[Bioperl-l] bioperl invades emacs -- bug report?

[Mark A. Jensen]

Thanks for all this work, Pablo. Am working hard on 21
back-compat. Will attempt some mac-friendly paths
and look at the perl5lib issue-

"No matches" are seeming to stem from failure to
find the Bio tree-- there's a workaround for this on
the wiki page as of right now. This will probably
not help the 21 problems, but the next commit
(tomorrow) will likely solve these. I will post to this
thread when that happens.
cheers Mark
----- Original Message ----- 
From: "Pablo Marin-Garcia" <pg4 at sanger.ac.uk>
To: <bioperl-l at lists.open-bio.org>
Sent: Wednesday, September 02, 2009 7:35 PM
Subject: Re: [Bioperl-l] bioperl invades emacs -- bug report?


>
>
> Hello Mark,
>
> It sounds fantastic,
>
> unfortunatelly I was unable to use it:
>
> It does not found pod2text in my macosX and fail to find my bioperl paths in 
> linux (probably due to a bug in the perl5lib parsing but I am a lisp novice so 
> I could be wrong)
>
> ==  macosX ==
>
> in my macbook macosX 10.5 emacs 22.3 it does not find the pod2text
> GNU Emacs 22.3.1 (i386-apple-darwin9.6.0, X toolkit)
>
>   -I have installed your modules in my local-lisp and added the requiere and 
> now emacs fails with the error:
>
>   File error: Searching for program, invalid argument, pod2text
>
>   -- I have pod2text in /usr/bin and this is in my $PATH (I use fink emacs in 
> not-window mode) but the same happens with the carbon emacs
>
> ==  debian etch with an old emacs 21 ==
>
> GNU Emacs 21.4.1 (i486-pc-linux-gnu, X toolkit, Xaw3d scroll bars) of 
> 2007-06-19 on ninsei, modified by Debian
>
> It loads ok but when asking for the pods
>
> [pod] Namespace: Bio::
>
> it does not autocomplete from there, and if I have the cursor over a 'use 
> Bio::xxx', and select [BP Docs] 'view methods' or 'view pod' it says 'no 
> match'
>
> # [pod mth] Namespace: Bio::PrimarySeq [No match]
>
> Reading bioperl-mode.el and bioperl-init.el I have seen that the variable that 
> stores the path to bioperl has not other paths added a part of current path:
>
> # c-h v bioperl-module-path [ret] => bioperl-module-path's value is "."
>
>
> == bug when parsing perl5lib? ==
>
> Please correct me if I am wrong but in bioperl-init.el when extracting the 
> Bioperl paths from PERL5LIB this is not working for me in linux.
>
> While debugging bioperl-init.el:
> # (setq pth (getenv "PERL5LIB"))
> # 
> "/nfs/home/pmg/ensembl-api/ensembl-compara/modules:...:/nfs/home/pmg/bioperl-live:..."
> # (setq pth (if (file-exists-p (concat pth "/" "Bio")) pth nil))
> # nil
>
> No file is found because it is looking for all the paths concatenated together 
> with a '/Bio' at the end:
>
>   libpaht1:libpath2:libpath3/Bio
>
> 'concat' adds /Bio to the pth that is a string with all the PERL5LIB paths. 
> Should this concat rather be applied to the splited perl5lib by ':' in unix or 
> ';' in windows and then tested for the existence of files?
>
> for example in unix:
>
> --- code --
> (defun addbio (bio_path)
>   "apend /Bio to each path"
>   (concat bio_path "/" "Bio"))
>
> (mapcar 'file-exists-p (mapcar 'addbio (split-string pth ":")))
> -- end code ---
>
> This would result in the list of T and F bioperl (and ensembl) paths
> (t t nil t t t t t t nil nil nil ...)
>
>
> Regards and thanks for the modules they would be very useful.
>
>    -Pablo
>
> =====================================================================
>                      Pablo Marin-Garcia, PhD
>
>                     \\//          (Argiope bruennichi
>                \/\/`(||>O:'\/\/   with stabilimentum)
>                     //\\
>
> Sanger Institute                |  PostDoc / Computer Biologist
> Wellcome Trust Genome Campus    |  team : 128/108 (Human Genetics)
> Hinxton, Cambridge CB10 1HH     |  room : N333
> United Kingdom                  |  email: pablo.marin at sanger.ac.uk
> ====================================================================
>
>
>
>
>
>
>
>
>
>
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a 
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