I get this message when I try to run a Perl script used in a bioinformatic package named DISOPRED3:
/usr/bin/perl: symbol lookup error: /software6/bioinfo/apps/mugqic_space/software/
perl/perl-5.18.2/lib/5.18.2/x86_64-linux-thread-multi/auto/Cwd/Cwd.so:
undefined symbol: Perl_xs_apiversion_bootcheck
I used the exact same script on my local computer and it works. Now I have to work on a super-computer from a distance and that's where I get this message. I checked, and the Perl versions are the same on both computers.
Sounds like you have two installs of Perl, the system one (/usr/bin/perl), and one in /software6/bioinfo/apps/mugqic_space/software/perl, and the former is using files installed by the latter. The former should not have been told to even look at the files installed by the latter.
Related
I copied a Perl module (DBD::Pg) from one system to another to run some quick checks on a Mojolicious project. On the new system, it all works fine when I run it under morbo (the Mojolicious test web daemon). But when I try to run the tests (via the Module::Build installer), I get the error:
Perl API version v5.16.0 of DBD::Pg does not match v5.20.0 at /usr/local/lib/perl/DynaLoader.pm line 216.
I researched why I am getting this, and read the explanation in the perldoc. But since the project runs under morbo, that seems to imply to me that the version mismatch may be trivial in this case. It looks like PerlXS does make some allowances for disabling VERSIONCHECK, but I don't see how that can be applied when running a Perl script.
You can't copy non-pure Perl modules from one system to the next (or into one group of perl lib directories into another perl's). Generally the code in those modules is compiled against the specific perl binary. That binary could have linked to different libraries, changed how it does things, used a different compiler, and many other things. It may not even work if the perl versions are the same.
Instead, install the DBD::Pg for each perl that needs to use it.
I have been trying to compile a script that was written in perl by someone other than myself into an executable format that can be used without having perl installed. There seems to be some sort of issue with Crypt::SSLeay packaging but I'm not sure what the error means. Here is a screenshot of the error message.
I've tried using PAR pp and cava to package, both will create executables that run just fine on the machine I'm using that has perl, but whenever I transfer it to a different computer I get the error seen in the screenshot. It's been the same error each time after changing compiler settings, and I'm not sure what to do at this point. If I have left anything out that may assist in answer please let me know and I will be happy to provide, coding is not my field so I am still learning and this is my first encounter with Perl.
First off, you probably do not need and should not use Crypt::SSLeay. However, both the modern Net::SSLeay and Crypt::SSLeay require OpenSSL binaries to be installed on the machine to run.
both will create executables that run just fine on the machine I'm using that has perl, but whenever I transfer it to a different computer I get the error ...
That's because the target machine does not have OpenSSL installed in the same location on which compiled the modules you are bundling.
I want to run my perl script which suppose to use the "Understand Scitool Perl API". I have included the statement "use Understand;" in the script have but when I tun the it on the terminal, it keeps showing me this error:
"Can't locate Understand/license.pm in #INC".
Does anyone know how can I install "Understand" module in order to be able to use its library knowing that I have already installed "Understand" tool.
Note: Im working on Mac operating system.
The SciTools Understand module requires a licence in the form of a license.pm file
If you're doing this at work then you should speak to your system administrator or manager to get hold of one. If you're working on your own then you need to talk to SciTools
Where did you get the main Understand module from?
I want to generate a ER Diagram sort of, of my spatial database i created inside of Postgresql. As i am also new to Postgresql, i am not too sure if the diagramming functionality can be done using whats offered by the PgAdmin (not referring to the Graphical Query Builder). However, it seems to me there is none. I read around that there is a perl based tool called postgresql_autodoc that can run through PostgreSQL system tables and return HTML, Dot, Dia and DocBook XML which describes the database. Now this is not exactly what i wanted but its the closest option i have. So i have successfully installed, ActivePerl 5.8 and DBD-Pg 2.10.0 for Perl 5.8 (DBD PG is a Perl DBI driver for the PostgreSQL database) and i have also downloaded the postgresql_autodoc.pl file. I have also added the path for Perl. But when i try to run the postgresql_autodoc.pl via the command prompt, i was getting this error: Possible Unintended Interpolation of #TEMPLATE in string at C:/Perl/bin/postgresql_autodoc.pl line 1831. Global symbol "#TEMPLATE" requires explicit package name at C:/Perl/bin/postgresql_autodoc.pl line 1831. Execution of C:/Perl/bin/postgresql_autodoc.pl aborted due to compilation errors.
I tried to view the postgresql_autodoc.pl using notepad++ however i have no experience with the perl language and so i cant figure out what is really wrong. All i could do is locate line 1831 but i dont know what i should do to fix this problem.
The postgresql_autodoc.pl file was downloaded from: http://www.rbt.ca/autodoc/
I would appreciate if anyone can help me here!
Thanks in advance
Barbara
That thingy, ##TEMPLATE-DIR##, is a string that is replaced when you build and install the module -- meaning you're not supposed to run it directly from the unpacked archive.
Most Perl modules are installed with a more or less simple three-step installation process, something like perl Makefile.PL ; make ; make install. However, this package is slightly different, you seem only to need make install.
Note that I have no experience with installing Perl modules on Windows with ActiveState. So the above may not work (e.g. if there's no make utility which is usually not part of Perl -- though it might be part of the ActiveState Perl distribution).
But there's a workaround. You can simply do what the install script does and replace the ##TEMPLATE-DIR## string yourself. It can be done easily with any text editor by replacing the two occurrences of ##TEMPLATE-DIR## with the path to where the postgresql_autodoc.pl script has been unpacked to -- meaning it's the path the script will look for the *.tmpl files in.
Note that Windows path names can be written with forward slashes in Perl, meaning C:/Temp/postgresql_autodoc should be OK.
I have downloaded strawberry PERL and writing one application with CGI Perl Apache on Winxp sp3).
One of the libraries (written by someone else) which I using uses XML::LibXML. When i load the page it gives Internal Server Error. From Apache error log i can see this error:
Can't load 'C:/strawberry/perl/site/lib/auto/XML/LibXML/LibXML.dll' for module XML::LibXML: load_file:The specified module could not be found at C:/strawberry/perl/lib/DynaLoader.pm line 190.
C:/strawberry/perl/site/lib/auto/XML/LibXML/LibXML.dll exists with all permissions.
Also this library works properly on Linux. My application also works fine if I remove all code that needs LibXML.
Can anyone tell me when can be possible issue here.
If you peek into the source for DynaLoader you'll find
Many dynamic extension loading problems will appear to come from
this section of code: XYZ failed at line 123 of DynaLoader.pm.
Often these errors are actually occurring in the initialisation
C code of the extension XS file. Perl reports the error as being
in this perl code simply because this was the last perl code
it executed.
You should have also gotten (but may not have noticed) the following dialog, which provides a more accurate error message:
The problem isn't that perl can't find LibXML.dll; it's that LibXML.dll can't find the real libxml. (The former is just a wrapper that provides Perl bindings for the latter.) To fix that you need to ensure that Strawberry Perl's c\bin folder is in your PATH. In your case, that would be C:\strawberry\c\bin.
You might have to check the environment variable settings in the windows,
make sure that the installation path of the module is present in the PATH variable.
The reason it works in linux is that make files usually set the environment variables for you in linux in windows it may not have set properly.
For eg;
go to Control Panel\System and Security\System click change settings then advanced tab in user variable section see if there is a variable called perl5lib.
if not create an new perl5lib variable and add the path of your library ( usuall C:\Perl\site\lib but may be different in your case)
I had the same issue after installing Strawberry perl. It was working fine when I run the script from server, but not remotely from a automation tool. The issue was because of the Environment variables not updated when we run it remotely. So I did server reboot, which resolved the issue.
I encountered the same problem recently, in my case it was not related to PATH variable (it was already correct). The thing is I was executing my script from Git Bash console and as it turned out git-bash perl was being used instead of Strawberry (see git-bash perl should not be first in path). Switching to standard Windows CMD terminal helped.