I need to build the same set of shared objects (the OpenSSL support) for many platform and Perl version (4x4). Install works well with Perlbrew and I can install various packages with cpan on the different version I'v created. The problem is that they all fail with a PL_unitcheckav not found in DynLoader.pm
I've found lots of similar issues, but no solutione so far. Is this a debug symbol? It only fails when I add (cpan) a package from my brew install and then try to tun it on other system. It works fine when compile "natively" using my local Perl
Just found the answer. As #ikegami said, I was compiling w/o --multi, --64int and --thread and running it on a version with all these flags compiled (version number was correct). The "multi" option was really the problem
Related
I trying to get set up with Variant Effect Predictor (VEP) on the command line. I'm following the setup tutorial but I'm encountering some errors around dependencies. I'm also quite new to the command line so if anyone is able to break down the solution too then I'd be very grateful. Thanks!
Tutorial: https://www.ensembl.org/info/docs/tools/vep/script/vep_tutorial.html
VEP requirements: http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#requirements
I also have Perl v5.32.1.
What I've done:
I installed dependencies (listed in the requirements page) with the following commands:
- sudo -s cpanm DBI
- sudo -s cpanm Archive::Zip
- sudo -s cpanm DBD::mysql
For DBD:mysql, I got the follwoing message:
--> Working on DBD::mysql
Fetching http://www.cpan.org/authors/id/D/DV/DVEEDEN/DBD-mysql-4.050.tar.gz ... OK
Configuring DBD-mysql-4.050 ... N/A
! Configure failed for DBD-mysql-4.050. See /root/.cpanm/work/1626111140.5937/build.log for details.
Trying it out anyway, I ran perl INSTALL.pl (from the tutorial page) and got the message below. I would like VEP to run in online mode too if possible.
`WARNING: DBD::mysql module not found. VEP can only run in offline (--offline) mode without DBD::mysql installed
http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#requirements
Hello! This installer is configured to install v104 of the Ensembl API for use by the VEP.
It will not affect any existing installations of the Ensembl API that you may have.
It will also download and install cache files from Ensembl's FTP server.
Checking for installed versions of the Ensembl API...done
Setting up directories
Destination directory ./Bio already exists.
Do you want to overwrite it (if updating VEP this is probably OK) (y/n)? y
- fetching BioPerl
- unpacking ./Bio/tmp/release-1-6-924.zip
ERROR: Unable to unpack file ./Bio/tmp/release-1-6-924.zip without Archive::Extract or tar/unzip/gzip`
You show us this error:
Configure failed for DBD-mysql-4.050. See /root/.cpanm/work/1626111140.5937/build.log for details.
So looking in there will give you more clues about what the problems are. Without that, we can only guess.
But we can make educated guesses. The DBD::mysql distribution comes with a file called DBD::mysql::INSTALL which will talk you through some of the problems you'll find while installing this module.
It's important to note that DBD::mysql is a wrapper around MySQL's client libraries. They are written in C, so you'll need a C compiler installed in order to build DBD::mysql. You'll also need the client libraries and the development versions of the client libraries (for the C header files that you'll need to compile the module). On Ubuntu, those packages are called "libmysqlclient" and "libmysqlclient-dev". If you don't have a C compiler, then you'll want to install "gcc" too.
But this is all getting a bit complicated. There's another, simpler, approach. If you're using the system version of Perl (the version that was installed as part of the operating system and probably lives in /usr/bin/perl) then I'd recommend using the pre-build Ubuntu version of the package, which you can install by running:
$ sudo apt-get install libdbd-mysql-perl
Installing that version uses the OS's own package manager, and the package manager knows which other packages are needed in order for it to work - so it will install those as well.
People will probably complain that you're better off installing the modules from CPAN as it gives you more flexibility and allows you to use more up-to-date packages than the versions from your OS repos. And they're right. But, honestly, if you're a non-Perl programmer who just wants to get an application up and running, this is by far the simplest approach.
(But, as I said above, this is all guesswork as you haven't shared the most important errors with us.)
I am using the windows 8 operating system and I am trying to install the WWW::Mechanize::Firefox module in ActiveState Perl, from CPAN. I have successfully downloaded and installed all the dependencies and also installed the MozRepl module on Firefox. I do not have noScript running on my firefox and hence I am assuming that Javascript is enabled across all files (I am not sure how or where to check that). Here is my error message when I try to install the module.
I also constantly receive this error throughout the installation - "Subroutine-MozRepl-Load Plugins redefined at line 104."
Any help is much appreciated ! Thank you !
EDIT - These are the errors -
As Kim suggested in comments, you will need Mozrepl and Firefox.
Please refer WWW::Mechanize::Firefox::Installation page for detailed instructions on how to install this module.
If you use ActiveStates package manager, you can find some pre-packaged but untested PPMs at https://github.com/Corion/www-mechanize-firefox/downloads .
I needed to use this module on Windows, and couldn't get it running with ActivePerl. So I installed http://strawberryperl.com/ and it worked. This version of perl seems to handle installs form the cpan command line utility better than Activestate, who expect you to use their perl package manager as the default module installer (and don't supply a dmake program). Strawberry Perl also comes with a C compiler so can build modules that are a mixture of Perl and C code.
And make sure mozrepl is running before you try to install.
I have a Perl module that handles localization tasks using the GNU gettext utilities xgettext, msgfmt, msginit, and msgmerge. I got some test failures from a SunOS system which, when I looked into it, seemed to be ancient. For now I am skipping tests when msgfmt and xgettext choke on a simple --version option. But I think it would be better to refuse to install unless a relatively modern version of the GNU Gettext utilities are installed.
So, what's the best way to do that? I'd like to just figure out what's installed and if it supports the options I need, and refuse to install the module if those dependencies are not met. Should I just run gettext --version and refuse to install if it exits with a non-0 value? Or might there be a more canonical solution?
Since "gettext --version" should always return a value on any "contemporary" version (for example, I just tried it on a circa 1997 Redhat ... and it worked!), that should be sufficient.
IMHO...
I am trying to install wxperl on strawberry. I can't install Alien::wxWidgets. I tried everything I can think of. Usually I get an error like this one:
Creating library file: ..\..\src\stc\..\..\..\lib\gcc_dll\libwxmsw28u_stc.a
compilet.exp:fake:(.edata+0x3c): undefined reference to `boot_compilet'
compilet.exp:fake:(.edata+0x40): undefined reference to `boot_compilet'
I don't know what that means. I tried with wxWidgets v 2.8.12 and 2.9.3 and various options. I started with cpanm and later evoking perl Build.PL manually with all kinds of options.
I am on Windows 7 64 bit. I tried with 5.14.2 32bit and 64bit. I am pretty sure that my path has no other perl installation than the one I currently using.
Any ideas? Thanks!
Using strawberry-perl-5.16.3.1-32bit on Windows 7.
It seems that even though the build process crashes with the error message above, Alien::wxWidgets has, in fact, been successfully made, and is ready to install.
Got the same error message building Alien::wxWidgets from SVN trunk. I ran 'build test' and the tests passed so I ran 'build install'. Wx compiled successfully, all tests passed. Padre editor compiled successfully, all tests passed, and it works well.
It is also possible to install via PPM in Strawberry perl:
ppm set repository wxPerl http://www.wxperl.co.uk/repo29 (for WxWidgets-2.9.4)
ppm install Alien::wxWidgets (version 0.61)
Unfortunately, the latest version of Padre editor requires Alien::wxWidgets 0.62, so building Alien::wxWidgets from source is necessary to make Padre from CPAN.
Alternately, you can use the Citrus Perl distribution created by Mark Dootson. One caveat, the version of Perl, 5.16.1, is not the latest, but it is more recent than DWIM Perl build of Strawberry Perl 5.14.2.1 RC.
I would recommend using the latest Strawberry Perl 5.16.3, or 5.14.4.1 for security reasons because it has a a fix for the rehashing flaw which could be used for denial of service attacks. Described here:
http://www.vuxml.org/freebsd/CVE-2013-1667.html
One idea is to install DWIM Perl, which is a Perl distribution which contains Strawberry preloaded with a whole lot of commonly used CPAN modules, and includes Alien::wxWidgets.
I am trying to install ruby version manager on a g4 ibook running 10.4 but I receive two error messages right off the bat when I try to run the first command:
$ bash -s stable < <(curl -s https://raw.github.com/wayneeseguin/rvm/master/binscripts/rvm-installer )
bash: line 6: set: errtrace: invalid option name
bash: line 13: conditional binary operator expected
I am new to ruby, rails, and fairly inexperienced with the command line too. I've done a bit of searching and have seen other people having problems installing a specific version of ruby on a powerpc using rvm, but no other examples of someone having a problem installing rvm first of all.
Does this seem like a powerpc issue? Or is there something simple with the command line that I am missing here?
I have also searched on these specific error messages but haven't found any solutions yet. Oh and I should also add that I have xcode installed and I also installed macports because I thought that might help...but it hasn't.
The most probable cause of the error you're getting is your bash version is far too old to be used with any relatively new RVM version. Also, the likelihood of you being able to easily compile rubies on a G4 now is very low. You'll likely end up needing to compile many tools and libraries from source which you'll have to do from the command-line. Finding the right combination of library versions that both support your arch and are still available for download might not be as easy as it sounds. Much of the ruby compilation on OS X depends on libraries that come with Xcode. So, you might hit a wall there too with rubies now requiring newer libraries that can be provided with a version of Xcode that can be installed on your system.
You can try upgrading your bash version and/or use a much older version of RVM, although, I don't remember RVM ever working on 10.4. Or, you can try to compile everything from source, including Ruby. You'll might be able to get Ruby 1.8.6, maybe 1.8.7 working but anything higher is very unlikely.
Good luck =/