Bug 173499

Summary:	Review Request: lagan: Local, global, and multiple alignment of DNA sequences
Product:	[Fedora] Fedora	Reporter:	Christian Iseli <Christian.Iseli>
Component:	Package Review	Assignee:	John Mahowald <jpmahowald>
Status:	CLOSED NEXTRELEASE	QA Contact:	David Lawrence <dkl>
Severity:	medium	Docs Contact:
Priority:	medium
Version:	rawhide	CC:	fedora-extras-list
Target Milestone:	---
Target Release:	---
Hardware:	All
OS:	Linux
URL:	http://lagan.stanford.edu
Whiteboard:
Fixed In Version:		Doc Type:	Bug Fix
Doc Text:		Story Points:	---
Clone Of:		Environment:
Last Closed:	2006-01-30 00:42:07 UTC	Type:	---
Regression:	---	Mount Type:	---
Documentation:	---	CRM:
Verified Versions:		Category:	---
oVirt Team:	---	RHEL 7.3 requirements from Atomic Host:
Cloudforms Team:	---	Target Upstream Version:
Embargoed:
Bug Depends On:
Bug Blocks:	163779

Description Christian Iseli 2005-11-17 17:17:45 UTC

Another bioinformatics package.  GPL licensed.  Builds in mock.
$ rpmlint /var/lib/mock/fedora-4-i386-core/result/lagan-1.21-0.i386.rpm
W: lagan non-standard-dir-in-usr libexec

Not sure what this warning is about...

Please review.  Thanks :-)

Spec Name or Url: ftp://ftp.licr.org/pub/software/unix/lagan.spec
SRPM Name or Url: ftp://ftp.licr.org/pub/software/unix/lagan-1.21-0.src.rpm
Description:
LAGAN toolkit is a set of tools for local, global, and multiple alignment of
DNA sequences.  Please visit http://lagan.stanford.edu for publications
describing LAGAN and its components.

The 4 main parts of LAGAN are:

1. CHAOS local alignment tool
2. LAGAN pairwise global alignment tool
3. MLAGAN multiple global alignment tool.
4. Shuffle-LAGAN pairwise glocal alignment

Comment 1 Ville Skyttä 2005-11-17 17:56:56 UTC

(In reply to comment #0)   
> $ rpmlint /var/lib/mock/fedora-4-i386-core/result/lagan-1.21-0.i386.rpm   
> W: lagan non-standard-dir-in-usr libexec   
>    
> Not sure what this warning is about...   
   
/usr/libexec is not standard as in "not FHS compliant".  This package would be  
far from alone in using it in FC/FE though, so not that much of a deal.    
Using %{_libdir}/lagan instead of it would be one possible fix if you  
like.

Comment 2 Christian Iseli 2005-11-17 21:53:11 UTC

(In reply to comment #1)

> /usr/libexec is not standard as in "not FHS compliant".

Ah, ok.

> This package would be  
> far from alone in using it in FC/FE though, so not that much of a deal.

Ok.

> Using %{_libdir}/lagan instead of it would be one possible fix if you  
> like.  

Yup, I'll probably do just that once the package is reviewed.

Thanks for the explanations.

Comment 3 John Mahowald 2006-01-29 16:21:31 UTC

Minor: Build has a bunch of  warning: ignoring return value of x, declared with
attribute warn_unused_result

Your patch sets the lagan dir but leaves the error messages that $LAGAN_DIR was
not set, although you don't use the env variables.

Good:

- rpmlint checks return:
W: lagan non-standard-dir-in-usr libexec
not too significant as per comment 1

- package meets naming guidelines
- package meets packaging guidelines
- license (GPL) OK, text in %doc, matches source
- spec file legible, in am. english
- source matches upstream
- package compiles on FC4 i386
- no missing BR
- no unnecessary BR
(can remove commented R and BR lines if desired)
- no locales
- not relocatable
- owns all directories that it creates
- no duplicate files
- permissions ok
- %clean ok
- macro use consistent
- code, not content
- no need for -docs
- nothing in %doc affects runtime
- no need for .desktop file

APPROVED

Comment 4 Christian Iseli 2006-01-30 00:42:07 UTC

Thanks for the review.  I agree the code is pretty dirty and lots of warnings
remain.  I'll see what I can do.

I've replaced _libexecdir with _libdir and rpmlint is now quiet.

I've redone the patch to kill all LAGAN_DIR occurences and related error messages.

Imported and built, so I'm closing the ticket.