[Debian-med-packaging] Bug#663889: [jwilk at debian.org: Bug#663889: qiime: FTBFS: FlowgramAli_4frame.lhs:10:10: Could not find module `System']

[Andreas Tille]

Hi Tim,

I tried your suggested patch but this did not really help.  I had the
idea that possibly the package libghc-unixutils-dev might provide the
module in question and wanted to add this as Build-Depends - but this
package fails to install at all because it depends from non-existing
packages (at least in Debian unstable).  So I'm waiting until Haskell
maintainers might have fixed this.

Any other hint is welcome.

Kind regards

      Andreas.

On Thu, Mar 15, 2012 at 03:44:41PM +0000, Tim Booth wrote:
> Hi Andreas,
> 
> It seems that 'import System' was previously legal but wrong, and the
> newer version of GHC is enforcing the rule properly.
> 
> As a guess, based on my very old and rusty knowledge of Haskell and a
> quick query of Google:
> 
> --- .orig/qiime/support_files/denoiser/FlowgramAlignment/FlowgramAli_4frame.lhs
> +++ .new/qiime/support_files/denoiser/FlowgramAlignment/FlowgramAli_4frame.lhs
> @@ -6,8 +6,7 @@
>  > import ADPCombinators
>  > import System(getArgs)
>  > import System.IO
> -> import System.Exit(exitWith)
> -> import System
> +> import System.Exit
>  > import Text.Printf(printf)
> ---
> 
> Does that help?  I don't have the newer GHC installed to test it myself.
> 
> Cheers,
> 
> TIM
> 
> On Wed, 2012-03-14 at 19:59 +0000, Andreas Tille wrote:
> > Hi Tim,
> > 
> > any idea what might went wrong here???
> > 
> > Kind regards
> > 
> >        Andreas.
> > 
> > ----- Forwarded message from Jakub Wilk <jwilk at debian.org> -----
> > 
> > Date: Wed, 14 Mar 2012 20:36:24 +0100
> > From: Jakub Wilk <jwilk at debian.org>
> > To: submit at bugs.debian.org
> > Subject: Bug#663889: qiime: FTBFS:
> > 	FlowgramAli_4frame.lhs:10:10: Could not find module `System'
> > X-Debian-PR-Message: followup 663889
> > X-Debian-PR-Package: src:qiime
> > X-Debian-PR-Keywords: 
> > X-Debian-PR-Source: qiime
> > X-Spam_score: -2.3
> > 
> > Source: qiime
> > Version: 1.3.0-2
> > Severity: serious
> > Justification: fails to build from source
> > 
> > qiime FTBFS:
> > | ghc --make -O2 FlowgramAli_4frame
> > |
> > | FlowgramAli_4frame.lhs:10:10:
> > |     Could not find module `System'
> > |     It is a member of the hidden package `haskell98-2.0.0.1'.
> > |     Use -v to see a list of the files searched for.
> > | make[1]: *** [FlowgramAli_4frame] Error 1
> > | make[1]: Leaving directory `/build/qiime-OSdDTF/qiime-1.3.0/qiime/support_files/denoiser/FlowgramAlignment'
> > | make[1]: Entering directory `/build/qiime-OSdDTF/qiime-1.3.0/qiime/support_files/denoiser/FlowgramAlignment'
> > | cp FlowgramAli_4frame ../bin/
> > | cp: cannot stat `FlowgramAli_4frame': No such file or directory
> > | make[1]: *** [install] Error 1
> > | make[1]: Leaving directory `/build/qiime-OSdDTF/qiime-1.3.0/qiime/support_files/denoiser/FlowgramAlignment'
> > 
> > Despite the error the build continued, finally failing with:
> > | running install_data
> > | creating /build/qiime-OSdDTF/qiime-1.3.0/debian/tmp/usr/qiime
> > | creating /build/qiime-OSdDTF/qiime-1.3.0/debian/tmp/usr/qiime/support_files
> > | creating /build/qiime-OSdDTF/qiime-1.3.0/debian/tmp/usr/qiime/support_files/denoiser
> > | creating /build/qiime-OSdDTF/qiime-1.3.0/debian/tmp/usr/qiime/support_files/denoiser/bin
> > | error: can't copy 'qiime/support_files/denoiser/bin/FlowgramAli_4frame': doesn't exist or not a regular file
> > | dh_auto_install: python2.6 setup.py install --force --root=/build/qiime-OSdDTF/qiime-1.3.0/debian/tmp --no-compile -O0 --install-layout=deb returned exit code 1
> > | make: *** [binary] Error 1
> > 
> > -- 
> > Jakub Wilk
> > 
> > 
> > 
> > _______________________________________________
> > Debian-med-packaging mailing list
> > Debian-med-packaging at lists.alioth.debian.org
> > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
> > 
> > 
> > ----- End forwarded message -----
> > 
> 
> -- 
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre 
> 
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB 
> 
> http://nebc.nerc.ac.uk
> +44 1491 69 2705
> 
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