I've already read related threads like these, but they do not fully capture our situation.
This is on a firewalled machine. No net access. We can ftp files to folders and install modules from there.
We have CHMOD 777 for our users on some folders. We can install Perl modules if we locally build them by downloading the relevant .pm files. But when these files cannot install, we do not have any cpan or cpanm.
I'd like to install, for example, HTML::Restrict. If I do the download + install thing, the Restrict.pm gives me this error:
/lib/HTML/Restrict.PM:328: Unknown command paragraph "=encoding UTF-8"
Reading a bit online suggests that this could be an old Perl problem. We use 5.8.x. Our own dev machines have the luxury of 5.16.x and internet access so installing module is a cinch. Anyway, one of my older machines also has 5.8.x, and installing the module via cpanminus worked there (with internet).
So, question: is it possible to install "cpanminus" (cpanm) through FTP, then upload specific module files to the server through FTP too, and then go into shell and install modules via cpanm by pointing it to respective .pm files?
Thank you for any pointers.
You should take a look at perldoc perlmodinstall which goes into detail about how to install a module from its distribution. It follows what should be a familiar incantation
Decompress
Unpack
Build
Test
Install
Assuming you're on a Linux system, this commonly takes take the form of
gzip -d My-Module-Distribution.tar.gz
tar -xof My-Module-Distribution.tar
perl Makefile.PL
make
make test
make install
But after the Unpack stage you will often find a README file or other text file that will describe any unusual steps to be taken
Clearly some of these steps can be combined. For instance, most people will probably want to use
tar -xvfz My-Module-Distribution.tar.gz
to avoid having to invoke gzip separately. Likewise, the make system will force a build phase as a prerequisite if you use just
make test
without the preceding make
The linked document has a lot to say about how to install on other platforms, should you not be running a Linux variant
I still don't really understand your thinking, but you can get a stand-alone version of cpanm using curl. For instance
curl -sS --location https://cpanmin.us/ --output cpanm
then you should be able to just copy it to your target machine, put it on your PATH, and do
cpanm HTML-Restrict-2.2.2.tar.gz
but I doubt if you will find any change to the specific errors you are getting
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'm working with an application that downloads its own copy of Perl from a 3rd party website as a sort of bootstrap. I'd like to get a different copy from a more trusted source like CPAN, but I can't find any precompiled copies of Perl (only full source distributions) and I don't know how to build from source. Is there anywhere I can get a precompiled copy?
Another problem is that I don't know for sure that this download is just "a compiled copy of Perl". I'm assuming that, but I don't know what it's supposed to look like.
It comes in a .tar.gz which really only has two directories populated:
/bin (contains perl, cpan, perldoc, enc2xs, etc)
/lib/5.16.3 (contains subdirectories for various CPAN modules)
So to summarize: 1) Is this what Perl looks like when it is compiled? 2) Where can I get a pre-compiled version of Perl for my OS (RHEL 7), or if this isn't possible, how can I best generate a compiled version?
PS: For those who are curious, this is the copy of Perl that is downloaded by Miyagawa's Heroku Perl buildpack (https://github.com/miyagawa/heroku-buildpack-perl), which I am using for a project. He downloads copies of Perl stored on a website cache.bulknews.net, which might just be his own hosting, not sure.
I don't know how to build from source
This is documented in INSTALL in the distribution.
It's quite simple on a unix system:
cd /tmp
wget https://cpan.metacpan.org/authors/id/S/SH/SHAY/perl-5.26.1.tar.bz2
tar xvjf perl-5.26.1.tar.bz2
cd perl-5.26.1
sh Configure -des -Dusethreads -Dprefix='/some/dir'
make
make test
make install
You might also want to pass -Duserelocatableinc to make the install relocatable.
You can also use perlbrew or plenv to assist you with installing perl and managing multiple installs of perl.
Because i have a long series of comments with #ikegami, I cleaning up the question, in a hope it will be more understandable. Unfortunately, english isn't my "main" language. :(
Let say, having an environment where:
no development tools are installed (no make, nor gcc or like)
perl is installed with its core packages, nothing more
no outgoing network access is allowed - e.g. the user couldn't use curl nor cpan to download/install perl dependencies
the user even doesn't have admin (root) rights
but want install and evaluate some perl based web-app, let call it as MyApp
The MyApp
doesn't uses any XS-based module. (at least, I hope - in the development me using plenv and cpanm, so never checked the installed dependencies in depth)
it is an pure PSGI app, the simple plackup app.psgi works OK
the app uses some data-files which should be included in the "deployment".
The main question is: how to prepare the MyApp, and the all used CPAN-modules, to be easily installed in such restricted environment?
The goal is:
i don't need save my efforts and my time
but i want save the user's time and want minimize the needed actions on his side, so the installation (deployment) should be simple-as-possible.
E.g. how to get an running web-app to the user's machine with minimum possible (his) steps.
- the simplest thing is could be something as:
- copy one file (zip, or tarbal)
- unpack it
- from the terminal execute some run.pl in the unpacked directory.
To get the above simple installation, my idea was the following:
1.) Create an tarball, and after the unpacking will contain 3 folders and 1 perl-script, let say:
myapp_repo/
myapp_repo/distlib #will contain all MyApp's perl modules also ALL used CPAN modules and their dependecies
myapp_repo/datafiles #will contain app-specific data files and such
myapp_repo/install.pl
myall_repo/lib #will contain modules directly used by the `install.pl`
2.) I will develop an install.pl script, and it will be used as the installer-tool, like
perl install.pl new /path/to/app_root
and it will (should):
create the all needed directories under the /path/to/app_root (especially the lib where the will install the perl modules)
will call "local" cpanm internally (from the myapp_repo/lib) to install the app's perl modules and their CPAN dependencies using only distribution files from the distlib.
will generate and install the needed runtime script and the app.psgi into the /path/to/app_root/bin
will install the needed data-files for the app.
3.) So, after this the user should be able to simply run:
/path/to/app_root/bin/plackup /path/to/app_root/bin/app.psgi
In short, the user should use:
the system-wide perl and the system-wide perl-core modules
and any other
runtime perl-scripts (like plackup)
and the required CPAN-modules
should be installed to an self-contained directory tree using only files (no net-access).
E.g. the install.pl should somewhat call internally the cpanm to achieve (as equivalent) for the following cpanm command
cpanm --mirror file://path/to/myapp_repo/distlib --mirror-only My::App
which, should install My::App and all dependencies without network access using only the files from the myapp_repo/distlib
Some questions:
Is possible to use cpanm (called as an locally installed module) without the make?
For creating the myapp_repo/distlib, me thinking about using Pinto. Is it the right tool for achieve the above?
forgot me something? or with other words:
Is the above an viable (read: working) way?
are are any other tools, which i could/should to use for simplifying the creation of such distribution tarball?
#ikegami suggesting some method:
- "install everything" in one fresh-directory on my machine
- transfer this self-contained directory to the target machine
It sound very good, because this directory could contain all the needed app-specific data-files too, unfortunately, I don't understand the details how his solution should be done.
The FatPacked solution looks interesting too - need learn about it.
Don't write your own make or installer. Just copy it make from a different machine (which is basically what apt/yum/etc do anyway, and which you'd have to do even if you wrote your own). You'd be able to use cpan in 5 minutes!
Also, that should allow you to install gcc if you need it (e.g. to install an XS module), although it doesn't sound like you do. If you do install gcc, I'd install my own perl to avoid having to deal with PERL5LIB.
Tools such as minicpan will allow you to install any module from CPAN without internet access. Of course, you can keep using the command you are already using it if mirrors the packages you need.
The above explains how to simply and quickly setup a machine so it can use cpan and thus install any module easily.
If you just want to install a specific module and its dependencies, you can completely avoid using cpan on the target machine. First, you need a fresh install of Perl (preferable of the same version as the one on the target system). Then, simply install the module to a fresh dir on your machine, and transfer that dir to the target machine. That's it; nothing else needs to be done. This even works for XS modules if the two machine are similar enough.
This is what ppm (ActiveState's Perl package manager) does.
Unfortunately, while this solution is almost as simple as the one above, it's not nearly as flexible, it doesn't run the test suite of the modules being installed, etc. It does have the advantage of not requiring the transfer of any binary (if you're not installing any XS modules).
I have a Linux server that has no access to the internet (access is prevented by a firewall). I would like to install a new Perl. What are my options and what is the best way to do this? The system Perl (included in OS installation) must remain unchanged.
I have been using perlbrew and I think it is the best way to do an online installation. But all the steps involved in perlbrew seem to require internet access: you download it from the net, it downloads new Perl versions from the net etc. and I haven't found a glue how to make it work offline.
If perlbrew is out of question I could build Perl from source into a custom location on the server. I assume that this could end up being complicated, time-consuming and error-prone. And every time I update Perl I have make a new build manually.
There can also be other ways to install that I'm not currently aware of. And of course I could stick with the system Perl but it is an outdated version and I'm already using the new syntax features. Or I could start negotiations to change the firewall policy to allow internet access for perlbrew.
But all the steps involved in perlbrew seem to require internet access
Not if properly configured.
To install perlbrew itself off-line, install the App-perlbrew dist. Following its dependencies manually is a chore, so instead prepare a MiniCPAN mirror (with -p to include Perl dists), take it over to the target machine and configure CPAN to use the local mirror. Run cpan App::perlbrew to install.
After perlbrew is installed, run its mirror command to configure a CPAN mirror into $PERLBREWROOT/Config.pm. Edit this file to change it to the local MiniCPAN mirror. Drop Perl dist tarballs into $PERLBREWROOT/dists/.
Be aware that compiling Perl requires a working C compiler toolchain, and optionally the development files for libdb (BerkeleyDB) and gdbm. (Read the INSTALL file once over, even though perlbrew's autoconfiguration and Perl's configure.SH defaults hide these details from you.)
The compiler toolchain is probably much more difficult to procure off-line, unless the OS installation has already been used before for compiling other C stuff.
There's nothing that special about perlbrew. If you aren't going to use it to download the Perl sources, it's not saving you that much. Once you have the Perl sources, you just need to configure and install it:
% ./Configure -des -Dprefix=/path/to/installation
% make install
Once done, everything for that Perl is under that installation path.
I dislike perlbrew mostly because it hides from people how amazingly simple this task is so they feel like they can't do it on their own.
Have you considered attacking it from a different direction? Keeping this up-to-date is going to be a pain if you have to request internet access each time. Likewise, if you've missed out/misconfigured any packages in your CPAN mirror it's difficult to correct once you're actually trying to use them.
Perhaps just build a small VM with a cut-down linux + perl + modules. Keep that up-to-date at your end and just take the whole lot in on a USB stick. You'd have a known-working easy-to-setup installation.
What I personally do is using git checkout when I'm offline (and not on vacation). Once you have the whole git work directory, it's trivial to build any released version by checking out the tags:
git checkout v5.17.4
git clean -f # cleanup previously compiled .o files etc
sh ./Configure ...
Depending on how you can transfer files to your host, this can be handy, since you you can also setup a private git repo there so other computer can git push new commits to there.
I am attempting to install a Perl Module entitled: File-Copy-Recursive and I am following these steps:
1) open cmd.exe
2) perl -MCPAN -e 'install File::Copy::Recursive;'
and I receive the message "It looks like you don't have a C compiler and make utility installed. Trying to install dmake and the MinGW gcc compiler using the Perl Package Manager. This may take a few minutes..."
"Downloading ActiveState Package Repository packlist...failed 500 Can't connect to ppm4.activestate.com:80 (connect: timeout).
Downloading File-Copy-Recursive packlist...not found
ppm.bat install failed: Can't find any package that provides MinGW"
These failed because I am behind a proxy, and I do know the proxy settings but I don't know how to apply them in this situation.
Is anyone aware of any alternative fixes to this solution?
Thank you.
It seems you are using ActiveState Perl, which comes with its own package manager (called PPM) to ease the pain of installing modules, especially those which would normally require a C compiler to be able to install.
Try following the instructions to set up your environment so that PPM knows about your proxy. For example, to set the proxy settings for a single instance of cmd.exe:
C:\>set http_proxy=http://username:password#proxy.example.org:8080
Then, in the same command prompt window, try this (it works for me, though I'm not behind a proxy):
C:\>ppm install File-Copy-Recursive
Note that it's probably a good idea (maybe even required?) to run cmd.exe "As Administrator" to make sure it has full authorization.
EDIT: The particular module you want to use is written in pure Perl. For a quick "installation", you can just download it from CPAN, extract the files, and copy the "Recursive.pm" file into a File\Copy directory structure placed in the same directory as your script:
yourscript.pl
File\
Copy\
Recursive.pm
As an alternative you could try the Strawberry Perl distribution which comes with tools for building XS modules.
Hi
I guess you are using Activestate Perl
look at
http://docs.activestate.com/activeperl/5.10/faq/ActivePerl-faq2.html#what_is_ppm
PPM is installed automatically with ActivePerl.
To use PPM, your computer must be connected to the internet, have access to a PPM repository on a local hard drive or network share, or have access to a mounted ActiveState ActiveDVD.
If you connect to the internet via firewall or proxy, you may need to set the http_proxy environment variable. See PPM, Proxies and Firewalls for more information.