I am running a toolkit named RNA Framework that requires ViennaRNA to be installed.
I have installed the ViennaRNA 2.4.14 to run a function named rf-fold, However, I constantly receive this error:
[!] Error: ViennaRNA package's Perl module RNA.pm is required.
Please ensure that `ViennaRNA package v2.2.0` (or greater) is installed and try again
When I check the missing RNA.pm module, I can see it is in this path:
/home/user/ViennaRNA/lib/site_perl/5.28.0/
when I check which Perl I am using (type: which Perl) it gives me:
/home/user/perl5/perlbrew/perls/perl-5.28.0/bin/perl
I tried different ways to install the ViennaRNA, including conda install -c bioconda viennarna, compile and make install from ViennaRNA-2.4.14.tar.gz file from the official website. But I cannot get over this error.
I saw a similar issue here and there is a solution (https://www.perlmonks.org/?node_id=1052814), but I don't fully understand the content. Thanks in advance for any help and sorry if it is a basic question!
I think the RNA.pm come with the package, when you download ViennaRNA-2.4.14.tar.gz and install following this link.
So I found my RNA.pm is in the directory:
/share/apps/ViennaRNA-2.1.7/compile-install/lib/site_perl/5.14.2/x86_64-linux-thread-multi/RNA.pm
And I modified the PERL5LIB environment variable by :
export PERL5LIB=/share/apps/ViennaRNA-2.1.7/compile-install/lib/
Problem solved!
Related
On Ubuntu 20.04, I had two operational copies of opus-tools 0.1.10-1 (amd64) and ffmpeg 7:4.2.4-1ubuntu0.1 (amd64). I installed lame 3.100-3 (amd64) and opus-tools / ffmpeg stopped working with the following errors:
ffmpeg: symbol lookup error: /lib/x86_64-linux-gnu/libavcodec.so.58: undefined symbol: opus_multistream_surround_encoder_create
opusenc: symbol lookup error: opusenc: undefined symbol: opus_multistream_surround_encoder_create
I uninstalled lame and got the same messages. Then I used the --auto-remove option to remove any dependency and faced the same issues. After that, I uninstalled and reinstalled opus-tools and ffmpeg and that didn't help. Almost giving up, I followed this FFmpeg-user thread and executed ldconfig. No luck either.
Finally, I tried building and installing opus-tools from the sources but got the following message:
configure: error: Package requirements (ogg >= 1.3) were not met:
No package 'ogg' found
Consider adjusting the PKG_CONFIG_PATH environment variable if you
installed software in a non-standard prefix.
Alternatively, you may set the environment variables OGG_CFLAGS
and OGG_LIBS to avoid the need to call pkg-config.
See the pkg-config man page for more details.
Thanks in advance for any help.
Do a backup of your files and reinstall ubuntu 20.04.
I was going to use Swift/t and normally I started to with HELLO WORLD code from the gallery. Unfortunately, I encountered compiling error as follow:
zsh: error while loading shared libraries: libtinfo.so.5: cannot open shared object file: No such file or directory
May you please provide me some hints that may help me to resolve the issue.
This kind of errors (bash/zsh: error while loading shared libraries: ...) appear when you don't have a library installed on your system.
In your case, your missing library is libtinfo, on its version 5. You should be able to search and install it throught your system's package manager.
Just as an example, in Ubuntu you can install it by:
sudo apt install libtinfo5
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
I tried to install module Class-Load-XS-0.04 manually. I saw the following error:
$ perl Build.PL
Warning: ExtUtils::CBuilder not installed or no compiler detected
Proceeding with configuration, but compilation may fail during Build
However, the execution of perl -e 'use ExtUtils::CBuilder' was perfectly fine. I even tried to re-install ExtUtils::CBuilder, but it still does not work.
Could you please help?
I tried on my Win 7 machine, and it shows some warnings like this when I do perl Build.pl:
collect2: ld returned 1 exit status
Checking prerequisites...
requires:
! Class::Load is not installed
build_requires:
! Class::Load is not installed
! Module::Implementation is not installed
! Test::Fatal is not installed
! Test::Requires is not installed
ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions
of the modules indicated above before proceeding with this installation
Then I installed the above mentioned modules, and things went fine then.
You may try install these modules first.
Hope it helps.
It looks to me like you don't have a compiler. Try this:
perl -e 'use ExtUtils::CBuilder; $cb = ExtUtils::CBuilder->new; print $cb->have_compiler ? "have\n" : "dont have\n";'
Can I guess that you are on Windows using ActiveState Perl? If so perhaps try Strawberry Perl which comes with a compiler.
Had a similar problem installing a different module (Win32::Mutex). This isn't a great fix, but it got the job done. From the build directory (e.g., ~/.cpan/build/The-Module-mYyzLx)
First, set the CC environment variable yourself
SET CC=C:\strawberry\c\bin\g++.exe [Windows]
export CC=/usr/bin/g++.exe [Cygwin]
and try to build (perl Build.PL, perl Build, ...). If it is still complaining about missing programs (g++, dlltool, etc.):
Second, copy pieces of your tool chain into the build directory
COPY C:\strawberry\c\bin\g++.exe . [Windows]
COPY C:\strawberry\c\bin\dlltool.exe .
cp /usr/bin/g++ . [Cygwin]
cp /usr/bin/dlltool .
If the build still complains about missing programs, copy those to your build directory too.
The fix and the symptoms are consistent with ExtUtils::CBuilder not being able to use the current PATH setting, though I have no idea what that would be so difficult.
I'd suggest installing these first:
apt-get install libc6-dev
and
apt-get install libtest-exception-perl
By the way you describe the problem it looks like you have these two perl modules missing. On the other hand it takes just a couple of seconds to double-check if those are installed, but these 'seconds' could help you save on a lot of head ache.