I am trying to install GeneMark-ES but when trying to run as specified in the documentation several PERL modules are missing. I have tried to point to all the necessary files by defining PERL5LIB variable.
However, I have come across several files which are installed but there is more than one file in various directories. Not only that, each file has different file sizes.
Why is that happening? What file should I use?
Here is a GUI search for files named Simple.pm
Those Simple.pm files are module files, and each one is for a different "distribution".
For example, the one highlighted in the image is for Locale::Maketext::Simple. Simple.pm is the actual module file itself. The first one in the image is for Bio::Location::Simple etc. The Bio/Location part of the path signifies the actual name of the distribution as you can see.
The installation instructions should outline exactly which distributions it requires. You don't just use the Simple.pm file directly.
You need to read Perl Modules from the documentation to understand how Perl uses module names
After absorbing that, you will see that there are in reality only three different library locations which together contain ten module files that end with Simple.pm
/home/pollo/perl5/lib/perl5
/usr/share/perl5/core_perl
/usr/share/perl5/vendor_perl
Nowhere is there anything that looks like GeneMark-ES, but it seems unlikely that it would end with ::Simple if it were even there
Please open a new question and describe your experience trying to install the module that you require instead of offering misleading and irrelevant facts
Related
The number of sub-packages I want to create are so many (about 300 over).
I think.. to make the sub-package, the files should be installed (%install) early.
So I installed whole files to some specific directories.
Now I want to pack the file for each directory name.
in summaries,
Is it possible to repeat rpm macros? (ex, %package %description %files)
If it's possible, what should I use to repeat? (ex for ??)
As I know, to use %files macro, the real files should be installed previously. then where should I write the codes?
Natively, no there isn't. You'll have to use an external templating language like jinja2 to create the spec file on-the-fly.
That being said, having 300 subpackages is going to be an absolute nightmare for both your CM folks and for your users. You might want to ask another question explaining the use case to see if there are better alternatives.
I just published my first perl program, unifdef+ (code::unifdefplus, v0.5.3), but I'm not sure if I've done it properly. The program is broken into two parts -- a script (script/unifdef+.pl), and a module (lib/unifdefplus.pm). The script is basically a wrapper for the module. This is supposed to act as a command line utility (which is in reality what I wanted to publish).
The README file I included documents the script, not the module. CPAN seems to be taking the version from the module rather than the script as well (which is undefined at the moment).
So, my questions is: if I want this to be indexed as a script rather than a module, do I need to do anything differently? Also, I'm taking it I should write some documentation for the module as well -- in which case I'm assuming it should be a README file in the lib directory?
Again, I apologize, but this is the first time I've done this, and I want to make sure I've done it right.
Right off the bat, please read On the naming of modules from the PAUSE admins. If you still have questions, or you're still unsure, reach out to modules <at> perl.org.
The simplest way is to use a name in the App:: namespace, such as App::MyMod.
Typically, I'd keep the script and module documentation within their separate files, but near the top of the module documentation, clearly link to the script's documentation, and state that most users will want to read that for normal use.
To build the README from the script documentation:
pod2readme bin/my_script
Likewise, if you change your mind and want README to reference the module instead:
pod2readme lib/App/MyMod.pm
Assuming you're using ExtUtils::MakeMaker for your builds, you can ensure that the script is installed by adding a directive:
EXE_FILES => [
'bin/my_script'
],
With of course your script in the top-level bin directory of your distribution. Other build systems have similar directives.
For example, in my main.scm file I have (load "util.scm"). util.scm is a file in the same folder as main.scm. Both files are located in ~/documents/myproject/.
Now when I'm in this directory, and I run $ chez-scheme main.scm everything works fine. However, if I'm in my home directory and run $chez-scheme documents/myproject/main.scm it complains, not being able to find the file util.scm. I suppose this is the case because the current directory was my relevant home directory, and as such util.scm is indeed not there, it is actually in documents/myproject/. That being said, I'm used (in other languages) to the functionality of looking these paths up relative to the file containing the instruction to import, and I'd like to have that here as well. I've tried prefixing it by ./ or defining the file as a libary and doing (import (util)) but none of it works outside of documents/myproject/. Is there any way to get this to work as I intend it to?
I assume this is Chez-Scheme-specific. If not I'd prefer an answer that is implementation-neutral.
load is kind of awkward in R5RS since the report states that system interfaces are off topic in the report, but they include load which is a half hearted solution. The report does not say if the load is relative to the current directory or the file the load form originates from so in order to be portable I guess you are required to run your script from the current directory and have your loaded file relative to both.
Since Chez Scheme implements R6RS load is not really the right form to use. R6RS removed load in favor of libraries. You should make your file a library and consult how to install it. In some systems that is just placing the files in the right path, adding library location in configuration or running install script. How one uses the library is the same in all implementations, by using import.
According to Chez documentation you can pass --libdirs to it to give it one or more paths to consider for loading libraries. You can see the paths it scans by evaluating (library-directories)
There are several different ways to accomplish what (I think) you are trying to do, but eventually they all boil down to letting Chez know where to look for things. When given relative paths, include and load use the source-directories parameter to search for the requested file. Libraries have their path automatically prepended to source-directories while they are being loaded or compiled, so if your main.scm were a library definition then it would find util.scm as you expect.
However, it sounds like main.scm isn't a library, it's a top-level program. Unfortunately, Chez doesn't have a command line option to set the source-directories like it does for library directories. That leaves you with a bit less flexibility. Any of the following will work:
Make util.scm a library and invoke Chez with the --libdirs option to let it know where to look for libraries.
Set source-directories and load main.scm from inside the REPL rather than from the command line.
Write a wrapper shell script that does the above by echoing the commands into scheme so you don't have to type it yourself. (Only suitable if you don't also need to then type into the scheme session).
Write a wrapper shell script that cds into your project directory before running scheme (and presumably cds back to the original directory when it's done).
im trying to add the module File-Copy-Recursive to my script as i have done with another module already, but when i try to use it i get an error i can not explain:
use lib "./cpan";
use Recursive qw(dircopy);
dircopy($path1, $path2);
the error i get is: Undefined subroutine &main::dircopy called at ...
I don't understand it, the module clearly has the function dircopy in it.
As other answers have already stated, this isn't working because you've moved the module's location in the include directory from File/Copy/Recursive.pm to just Recursive.pm.
Here's why that doesn't work:
A Perl module (file with a .pm extension) and a Perl package (collection of code under a specific namespace) are two completely different things. Normally, we'll put a package into a module which happens to have the same name, but this is really just to help us humans maintain our sanity. perl doesn't care one way or the other - one module can contain multiple packages, one package can be split across multiple files, and the names of the packages and the modules can be completely unrelated for all perl cares.
But, still... there's that convention of using the same name for both, which the use command exploits to make things a little more convenient. Behind the scenes, use Module; means require Module.pm; Module->import; - note that it calls import on the module name, not the name of the package contained within the module!
And that's the key to your issue. Even though you've moved the file out of the File/Copy/ directory, its contents still specify package File::Copy::Recursive, so that's where all of its code ends up. use Recursive attempts to call Recursive->import, which doesn't exist, so nothing gets imported. The dircopy function would be imported by File::Copy::Recursive->import, but that never gets called.
So, yeah. Move ./cpan/Recursive.pm to ./cpan/File/Copy/Recursive.pm so that the package name and the module name will match up again and sanity will be restored. (If you've been paying attention, you should be able to come up with at least two or three other ways to get this working, but moving the file to the proper place under ./cpan really is your best option if you need to keep the File::Copy::Recursive source in a subdirectory of your project's code.)
Use FindBin for relative lib path:
use FindBin;
use lib "$FindBin::Bin/./cpan";
use File::Copy::Recursive;
And you have to keep the whole 'tree' under ./cpan and the use line have to remain the same.
Files under ./cpan dir:
find ./cpan/
./cpan/File/Copy/Recursive.pm
The module name in Perl comes not only from the path, but also from its package declaration. You installed the module to ./cpan, but the package name specified is still File::Copy::Recursive.
I am currently creating a Perl module for in house use. I used ExtUtils::ModuleMaker to generate a build script and skeleton for my Perl module. I would like to include .ini config files that my core modules need to run properly. Where do I put these files so they are installed with my module? What path do I need to use to access these config files across the main and sub modules?
P.S. this is the directory frame:
|-lib
|---Main.pm
|---Main
|-----subModule1.pm
|-----subModule2.pm
|-----subModule3.pm
|-scripts
|-t
If you are using Module::Install, you can use Module::Install::Share and File::ShareDir.
If you are using Module::Build, you may want to use its config_data tool and and a *::ConfigData module.
Taking a look at the generated Makefile, I would bet the better place to put it is under lib/Main and then you can direct your module to look at ~/.modulerc first, then PERLLIB/Main/modulerc.ini or something like that.
You could also embed the defaults in your module in a way that, in absence of ~/.modulerc, the module works using the default data.
To find the home directory, see File::HomeDir. You'll not want to use ~ (since that's a shell thing anyway).
I would suggest having your module work without the rc file as much as possible. If it doesn't exist, the code should fall back to defaults. This should be true, too, even if the file exists, but a particular flag is missing - it should fall back to the default, too.
You may want to look at Config::Any while you're at it. No point reinventing that wheel.