[Bioperl-l] ./Build install doesn't install bioperl-run

Chris Fields cjfields at illinois.edu
Sun Jun 6 12:25:59 EDT 2010

On Jun 6, 2010, at 10:15 AM, Peng Yu wrote:

> On Sun, Jun 6, 2010 at 9:16 AM, Dave Messina <David.Messina at sbc.su.se> wrote:
>>> My perl is installed in a directory in my home. I think that bioperl
>>> will be installed in the directory in the perl directory in my home,
>>> right?
>> Hmm, I think you still have to tell Build that you want it to install in your private directory.
>> Have you read
>> http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_IN_A_PERSONAL_MODULE_AREA
> I actually read the description. But I don't understand why it is the case.
> When I download other packages from CPAN. I don't need to specify
> anything. They get automatically installed in a directory (I think it
> is site_perl?) in my local perl installation directory. Why I have to
> explicitly say where bioperl should be installed ?

That's not the point.  You are not installing code from CPAN; you are installing code in development from our git/github repository.  We can't always guarantee that it would pass tests, as the CPAN release does, nor should we need to.

I know there is a need to install the latest and greatest bleeding-edge code, but there is a reason it's called 'bleeding edge'.  It may not always pass tests, so installing it system-wide is definitely not recommended.  I would go as far as saying that installing it locally is probably also not a good idea unless you know what you are doing.

>> ?
>>> BTW, the following web address better be changed to 'Using_git".
>>> http://www.bioperl.org/wiki/Using_Subversion
>> Actually, the page is Using_git, but we're redirecting Using_Subversion to it; that's why it looks like URL is wrong.
>> Also, I think we tried to change all of the links on the website to point to Using_git. May I ask where did you see — that is, how did you come to — the link to Using_subversion?
> Please see the following webpage.Search for "Using Subversion".
> http://www.bioperl.org/wiki/HOWTO:BlastPlus

Looks like that was corrected to point to the proper location.  

I just want to point out something: we've now been on git/github for just over a month now.  It's very possible there are links on the wiki that point to the older page.  It's also possible to simply edit said pages to point to the proper page; it is a wiki, after all.  If you see a link to the wrong page, feel free to edit it after logging in (anyone can get an account).

>>>> Can you post the whole transcript of your failed install?
>>> I assume that you are asking the Build script. Please see the
>>> attachment. Let me know if you mean something else.
>> No, I mean could you copy and paste the command line text showing the commands you ran (starting with 'perl Build.PL' and up to and including './Build install'), and including the output from running those commands?
> Once, I saw some installing command after "Building BioPerl-Run" when
> I run '.Build install". But I can not reproduce it any more.
> I delete the download and run the installation process again. But it
> still doesn't seem to work.
> $ git clone git://github.com/bioperl/bioperl-run.git
> Initialized empty Git repository in
> /pearson/data/pengy/download/bioperl_svn/bioperl-run/.git/
> remote: Counting objects: 11230, done.
> remote: Compressing objects: 100% (2502/2502), done.
> remote: Total 11230 (delta 7360), reused 11184 (delta 7322)
> Receiving objects: 100% (11230/11230), 25.84 MiB | 18.20 MiB/s, done.
> Resolving deltas: 100% (7360/7360), done.
> Checking out files: 100% (379/379), done.
> $ perl Build.PLInstall scripts? y/n [n ]
> n
> Do you want to run tests that require connection to servers across the internet
> (likely to cause some failures)? y/n [n ]
> n
>  - will not run internet-requiring tests
> Creating new 'MYMETA.yml' with configuration results
> Can't find dist packages without a MANIFEST file
> Run 'Build manifest' to generate one
> WARNING: Possible missing or corrupt 'MANIFEST' file.
> Nothing to enter for 'provides' field in metafile.
> Creating new 'Build' script for 'BioPerl-Run' version '1.006900'
> $ ./Build manifest
> File 'MANIFEST.SKIP' does not exist: Creating a temporary 'MANIFEST.SKIP'
> Added to MANIFEST: Build.PL
> Added to MANIFEST: Changes
> .....
> Added to MANIFEST: t/TCoffee.t
> Added to MANIFEST: t/TigrAssembler.t
> Added to MANIFEST: t/Tmhmm.t
> Added to MANIFEST: t/TribeMCL.t
> Added to MANIFEST: t/tRNAscanSE.t
> Added to MANIFEST: t/Vista.t
> $ ./Build install
> Building BioPerl-Run
> $
> -- 
> Regards,
> Peng

I added a default MANIFEST, just in case.  However, this shouldn't prevent installation, it just builds one for packaging up the distribution for CPAN.  This does install on my machine locally (see below).  If you reinstall (also demonstrated below) you won't see any install messages b/c no modules have changed from the build process.  

So, maybe it already installed successfully, and you haven't set the include path correctly so it isn't showing up?  Make sure you are setting PERL5LIB or your 'use lib' directive to point to the proper location; in the below, that would be '/Users/cjfields/local/lib/perl5'.


pyrimidine1:bioperl-run cjfields$ perl Build.PL --install-base ~/local/
Install scripts? y/n [n ]y
Do you want to run tests that require connection to servers across the internet
(likely to cause some failures)? y/n [n ]y
  - will run internet-requiring tests
Do you want to run tests requiring a valid email address? y/n [n ]y
Enter email address:  cjfields at bioperl.org
Creating new 'MYMETA.yml' with configuration results
Creating new 'Build' script for 'BioPerl-Run' version '1.006900'
pyrimidine1:bioperl-run cjfields$ ./Build
Building BioPerl-Run
pyrimidine1:bioperl-run cjfields$ ./Build install
Building BioPerl-Run
Installing /Users/cjfields/local/man/man1/bp_bioperl_application_installer.pl.1
Installing /Users/cjfields/local/man/man1/bp_multi_hmmsearch.pl.1
Installing /Users/cjfields/local/man/man1/bp_panalysis.pl.1
Installing /Users/cjfields/local/man/man1/bp_papplmaker.pl.1
Installing /Users/cjfields/local/man/man1/bp_run_neighbor.pl.1
Installing /Users/cjfields/local/man/man1/bp_run_protdist.pl.1
Installing /Users/cjfields/local/lib/perl5/Bio/DB/ESoap.pm
Installing /Users/cjfields/local/lib/perl5/Bio/DB/SoapEUtilities.pm
Installing /Users/cjfields/local/lib/perl5/Bio/DB/ESoap/WSDL.pm
....<snipped out lots of install stuff>
Installing /Users/cjfields/local/man/man3/Bio::Tools::Run::tRNAscanSE.3
Installing /Users/cjfields/local/man/man3/Bio::Tools::Run::Vista.3
Installing /Users/cjfields/local/bin/bp_bioperl_application_installer.pl
Installing /Users/cjfields/local/bin/bp_multi_hmmsearch.pl
Installing /Users/cjfields/local/bin/bp_panalysis.pl
Installing /Users/cjfields/local/bin/bp_papplmaker.pl
Installing /Users/cjfields/local/bin/bp_run_neighbor.pl
Installing /Users/cjfields/local/bin/bp_run_protdist.pl
pyrimidine1:bioperl-run cjfields$ ./Build install
Building BioPerl-Run
pyrimidine1:bioperl-run cjfields$ cd
pyrimidine1:~ cjfields$ perldoc -l Bio::Tools::Run::StandAloneBlastPlus

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