Bioperl Installation

[stephenmcgowan1]

Hi,

I seem to be having trouble with Installing Bioperl 1.6 in CPAN.

I have attached a log of the install, i just can't see why it seems to be falling over.

Thanks,

Stephen

BioPerl+Install.rtf
BioPerl+Install.doc

[Robert Buels]

Hi Stephen,

It looks to me like your CPAN installation has gotten a bit confused,
possibly from it getting stopped in the middle of doing something.  Try
doing rm -rf ~/.cpan/build/* and trying the installation again.

Also, it's usually best to just cut and paste logs like this into the
body of an email, but try to paste only the most relevant parts.

Rob


--
Robert Buels
Bioinformatics Analyst, Sol Genomics Network
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca, NY  14853
Tel: [phone]
rmb32@...
http://www.sgn.cornell.edu


stephenmcgowan1 wrote:

> Hi,
>
> I seem to be having trouble with Installing Bioperl 1.6 in CPAN.
>
> I have attached a log of the install, i just can't see why it seems to be
> falling over.
>
> Thanks,
>
> Stephen
>
> http://www.nabble.com/file/p24360594/BioPerl%2BInstall.rtf
> BioPerl+Install.rtf
> http://www.nabble.com/file/p24360594/BioPerl%2BInstall.doc
> BioPerl+Install.doc

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[Kevin Brown-8]

Well, without the error messages that should have been printed out not
sure how much help we can be. No idea what OS you're running, perl
version, etc...

> -----Original Message-----
> From: bioperl-l-bounces@...
> [mailto:bioperl-l-bounces@...] On Behalf Of
> stephenmcgowan1
> Sent: Monday, July 06, 2009 11:31 AM
> To: Bioperl-l@...
> Subject: [Bioperl-l] Bioperl Installation
>
>
> Hi,
>
> I seem to be having trouble with Installing Bioperl 1.6 in CPAN.
>
> I have attached a log of the install, i just can't see why it
> seems to be
> falling over.
>
> Thanks,
>
> Stephen
>
> http://www.nabble.com/file/p24360594/BioPerl%2BInstall.rtf
> BioPerl+Install.rtf
> http://www.nabble.com/file/p24360594/BioPerl%2BInstall.doc
> BioPerl+Install.doc
> --
> View this message in context:
> http://www.nabble.com/Bioperl-Installation-tp24360594p24360594.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

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[Dave Messina-3]

Hi Stephen,
This is on a Mac, correct?

You need to install the developer tools first. The key line in your log is:

  Can't test without successful make


Admittedly, that's cryptic. What it means is that it needs the program
called make. That program is installed when you install the developer tools.


Go to developer.apple.com and create an account if you don't already have
one.


Go to the Mac Dev Center, and click on "Xcode 3".


This should be the right link:

Xcode 3<https://connect.apple.com/cgi-bin/WebObjects/MemberSite.woa/wa/getSoftware?bundleID=20414>

You'll need to login to get to it, and then you'll get to the download page
for the massive 986 MB Xcode 3.1.3 download.

After you run the Xcode installer, you can check in Terminal that you've got
'make' installed by typing:

which make

on the command line. It should give you the answer
make is /usr/bin/make

If it does, then you're good to try again with the bioperl install.

Dave
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[Scott Cain-3]

After you get make installed, you may need to reconfigure cpan so it  
knows where to find it.  Do this:

   sudo cpan

(Assuming you want the libraries installed in the system paths)

   cpan> o conf init

You can probably answer yes to the "do you want me to automatically  
configure" question, and it should sense that make is now present.  If  
not, do it again and answer "no" and accept all of the defaults until  
it gets to the part about where make is.

Scott

On Jul 6, 2009, at 3:38 PM, Dave Messina wrote:

> Hi Stephen,
> This is on a Mac, correct?
>
> You need to install the developer tools first. The key line in your  
> log is:
>
>  Can't test without successful make
>
>
> Admittedly, that's cryptic. What it means is that it needs the program
> called make. That program is installed when you install the  
> developer tools.
>
>
> Go to developer.apple.com and create an account if you don't already  
> have
> one.
>
>
> Go to the Mac Dev Center, and click on "Xcode 3".
>
>
> This should be the right link:
>
> Xcode 3<https://connect.apple.com/cgi-bin/WebObjects/MemberSite.woa/wa/getSoftware?bundleID=20414 
> >
>
> You'll need to login to get to it, and then you'll get to the  
> download page
> for the massive 986 MB Xcode 3.1.3 download.
>
> After you run the Xcode installer, you can check in Terminal that  
> you've got
> 'make' installed by typing:
>
> which make
>
> on the command line. It should give you the answer
> make is /usr/bin/make
>
> If it does, then you're good to try again with the bioperl install.
>
> Dave
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-----------------------------------------------------------------------
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GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research




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[Scott Cain-4]

Always, always, always reply to the list, as the original author of  
the email that you are replying to doesn't always know the answer,  
like now.  I don't recall how I installed libxslt.  In fact, I don't  
remember doing it.  Have you searched your hard drive?  I think it  
gets installed with the developers tools.

Scott

On Jul 6, 2009, at 4:01 PM, Steven McGowan wrote:

> Hi Scott,
>
> I removed my previous install with rm -rf ~/.cpan/build/*
>
> I've tried re-installing (install C/CJ/CJFIELDS/BioPerl-
> db-1.6.0.tar.gz), and upon installing have noticed the error:
>
> Checking prerequisites...
>  - ERROR: Data::Stag is not installed
>
> so i have then quit out of the install, and entered "install  
> Data::Stag" in>CPAN
>
> but receive the following error messages:
>
> External Module XML::LibXSLT, XSLT,
>  is not installed on this computer.
>   Data::Stag::XSLTHandler in Data::Stag needs it for XSLT  
> Transformations
>
> External Module XML::Parser::PerlSAX, SAX Handler,
>  is not installed on this computer.
>   Data::Stag::XMLParser in Data::Stag needs it for parsing XML
>
> External Module GD, Graphical Drawing Toolkit,
>  is not installed on this computer.
>   stag-drawtree.pl in Data::Stag needs it for drawing trees
>
> External Module Graph::Directed, Generic Graph data stucture and  
> algorithms,
>  is not installed on this computer.
>   Data::Stag::GraphHandler in Data::Stag needs it for transforming  
> stag trees to graphs
>
> External Module Tk, Tk,
>  is not installed on this computer.
>   stag-view.pl in Data::Stag needs it for tree viewer
>
> ok so for the C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz install, it's  
> lacking Data::Stag who's install is lacking the list above. How  
> would i go about installing the above list? is there an easier way  
> or something i'm doing wrong?
>
> Thanks,
>
> Stephen
>
> > From: cain.cshl@...
> > To: David.Messina@...
> > Subject: Re: [Bioperl-l] Bioperl Installation
> > Date: Mon, 6 Jul 2009 15:48:21 -0400
> > CC: stevey_mac2k2@...; Bioperl-l@...
> >
> > After you get make installed, you may need to reconfigure cpan so it
> > knows where to find it. Do this:
> >
> > sudo cpan
> >
> > (Assuming you want the libraries installed in the system paths)
> >
> > cpan> o conf init
> >
> > You can probably answer yes to the "do you want me to automatically
> > configure" question, and it should sense that make is now present.  
> If
> > not, do it again and answer "no" and accept all of the defaults  
> until
> > it gets to the part about where make is.
> >
> > Scott
> >
> > On Jul 6, 2009, at 3:38 PM, Dave Messina wrote:
> >
> >> Hi Stephen,
> >> This is on a Mac, correct?
> >>
> >> You need to install the developer tools first. The key line in your
> >> log is:
> >>
> >> Can't test without successful make
> >>
> >>
> >> Admittedly, that's cryptic. What it means is that it needs the  
> program
> >> called make. That program is installed when you install the
> >> developer tools.
> >>
> >>
> >> Go to developer.apple.com and create an account if you don't  
> already
> >> have
> >> one.
> >>
> >>
> >> Go to the Mac Dev Center, and click on "Xcode 3".
> >>
> >>
> >> This should be the right link:
> >>
> >> Xcode 3<https://connect.apple.com/cgi-bin/WebObjects/MemberSite.woa/wa/getSoftware?bundleID=20414
> >>>
> >>
> >> You'll need to login to get to it, and then you'll get to the
> >> download page
> >> for the massive 986 MB Xcode 3.1.3 download.
> >>
> >> After you run the Xcode installer, you can check in Terminal that
> >> you've got
> >> 'make' installed by typing:
> >>
> >> which make
> >>
> >> on the command line. It should give you the answer
> >> make is /usr/bin/make
> >>
> >> If it does, then you're good to try again with the bioperl install.
> >>
> >> Dave
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l@...
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >  
> -----------------------------------------------------------------------
> > Scott Cain, Ph. D. scott at scottcain dot net
> > GMOD Coordinator (http://gmod.org/) 216-392-3087
> > Ontario Institute for Cancer Research
> >
> >
> >
> >
>
> View your Twitter and Flickr updates from one place – Learn more!

-----------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research





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[stephenmcgowan1]

I managed to sort it and have had a go at installing: (install C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz), but upon installing have noticed the error:
Checking prerequisites... - ERROR: Data::Stag is not installed
so i have then quit out of the install, and entered "install Data::Stag" in>CPAN
but receive the following error messages:
External Module XML::LibXSLT, XSLT, is not installed on this computer.  Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations
External Module XML::Parser::PerlSAX, SAX Handler, is not installed on this computer.  Data::Stag::XMLParser in Data::Stag needs it for parsing XML
External Module GD, Graphical Drawing Toolkit, is not installed on this computer.  stag-drawtree.pl in Data::Stag needs it for drawing trees
External Module Graph::Directed, Generic Graph data stucture and algorithms, is not installed on this computer.  Data::Stag::GraphHandler in Data::Stag needs it for transforming stag trees to graphs
External Module Tk, Tk, is not installed on this computer.  stag-view.pl in Data::Stag needs it for tree viewer
ok so for the C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz install, it's lacking Data::Stag who's install is lacking the list above. How would i go about installing the above list? is there an easier way or something i'm doing wrong?
Thanks,
Stephen
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[Dave Messina-3]

Hi Steven,
Forwarding this to the list so that everyone can follow along...please keep
the list on any replies.

Don't quit out of the install -- cpan can automatically detect required
dependencies and will try to install them first.

Amidst all of the kerfuffle in your previous install there was this bit:

---- Unsatisfied dependencies detected during
[C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz] -----

    Test::Harness

    Data::Stag

    CPAN

Shall I follow them and prepend them to the queue

of modules we are processing right now? [yes]


So if you go back into cpan, try the Bioperl-1.6 install again, you should
be prompted again about those missing dependencies.



A note to the Bioperl core-devs:

Data::Stag seems to have a couple of tricky dependencies of its own, namely
GD and Tk, and it looks like they're for a couple of included scripts which
I'm guessing Bioperl doesn't use.

Perhaps we should send a request to the Data::Stag author to make GD and Tk
optional instead of required?


Dave




---------- Forwarded message ----------
From: Steven McGowan <stevey_mac2k2@...>
Date: Mon, Jul 6, 2009 at 22:02
Subject: RE: [Bioperl-l] Bioperl Installation
To: david.messina@...


 Hi Dave,

I managed to sort it and have had a go at
installing: (install C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz), but upon
installing have noticed the error:

Checking prerequisites...
 - ERROR: Data::Stag is not installed

so i have then quit out of the install, and entered "install Data::Stag"
in>CPAN

but receive the following error messages:

External Module XML::LibXSLT, XSLT,
 is not installed on this computer.
  Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations

External Module XML::Parser::PerlSAX, SAX Handler,
 is not installed on this computer.
  Data::Stag::XMLParser in Data::Stag needs it for parsing XML

External Module GD, Graphical Drawing Toolkit,
 is not installed on this computer.
  stag-drawtree.pl in Data::Stag needs it for drawing trees

External Module Graph::Directed, Generic Graph data stucture and algorithms,
 is not installed on this computer.
  Data::Stag::GraphHandler in Data::Stag needs it for transforming stag
trees to graphs

External Module Tk, Tk,
 is not installed on this computer.
  stag-view.pl in Data::Stag needs it for tree viewer

ok so for the C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz install, it's lacking
Data::Stag who's install is lacking the list above. How would i go about
installing the above list? is there an easier way or something i'm doing
wrong?

Thanks,

Stephen

------------------------------
From: David.Messina@...
Date: Mon, 6 Jul 2009 21:38:09 +0200
Subject: Re: [Bioperl-l] Bioperl Installation
To: stevey_mac2k2@...
CC: Bioperl-l@...


Hi Stephen,
This is on a Mac, correct?

You need to install the developer tools first. The key line in your log is:

  Can't test without successful make


Admittedly, that's cryptic. What it means is that it needs the program
called make. That program is installed when you install the developer tools.


Go to developer.apple.com and create an account if you don't already have
one.


Go to the Mac Dev Center, and click on "Xcode 3".


This should be the right link:

Xcode 3

You'll need to login to get to it, and then you'll get to the download page
for the massive 986 MB Xcode 3.1.3 download.

After you run the Xcode installer, you can check in Terminal that you've got
'make' installed by typing:

which make

on the command line. It should give you the answer
make is /usr/bin/make

If it does, then you're good to try again with the bioperl install.

Dave


------------------------------
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[stephenmcgowan1]

I have since initialised the install and receive the message:

Checking prerequisites...
 - ERROR: Data::Stag is not installed
(I think I'm being run by CPAN, so will rely on CPAN to handle prerequisite installation)
   I'll get CPAN to prepend the installation of this
 - ERROR: Test::Harness (2.56) is installed, but we need version>= 2.62
   I'll get CPAN to prepend the installation of this
 - ERROR: CPAN (1.7602) is installed, but we need version>= 1.81
   I'll get CPAN to prepend the installation of this
Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n]
do i now want to Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n]
i'm guessing installing all external modules will include Data::Stag?
StephenFrom: David.Messina@...
Date: Mon, 6 Jul 2009 22:26:55 +0200
Subject: Fwd: [Bioperl-l] Bioperl Installation
To: bioperl-l@...
CC: stevey_mac2k2@...

Hi Steven,
Forwarding this to the list so that everyone can follow along...please keep the list on any replies.
Don't quit out of the install -- cpan can automatically detect required dependencies and will try to install them first.


Amidst all of the kerfuffle in your previous install there was this bit:
---- Unsatisfied dependencies detected during [C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz] -----


    Test::Harness
    Data::Stag
    CPAN
Shall I follow them and prepend them to the queue
of modules we are processing right now? [yes]



So if you go back into cpan, try the Bioperl-1.6 install again, you should be prompted again about those missing dependencies.




A note to the Bioperl core-devs:
Data::Stag seems to have a couple of tricky dependencies of its own, namely GD and Tk, and it looks like they're for a couple of included scripts which I'm guessing Bioperl doesn't use.


Perhaps we should send a request to the Data::Stag author to make GD and Tk optional instead of required?

Dave





---------- Forwarded message ----------
From: Steven McGowan <stevey_mac2k2@...>


Date: Mon, Jul 6, 2009 at 22:02
Subject: RE: [Bioperl-l] Bioperl Installation
To: david.messina@...







Hi Dave,
I managed to sort it and have had a go at installing: (install C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz), but upon installing have noticed the error:


Checking prerequisites... - ERROR: Data::Stag is not installed
so i have then quit out of the install, and entered "install Data::Stag" in>CPAN


but receive the following error messages:
External Module XML::LibXSLT, XSLT, is not installed on this computer.

  Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations
External Module XML::Parser::PerlSAX, SAX Handler,

 is not installed on this computer.  Data::Stag::XMLParser in Data::Stag needs it for parsing XML


External Module GD, Graphical Drawing Toolkit, is not installed on this computer.  stag-drawtree.pl in Data::Stag needs it for drawing trees


External Module Graph::Directed, Generic Graph data stucture and algorithms, is not installed on this computer.

  Data::Stag::GraphHandler in Data::Stag needs it for transforming stag trees to graphs
External Module Tk, Tk,

 is not installed on this computer.  stag-view.pl in Data::Stag needs it for tree viewer
ok so for the C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz install, it's lacking Data::Stag who's install is lacking the list above. How would i go about installing the above list? is there an easier way or something i'm doing wrong?


Thanks,
Stephen
From: David.Messina@...
Date: Mon, 6 Jul 2009 21:38:09 +0200


Subject: Re: [Bioperl-l] Bioperl Installation
To: stevey_mac2k2@...
CC: Bioperl-l@...



Hi Stephen,
This is on a Mac, correct?
You need to install the developer tools first. The key line in your log is:




  Can't test without successful make
Admittedly, that's cryptic. What it means is that it needs the program called make. That program is installed when you install the developer tools.




Go to developer.apple.com and create an account if you don't already have one.


Go to the Mac Dev Center, and click on "Xcode 3".


This should be the right link:Xcode 3


You'll need to login to get to it, and then you'll get to the download page for the massive 986 MB Xcode 3.1.3 download.


After you run the Xcode installer, you can check in Terminal that you've got 'make' installed by typing:
which make


on the command line. It should give you the answermake is /usr/bin/make
If it does, then you're good to try again with the bioperl install.


Dave

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[Dave Messina-3]

> do i now want to Install [a]ll optional external modules, [n]one, or choose
> [i]nteractively? [n]
>
>
Data::Stag, Test::Harness, and CPAN are required, not optional. So I think
they'll be installed even if you answer n to the question about the
optional external modules.


Dave
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[Scott Cain-4]

Hi Dave,

I think you are confused about the prereqs for Data::Stag: I have it
installed and working and don't have Tk.  cpantesters.org also thinks
that IO::String is the only dependency:

  http://deps.cpantesters.org/?module=Data::Stag;perl=latest

Scott


On Mon, Jul 6, 2009 at 4:26 PM, Dave Messina<David.Messina@...> wrote:

> Hi Steven,
> Forwarding this to the list so that everyone can follow along...please keep
> the list on any replies.
>
> Don't quit out of the install -- cpan can automatically detect required
> dependencies and will try to install them first.
>
> Amidst all of the kerfuffle in your previous install there was this bit:
>
> ---- Unsatisfied dependencies detected during
> [C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz] -----
>
>    Test::Harness
>
>    Data::Stag
>
>    CPAN
>
> Shall I follow them and prepend them to the queue
>
> of modules we are processing right now? [yes]
>
>
> So if you go back into cpan, try the Bioperl-1.6 install again, you should
> be prompted again about those missing dependencies.
>
>
>
> A note to the Bioperl core-devs:
>
> Data::Stag seems to have a couple of tricky dependencies of its own, namely
> GD and Tk, and it looks like they're for a couple of included scripts which
> I'm guessing Bioperl doesn't use.
>
> Perhaps we should send a request to the Data::Stag author to make GD and Tk
> optional instead of required?
>
>
> Dave
>
>
>
>
> ---------- Forwarded message ----------
> From: Steven McGowan <stevey_mac2k2@...>
> Date: Mon, Jul 6, 2009 at 22:02
> Subject: RE: [Bioperl-l] Bioperl Installation
> To: david.messina@...
>
>
>  Hi Dave,
>
> I managed to sort it and have had a go at
> installing: (install C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz), but upon
> installing have noticed the error:
>
> Checking prerequisites...
>  - ERROR: Data::Stag is not installed
>
> so i have then quit out of the install, and entered "install Data::Stag"
> in>CPAN
>
> but receive the following error messages:
>
> External Module XML::LibXSLT, XSLT,
>  is not installed on this computer.
>  Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations
>
> External Module XML::Parser::PerlSAX, SAX Handler,
>  is not installed on this computer.
>  Data::Stag::XMLParser in Data::Stag needs it for parsing XML
>
> External Module GD, Graphical Drawing Toolkit,
>  is not installed on this computer.
>  stag-drawtree.pl in Data::Stag needs it for drawing trees
>
> External Module Graph::Directed, Generic Graph data stucture and algorithms,
>  is not installed on this computer.
>  Data::Stag::GraphHandler in Data::Stag needs it for transforming stag
> trees to graphs
>
> External Module Tk, Tk,
>  is not installed on this computer.
>  stag-view.pl in Data::Stag needs it for tree viewer
>
> ok so for the C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz install, it's lacking
> Data::Stag who's install is lacking the list above. How would i go about
> installing the above list? is there an easier way or something i'm doing
> wrong?
>
> Thanks,
>
> Stephen
>
> ------------------------------
> From: David.Messina@...
> Date: Mon, 6 Jul 2009 21:38:09 +0200
> Subject: Re: [Bioperl-l] Bioperl Installation
> To: stevey_mac2k2@...
> CC: Bioperl-l@...
>
>
> Hi Stephen,
> This is on a Mac, correct?
>
> You need to install the developer tools first. The key line in your log is:
>
>  Can't test without successful make
>
>
> Admittedly, that's cryptic. What it means is that it needs the program
> called make. That program is installed when you install the developer tools.
>
>
> Go to developer.apple.com and create an account if you don't already have
> one.
>
>
> Go to the Mac Dev Center, and click on "Xcode 3".
>
>
> This should be the right link:
>
> Xcode 3
>
> You'll need to login to get to it, and then you'll get to the download page
> for the massive 986 MB Xcode 3.1.3 download.
>
> After you run the Xcode installer, you can check in Terminal that you've got
> 'make' installed by typing:
>
> which make
>
> on the command line. It should give you the answer
> make is /usr/bin/make
>
> If it does, then you're good to try again with the bioperl install.
>
> Dave
>
>
> ------------------------------
> View your Twitter and Flickr updates from one place – Learn
> more!<http://clk.atdmt.com/UKM/go/137984870/direct/01/>
>
> _______________________________________________
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> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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[stephenmcgowan1]

ok i've hit [n]
the next bypasses a list of optional prerequisites...apart from:
 * XML::SAX (0.14) is installed, but we prefer to have 0.15   (wanted for parsing xml, used by Bio::SearchIO::blastxml, Bio::SeqIO::tigrxml and Bio::SeqIO::bsml_sax)
this does not seem to be an optional prerequisite but seems to be bypassed?
and then i receive:
ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the versionsof the modules indicated above before proceeding with this installation
Checking features:  Network..................enabled  BioDBSeqFeature_mysql....enabled  BioDBGFF.................enabled  BioDBSeqFeature_BDB......enabled
Do you want to run the Bio::DB::GFF or Bio::DB::SeqFeature::Store live database tests? y/n [n] n  - will not run the BioDBGFF or BioDBSeqFeature live database tests
Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a]  
From: David.Messina@...
Date: Mon, 6 Jul 2009 22:47:06 +0200
Subject: Re: [Bioperl-l] Bioperl Installation
To: stevey_mac2k2@...
CC: bioperl-l@...




do i now want to Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n]
Data::Stag, Test::Harness, and CPAN are required, not optional. So I think they'll be installed even if you answer n to the question about the optional external modules.



Dave

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[Chris Fields-5]

(cc'ing Chris M about this)

The Tk and GD dependencies should probably be optional if they are  
only required for the Data::Stag scripts.  As for the libxslt, I'm not  
sure but I believe that's available with the dev kit; if not it's  
available via fink/macports.

The inclusion of those as a requirement is a bit troubling for me, but  
this is the first time I've seen issues with it pop up.

chris

On Jul 6, 2009, at 3:26 PM, Dave Messina wrote:

> Hi Steven,
> Forwarding this to the list so that everyone can follow  
> along...please keep
> the list on any replies.
>
> Don't quit out of the install -- cpan can automatically detect  
> required
> dependencies and will try to install them first.
>
> Amidst all of the kerfuffle in your previous install there was this  
> bit:
>
> ---- Unsatisfied dependencies detected during
> [C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz] -----
>
>    Test::Harness
>
>    Data::Stag
>
>    CPAN
>
> Shall I follow them and prepend them to the queue
>
> of modules we are processing right now? [yes]
>
>
> So if you go back into cpan, try the Bioperl-1.6 install again, you  
> should
> be prompted again about those missing dependencies.
>
>
>
> A note to the Bioperl core-devs:
>
> Data::Stag seems to have a couple of tricky dependencies of its own,  
> namely
> GD and Tk, and it looks like they're for a couple of included  
> scripts which
> I'm guessing Bioperl doesn't use.
>
> Perhaps we should send a request to the Data::Stag author to make GD  
> and Tk
> optional instead of required?
>
>
> Dave
>
>
>
>
> ---------- Forwarded message ----------
> From: Steven McGowan <stevey_mac2k2@...>
> Date: Mon, Jul 6, 2009 at 22:02
> Subject: RE: [Bioperl-l] Bioperl Installation
> To: david.messina@...
>
>
> Hi Dave,
>
> I managed to sort it and have had a go at
> installing: (install C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz), but upon
> installing have noticed the error:
>
> Checking prerequisites...
> - ERROR: Data::Stag is not installed
>
> so i have then quit out of the install, and entered "install  
> Data::Stag"
> in>CPAN
>
> but receive the following error messages:
>
> External Module XML::LibXSLT, XSLT,
> is not installed on this computer.
>  Data::Stag::XSLTHandler in Data::Stag needs it for XSLT  
> Transformations
>
> External Module XML::Parser::PerlSAX, SAX Handler,
> is not installed on this computer.
>  Data::Stag::XMLParser in Data::Stag needs it for parsing XML
>
> External Module GD, Graphical Drawing Toolkit,
> is not installed on this computer.
>  stag-drawtree.pl in Data::Stag needs it for drawing trees
>
> External Module Graph::Directed, Generic Graph data stucture and  
> algorithms,
> is not installed on this computer.
>  Data::Stag::GraphHandler in Data::Stag needs it for transforming stag
> trees to graphs
>
> External Module Tk, Tk,
> is not installed on this computer.
>  stag-view.pl in Data::Stag needs it for tree viewer
>
> ok so for the C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz install, it's  
> lacking
> Data::Stag who's install is lacking the list above. How would i go  
> about
> installing the above list? is there an easier way or something i'm  
> doing
> wrong?
>
> Thanks,
>
> Stephen
>
> ------------------------------
> From: David.Messina@...
> Date: Mon, 6 Jul 2009 21:38:09 +0200
> Subject: Re: [Bioperl-l] Bioperl Installation
> To: stevey_mac2k2@...
> CC: Bioperl-l@...
>
>
> Hi Stephen,
> This is on a Mac, correct?
>
> You need to install the developer tools first. The key line in your  
> log is:
>
>  Can't test without successful make
>
>
> Admittedly, that's cryptic. What it means is that it needs the program
> called make. That program is installed when you install the  
> developer tools.
>
>
> Go to developer.apple.com and create an account if you don't already  
> have
> one.
>
>
> Go to the Mac Dev Center, and click on "Xcode 3".
>
>
> This should be the right link:
>
> Xcode 3
>
> You'll need to login to get to it, and then you'll get to the  
> download page
> for the massive 986 MB Xcode 3.1.3 download.
>
> After you run the Xcode installer, you can check in Terminal that  
> you've got
> 'make' installed by typing:
>
> which make
>
> on the command line. It should give you the answer
> make is /usr/bin/make
>
> If it does, then you're good to try again with the bioperl install.
>
> Dave
>
>
> ------------------------------
> View your Twitter and Flickr updates from one place – Learn
> more!<http://clk.atdmt.com/UKM/go/137984870/direct/01/>
>
> _______________________________________________
> Bioperl-l mailing list
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> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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[Chris Fields-5]

Okay, that makes more sense to me (and also makes sense looking at the  
Data::Stag makefile).  None of those additional modules are required  
for bioperl core functionality.

chris

On Jul 6, 2009, at 3:50 PM, Scott Cain wrote:

> Hi Dave,
>
> I think you are confused about the prereqs for Data::Stag: I have it
> installed and working and don't have Tk.  cpantesters.org also thinks
> that IO::String is the only dependency:
>
>  http://deps.cpantesters.org/?module=Data::Stag;perl=latest
>
> Scott
>
>
> On Mon, Jul 6, 2009 at 4:26 PM, Dave  
> Messina<David.Messina@...> wrote:
>> Hi Steven,
>> Forwarding this to the list so that everyone can follow  
>> along...please keep
>> the list on any replies.
>>
>> Don't quit out of the install -- cpan can automatically detect  
>> required
>> dependencies and will try to install them first.
>>
>> Amidst all of the kerfuffle in your previous install there was this  
>> bit:
>>
>> ---- Unsatisfied dependencies detected during
>> [C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz] -----
>>
>>    Test::Harness
>>
>>    Data::Stag
>>
>>    CPAN
>>
>> Shall I follow them and prepend them to the queue
>>
>> of modules we are processing right now? [yes]
>>
>>
>> So if you go back into cpan, try the Bioperl-1.6 install again, you  
>> should
>> be prompted again about those missing dependencies.
>>
>>
>>
>> A note to the Bioperl core-devs:
>>
>> Data::Stag seems to have a couple of tricky dependencies of its  
>> own, namely
>> GD and Tk, and it looks like they're for a couple of included  
>> scripts which
>> I'm guessing Bioperl doesn't use.
>>
>> Perhaps we should send a request to the Data::Stag author to make  
>> GD and Tk
>> optional instead of required?
>>
>>
>> Dave
>>
>>
>>
>>
>> ---------- Forwarded message ----------
>> From: Steven McGowan <stevey_mac2k2@...>
>> Date: Mon, Jul 6, 2009 at 22:02
>> Subject: RE: [Bioperl-l] Bioperl Installation
>> To: david.messina@...
>>
>>
>>  Hi Dave,
>>
>> I managed to sort it and have had a go at
>> installing: (install C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz), but upon
>> installing have noticed the error:
>>
>> Checking prerequisites...
>>  - ERROR: Data::Stag is not installed
>>
>> so i have then quit out of the install, and entered "install  
>> Data::Stag"
>> in>CPAN
>>
>> but receive the following error messages:
>>
>> External Module XML::LibXSLT, XSLT,
>>  is not installed on this computer.
>>  Data::Stag::XSLTHandler in Data::Stag needs it for XSLT  
>> Transformations
>>
>> External Module XML::Parser::PerlSAX, SAX Handler,
>>  is not installed on this computer.
>>  Data::Stag::XMLParser in Data::Stag needs it for parsing XML
>>
>> External Module GD, Graphical Drawing Toolkit,
>>  is not installed on this computer.
>>  stag-drawtree.pl in Data::Stag needs it for drawing trees
>>
>> External Module Graph::Directed, Generic Graph data stucture and  
>> algorithms,
>>  is not installed on this computer.
>>  Data::Stag::GraphHandler in Data::Stag needs it for transforming  
>> stag
>> trees to graphs
>>
>> External Module Tk, Tk,
>>  is not installed on this computer.
>>  stag-view.pl in Data::Stag needs it for tree viewer
>>
>> ok so for the C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz install, it's  
>> lacking
>> Data::Stag who's install is lacking the list above. How would i go  
>> about
>> installing the above list? is there an easier way or something i'm  
>> doing
>> wrong?
>>
>> Thanks,
>>
>> Stephen
>>
>> ------------------------------
>> From: David.Messina@...
>> Date: Mon, 6 Jul 2009 21:38:09 +0200
>> Subject: Re: [Bioperl-l] Bioperl Installation
>> To: stevey_mac2k2@...
>> CC: Bioperl-l@...
>>
>>
>> Hi Stephen,
>> This is on a Mac, correct?
>>
>> You need to install the developer tools first. The key line in your  
>> log is:
>>
>>  Can't test without successful make
>>
>>
>> Admittedly, that's cryptic. What it means is that it needs the  
>> program
>> called make. That program is installed when you install the  
>> developer tools.
>>
>>
>> Go to developer.apple.com and create an account if you don't  
>> already have
>> one.
>>
>>
>> Go to the Mac Dev Center, and click on "Xcode 3".
>>
>>
>> This should be the right link:
>>
>> Xcode 3
>>
>> You'll need to login to get to it, and then you'll get to the  
>> download page
>> for the massive 986 MB Xcode 3.1.3 download.
>>
>> After you run the Xcode installer, you can check in Terminal that  
>> you've got
>> 'make' installed by typing:
>>
>> which make
>>
>> on the command line. It should give you the answer
>> make is /usr/bin/make
>>
>> If it does, then you're good to try again with the bioperl install.
>>
>> Dave
>>
>>
>> ------------------------------
>> View your Twitter and Flickr updates from one place – Learn
>> more!<http://clk.atdmt.com/UKM/go/137984870/direct/01/>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l@...
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at  
> scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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[Dave Messina-3]

>
>  * XML::SAX (0.14) is installed, but we prefer to have 0.15
>    (wanted for parsing xml, used by Bio::SearchIO::blastxml,
> Bio::SeqIO::tigrxml and Bio::SeqIO::bsml_sax)
>

> [snip]
>
> ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the
> versions
> of the modules indicated above before proceeding with this installation
>

This "error/warning" refers to XML::SAX. I'm pretty sure that's optional.
Not exactly sure why it's getting called out specifically here, but I think
you can safely ignore it.



Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a]
>
>

You went ahead and answered this question, right? The installation should
have started at this point.


D
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[stephenmcgowan1]

I'm just hanging on the question at the moment.. not sure whether to install all [a] or [n]one. I'm probably going to go with [a]ll

From: David.Messina@...
Date: Mon, 6 Jul 2009 23:09:05 +0200
Subject: Re: [Bioperl-l] Bioperl Installation
To: stevey_mac2k2@...
CC: bioperl-l@...

 * XML::SAX (0.14) is installed, but we prefer to have 0.15   (wanted for parsing xml, used by Bio::SearchIO::blastxml, Bio::SeqIO::tigrxml and Bio::SeqIO::bsml_sax)


[snip]


ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the versionsof the modules indicated above before proceeding with this installation


This "error/warning" refers to XML::SAX. I'm pretty sure that's optional. Not exactly sure why it's getting called out specifically here, but I think you can safely ignore it.




Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a]  


You went ahead and answered this question, right? The installation should have started at this point.

D

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[Dave Messina-3]

>
> I'm just hanging on the question at the moment.. not sure whether to
> install all [a] or [n]one. I'm probably going to go with [a]ll
>

Yes, you'll probably want all the scripts.
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[stephenmcgowan1]

ok...
after choosing to install all scripts, i receive:
Creating new 'Build' script for 'BioPerl' version '1.006000'Warning: PREREQ_PM mentions Test::Harness more than once, last mention wins at /System/Library/Perl/5.8.8/CPAN.pm line 4689, <GEN5> line 1.Warning: PREREQ_PM mentions CPAN more than once, last mention wins at /System/Library/Perl/5.8.8/CPAN.pm line 4689, <GEN5> line 1.---- Unsatisfied dependencies detected during [C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz] -----    Test::Harness    Data::Stag    CPAN
Shall I follow them and prepend them to the queueof modules we are processing right now? [yes] y

-------------TEST HARNESS-------------
Running install for module Test::Harness

CPAN.pm: Going to build A/AN/ANDYA/Test-Harness-3.17.tar.gz
Checking if your kit is complete...Looks goodWriting Makefile for Test::Harness    -- NOT OKRunning make test  Can't test without successful makeRunning make install  make had returned bad status, install seems impossible
---------DATA::STAG----------
Running install for module Data::StagRunning make for C/CM/CMUNGALL/Data-Stag-0.11.tar.gz
CPAN.pm: Going to build C/CM/CMUNGALL/Data-Stag-0.11.tar.gz

External Module XML::LibXSLT, XSLT, is not installed on this computer.  Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations
External Module XML::Parser::PerlSAX, SAX Handler, is not installed on this computer.  Data::Stag::XMLParser in Data::Stag needs it for parsing XML
External Module GD, Graphical Drawing Toolkit, is not installed on this computer.  stag-drawtree.pl in Data::Stag needs it for drawing trees
External Module Graph::Directed, Generic Graph data stucture and algorithms, is not installed on this computer.  Data::Stag::GraphHandler in Data::Stag needs it for transforming stag trees to graphs
External Module Tk, Tk, is not installed on this computer.  stag-view.pl in Data::Stag needs it for tree viewer
There are some external packages and perl modules, listed above, which    stag uses. This only effects the functionality which is listed above:   the rest of stag will work fine, which includes nearly all of the   core functionality.
   Enjoy the rest of stag, which you can use after going 'make install'
Checking if your kit is complete...Looks goodWriting Makefile for Data    -- NOT OKRunning make test  Can't test without successful makeRunning make install  make had returned bad status, install seems impossible
-------------CPAN--------------
CPAN.pm: Going to build A/AN/ANDK/CPAN-1.9402.tar.gz
Checking if your kit is complete...Looks goodWarning: prerequisite File::HomeDir 0.69 not found.Warning: prerequisite Test::Harness 2.62 not found. We have 2.56.Writing Makefile for CPAN---- Unsatisfied dependencies detected during [A/AN/ANDK/CPAN-1.9402.tar.gz] -----    Test::Harness    File::HomeDirShall I follow them and prepend them to the queueof modules we are processing right now? [yes] yRunning make test  Delayed until after prerequisitesRunning make install  Delayed until after prerequisitesRunning install for module Test::HarnessRunning make for A/AN/ANDYA/Test-Harness-3.17.tar.gz  Is already unwrapped into directory /Users/stevey_mac2k2/.cpan/build/Test-Harness-3.17  Has already been processed within this sessionRunning make test  Can't test without successful makeRunning make install  make had returned bad status, install seems impossible

-------Further On------->
CPAN.pm: Going to build A/AD/ADAMK/File-HomeDir-0.86.tar.gz
Checking if your kit is complete...Looks goodWriting Makefile for File::HomeDir    -- NOT OKRunning make test  Can't test without successful makeRunning make install  make had returned bad status, install seems impossibleRunning make for A/AN/ANDK/CPAN-1.9402.tar.gz  Is already unwrapped into directory /Users/stevey_mac2k2/.cpan/build/CPAN-1.9402
  CPAN.pm: Going to build A/AN/ANDK/CPAN-1.9402.tar.gz
    -- NOT OKRunning make test  Can't test without successful makeRunning make install  make had returned bad status, install seems impossibleRunning make for C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz  Is already unwrapped into directory /Users/stevey_mac2k2/.cpan/build/BioPerl-1.6.0
  CPAN.pm: Going to build C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz
    -- NOT OKRunning make test  Can't test without successful makeRunning make install  make had returned bad status, install seems impossible


From: David.Messina@...
Date: Mon, 6 Jul 2009 23:16:00 +0200
Subject: Re: [Bioperl-l] Bioperl Installation
To: stevey_mac2k2@...
CC: bioperl-l@...

I'm just hanging on the question at the moment.. not sure whether to install all [a] or [n]one. I'm probably going to go with [a]ll


Yes, you'll probably want all the scripts.
 
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[Dave Messina-3]

Did you confirm that make is available to cpan before you started, by
following Scott's earlier instructions?
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[Koen van der Drift-3]

Hi,

Installation problems on a Mac seems to be a recurring question on  
this mailing list. Just as a reminder, besides CPAN, one of the  
easiest ways to install bioperl on a Mac is through fink. The  
instructions are available on the bioperl website here: http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink 
, but are rather hidden.

Maybe http://www.bioperl.org/wiki/Installing_BioPerl can be edited to  
state Installing Bioperl for Unix (including Mac OS X)? I don't seem  
to have privileges to edit that page, so I'll leave that up to the team.

Also, the file PACKAGES contains a link about installation on Mac OS X  
that is *very* outdated. Can this be removed from the package, I think  
it only creates confusion?

Cheers,

- Koen.
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