtT`
Caused by:
could not compile `diesel_cli`.
I'm running postgres in a docker container and have the binaries on my C:\pgsql with the lib and bin directories both on the PATH so I can't figure out why it's not linking. What else could be required they didn't mention in the docs?
In my case the installation was successful but when I tried to run it this error occured.
maybe this would work for others who have the same problem:
open PowerShell
type in setx PQ_LIB_DIR "C:\Program Files\PostgreSQL\13\lib" (or any other path to your PostgreSQL lib)
restart your PC
run again
I had the same issue with WSL, if you're on Linux probably you could find PostgreSQL lib location and add it to your environment variables.
Update:
The answer below is a work around for older versions. Please check the possibility to execute cargo clean first
Original Version
Adding the folder to the PATH variable didn't help, at least in my case, as by some reason it is not used in the /LIBPATH parameter passed to link.exe.
In my case it was C:\Users\<username>\.rustup\toolchains\stable-x86_64-pc-windows-msvc\lib\rustlib\x86_64-pc-windows-msvc\lib
You can see it in the beginning of the error message.
Copy libpq.lib in there and it will be used from there.
After installation diesel would require some other assemblies. Copy libcrypto-1_1-x64.dll, libiconv-2.dll and libssl-1_1-x64.dll into the folder showed after where diesel command execution
I had the same error on Ubuntu and for me the following install fixed the issue:
sudo apt install libpq-dev
No need to move files around, just add C:\Program Files\PostgreSQL\14\lib and C:\Program Files\PostgreSQL\14\bin to your PATH. Installing and running diesel should have no problems.
Note: your paths may be different, and remember to close/reopen your terminal so the PATH variable is updated.
(Tested on Windows 10)
To give clear steps for windows:
Add C:\Users<username>.rustup\toolchains\stable-x86_64-pc-windows-msvc\lib\rustlib\x86_64-pc-windows-msvc\lib in the path in environment variables
Copy libpq.lib that is in C:\Program Files\PostgreSQL\14\lib (obviously this is with version 14) and paste it in C:\Users<username>.rustup\toolchains\stable-x86_64-pc-windows-msvc\lib\rustlib\x86_64-pc-windows-msvc\lib
If you've attempted to cargo build (or anything that runs the build scripts for libpq rust crate) when your environment was invalid, then you need to do a cargo clean after fixing your environment otherwise you'll still get the libpq.lib not found error even when it's in your PATH. The other answers where you copy the file into another directory are just hacks
You can instead add the path to .../lib to the compilers' library search paths, using RUSTFLAGS environment variable. It works both for installing diesel_cli and for building your projects.
RUSTFLAGS='-L /usr/local/pgsql/lib' cargo build
On Windows with EDB installer, the path contains a space, so use CARGO_ENCODED_RUSTFLAGS instead. For PowerShell:
$env:CARGO_ENCODED_RUSTFLAGS = "-L`u{1f}C:\Program Files\PostgreSQL\14\lib"
I am trying to compile matconvnet-1.0-beta20 with Matlab 2016a on Ubuntu 16.04. Initial phase of compilation works fine:
untar('http://www.vlfeat.org/matconvnet/download/matconvnet-1.0-beta20.tar.gz') ;
cd matconvnet-1.0-beta20
run matlab/vl_compilenn
The error happens when I run vl_simplenn(network, image) which gives following error:
Invalid MEX-file '/home/matconvnet-1.0-beta20/matlab/mex/vl_nnconv.mexa64':
/usr/local/MATLAB/R2016a/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6: version
`GLIBCXX_3.4.21' not found (required by /home/matconvnet-1.0-beta20/matlab/mex/vl_nnconv.mexa64)
To understand the cause of problem, I run /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBC which doesn't give any output bash: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: Permission denied
Also more /usr/lib/x86_64-linux-gnu/libstdc++.so.6 gives no output:
******** /usr/lib/x86_64-linux-gnu/libstdc++.so.6: Not a text file ********
I did some research and found some possible solutions:
http://it.mathworks.com/matlabcentral/newsreader/view_thread/162466
The problem is that MATLAB secretly changes LD_LIBRARY_PATH on startup
to point to the MATLAB version of GLIBC++, so that GLIBC++ 3.4.9 can
no longer be found. The solution is to modify matlab/bin/.matlab7rc.sh
so that "LDPATH_PREFIX" contains the path to the version of GLIB
installed with your compiler, then this is found before the
matlab-supplied library.
so I edited /usr/local/MATLAB/R2016a/bin/.matlab7rc.sh and modified LDPATH_PREFIX='' in 195th line to LDPATH_PREFIX='/usr/lib/x86_64-linux-gnu'.
After applying this change, the problem still exist.
As suggested here, I copied .matlab7rc.sh to current working directory of project, but still error persist.
https://askubuntu.com/questions/719028/version-glibcxx-3-4-21-not-found
According to first answer, running this command
ln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6 usr/local/MATLAB/R2014a/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6
gives an error:
ln: failed to create symbolic link 'usr/local/MATLAB/R2014a/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6': No such file or directory
Seems like second solution suggests changes of LD_PRELOAD path in .matlab7rc.sh, but it is not anywhere inside the file.
How to tell mex to link with the libstdc++.so.6 in /usr/lib instead of the one in the MATLAB directory?
From Matlab directory in /usr/local/MATLAB/R2016a/bin$ I run
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu/libstdc++.so.6
but the problem still exist.
Maybe there I didn't apply the solution in the correct way Or maybe there is another solution elsewhere that I didn't find. Please let me know, I am very confused!!!
You need before execute (matlab in my case) add path of library:
In console execute this:
LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6 matlab
I had the same problem.
In my case, to solve it, I first ran "locate" to list all the possible versions of the library in the system.
locate libstdc++
As an example, I report the result on my system
I then set the most recent version of "lib" by exporting the environment variable:
export LD_PRELOAD="/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21"
So, the fullpath of the library to be set depends on where it is allocated in your system.
There are 2 possible solutions:
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu/libstdc++.so.6
Install this package:
sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update
sudo apt-get upgrade
sudo apt-get dist-upgrade
MAYBE the second solution you mentioned really works, but you have done it before. So you cannot operate in the same way again because you have ever linked /usr/lib/x86_64-linux-gnu/libstdc++.so.6 to usr/local/MATLAB/R2014a/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6. TRY rebooting?
Also, you use MATLAB R2016a, but this command applies to R2014a. Was it that you ignore this point?
I'm trying to get postgres server status with:
sudo /etc/init.d/postgres status -u postgres
But getting following error:
/home/alex/olddisk/usr/local/pgsql/bin/pg_ctl: error while loading shared libraries: libpq.so.5: cannot open shared object file: No such file or directory
I added:
export LD_LIBRARY_PATH=""
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib/"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/alex/olddisk/usr/local/pgsql/lib/"
to my .bashrc, but it didn't help.
Thank you.
I ran into this error when I built postgresql from source using the --prefix flag. Building from source installs the necessary shared libs to the libs folder under the prefix directory you specified, instead of the usual place installations put shared libs. To solve the problem I just added the [prefix].libs folder to the LD_LIBRARY_PATH environment variable. For example, after building postgres using --prefix /mike/sandbox/postgres, the below command solved the issue:
export LD_LIBRARY_PATH=/mike/sandbox/postgres/lib:$LD_LIBRARY_PATH
I think this issue is duplicated, I faced the same problem and posted a solution here.
try this:
1: Know the path of "libpq.so.5"
find / -name libpq.so.5
Output example: "/usr/pgsql-9.4/lib/libpq.so.5" If found nothing, check if you have already installed the suitable postgresql-libs for your postgresql version and your OS platform
2: Symbolic link that library in a "well known" library path like "/usr/lib":
ln -s /usr/pgsql-9.4/lib/libpq.so.5 /usr/lib/libpq.so.5
Attention: If your platform is 64 bit, you MUST also symbolic link to 64 bit libraries path:
ln -s /usr/pgsql-9.4/lib/libpq.so.5 /usr/lib64/libpq.so.5
3: Be happy !
Please ensure you have 'postgresql94' package installed as well (in addition to postgresql94-server, postgresql94-lib, postgresql94-devel and whatever other PG related package you already have). These libraries get installed along with that package.
Some ideas:
Your modified ~/.bashrc only takes effect when you start a new (interactive) shell. Though catching up on that will not help you because:
/etc/sudoers, your configuration file of sudo, probably specifies env_reset. This means, that /etc/init.d/postgres will not see the content of $LD_LIBRARY_PATH of your shell.
Insert debug statements in /etc/init.d/postgres to verify what I told you: echo "LDPATH: $LD_LIBRARY_PATH" >&2
Check /etc/init.d/postgres. Probably you will have to insert the third one of your export statements near the start of this script. Or you will have to update an existing export LD_LIBRARY_PATH= statement.
Have you installed the necessary libraries?
If you are using ubuntu try:
sudo apt-get install libpq libpq-dev
My ultimate goal is to run a twiki website for my research group.
I have space on RedHat server that is running Apache, etc., but upon which I do not have root access. Since I cannot install perl modules with the current permissions, I've decided to manually install a local version of perl. Got that working no problem. The following modules are required to get twiki to work:
FreezeThaw - http://search.cpan.org/~ilyaz/FreezeThaw
CGI::Session - http://search.cpan.org/~markstos/CGI-Session
Error - http://search.cpan.org/~shlomif/Error
GD - http://search.cpan.org/~lds/GD
HTML::Tree - http://search.cpan.org/~petek/HTML-Tree
Time-modules - http://search.cpan.org/~muir/Time-modules
I have installed FreezeThaw, CGI, Error, and it fails on GD with the following error:
UNRECOVERABLE ERROR Could not find gdlib-config in the search path.
Please install libgd 2.0.28 or higher. If you want to try to
compile anyway, please rerun this script with the option --ignore_missing_gd.
In searching for how to get around this newest obstacle, I found a previous SO question: How to install GD library with Strawberry Perl asked about installing this and the top answer suggested manually compiling gdlib. You'll note, however, that that link is broken. The base site: http://www.libgd.org/ is basically down saying to go to the project's bitbucket page.
So I got the tarball from that page and am trying to install it. The following problems occur when I follow the instructions included. README.TXT says: "If the sources have been fetched from CVS, run bootstrap.sh [options]."
Running bootstrap.sh yields:
configure.ac:64: warning: macro `AM_ICONV' not found in library
configure.ac:10: required directory ./config does not exist cp: cannot
create regular file `config/config.guess': No such file or directory
configure.ac:11: installing `config/config.guess' configure.ac:11:
error while copying cp: cannot create regular file
`config/config.sub': No such file or directory configure.ac:11:
installing `config/config.sub' configure.ac:11: error while
copying cp: cannot create regular file `config/install-sh': No such
file or directory configure.ac:28: installing `config/install-sh'
configure.ac:28: error while copying cp: cannot create regular
file `config/missing': No such file or directory configure.ac:28:
installing `config/missing' configure.ac:28: error while copying
configure.ac:577: required file `config/Makefile.in' not found
configure.ac:577: required file `config/gdlib-config.in' not found
configure.ac:577: required file `test/Makefile.in' not found
Makefile.am:14: Libtool library used but `LIBTOOL' is undefined
Makefile.am:14: The usual way to define `LIBTOOL' is to add
AC_PROG_LIBTOOL' Makefile.am:14: to configure.ac' and run
aclocal' and autoconf' again. Makefile.am:14: If `AC_PROG_LIBTOOL'
is in `configure.ac', make sure Makefile.am:14: its definition is in
aclocal's search path. cp: cannot create regular file
`config/depcomp': No such file or directory Makefile.am: installing
`config/depcomp' Makefile.am: error while copying Failed
And it says I should also install the following 3rd party libraries:
zlib, available from http://www.gzip.org/zlib/
Data compression library
libpng, available from http://www.libpng.org/pub/png/
Portable Network Graphics library; requires zlib
FreeType 2.x, available from http://www.freetype.org/
Free, high-quality, and portable font engine
JPEG library, available from http://www.ijg.org/
Portable JPEG compression/decompression library
XPM, available from http://koala.ilog.fr/lehors/xpm.html
X Pixmap library
Which I am ignoring for now.
Switching to the generic instructions it says follow the advice in the INSTALL file; which says: "cd to the directory containing the package's source code and type ./configure to configure the package for your system." Which flat does not work: I've cd'ed into every directory of the tarball and running that command does nothing.
So, trying to install twiki required me to install perl, which required me to install the perl modules: FreezeThaw, CGI, Error, HTML, Time-modules, and GD -- which itself required me to install gdlib -- which further suggested I install zlib, libpng, FreeType 2.x, JPEG library, and XPM. And of course, I'm stuck at the installing gdlib stage.
My question is: what other process can possibly demean humanity to such a level? I cannot fathom the depths of cruelty that lay ahead of me as I dive ever deeper into this misery onion. Should I just end it all? Can meaning be brought from this madness? Will the sun come up tomorrow, and if so, does it even matter?
But seriously, any suggestions on what to do differently/better would be much appreciated -- I can't remember what a child's laughter sounds like anymore.
Install the package gd-devel, it contains /usr/bin/gdlib-config.
This should work:
sudo apt-get -y install libgd2-xpm-dev build-essential