There are two issues you are running into:

1) the interface changed between tagsoup 0.6 and 0.8
2) QuickCheck 2 is different from QC 1

In the current biolib (i.e. my darcs repo), the dependencies look like:

| Build-Depends: base>=4 && <5, QuickCheck>=2, binary==0.4.*, tagsoup>=0.4 && <0.8, bytestring >= 0.9.1,
| containers, array, parallel, parsec, random, old-time, mtl

I have also received a patch for biolib to work with both old and new tagsoup, which would obliviate the need for the upper limit to tagsoup versions.

I think the biggest problem here is that I haven’t kept up on Hackage, the 0.4 version is quite old. I’ve rolled out a new tarball (bio-0.4.4 at Hackage). You can usually get updated sources from “darcs get http://malde.org/biohaskell/biolib”

-k

you need to download and to install tagsoup 0.4

download from here:

http://hackage.haskell.org/package/tagsoup-0.4

then, you need to install using:

runhaskell Setup configure or
runhaskell Setup configure –user
runhaskell Setup build
runhaskell Setup install

so, download bio-0.4 haskell tar source package and untar package.

backup and edit bio.cabal following line:

Build-Depends: base>=3 && =1.2.0.0, binary, tagsoup= 0.9.1, containers, array,
parallel, parsec, random, old-time, mtl

I changed QuickCheck to >=1.2 and tagsoup =1.2.0.0: using QuickCheck-2.1.0.3
Dependency tagsoup <=0.4: using tagsoup-0.4

ok, good then install biohaskell lib using:

runhaskell Setup configure –user
runhaskell Setup build

opps so, you will see and error

[18 of 43] Compiling Bio.Sequence.TwoBit ( Bio/Sequence/TwoBit.hs, dist/build/Bio/Sequence/TwoBit.o )

Bio/Sequence/TwoBit.hs:37:31:
Module `Test.QuickCheck' does not export `check'

to fix error open Bio/Sequence/TwoBit.hs haskell source file and locate line 37 with your vi or emacs editor

by default you will see:

import Test.QuickCheck hiding (check) — QC 1.0
–import Test.QuickCheck hiding ((.&.)) — QC 2.0

please make changes like this:

– import Test.QuickCheck hiding (check) — QC 1.0
import Test.QuickCheck hiding ((.&.)) — QC 2.0

this is because I am using QuickCheck 2

ok, good , try to build once again :

runhaskell Setup build

opps error

[35 of 43] Compiling Bio.Util.TestBase ( Bio/Util/TestBase.hs, dist/build/Bio/Util/TestBase.o )

Bio/Util/TestBase.hs:81:4:
`coarbitrary' is not a (visible) method of class `Arbitrary'

Bio/Util/TestBase.hs:85:4:
`coarbitrary' is not a (visible) method of class `Arbitrary'

Bio/Util/TestBase.hs:90:4:
`coarbitrary' is not a (visible) method of class `Arbitrary'

Bio/Util/TestBase.hs:98:4:
`coarbitrary' is not a (visible) method of class `Arbitrary'

Bio/Util/TestBase.hs:105:4:
`coarbitrary' is not a (visible) method of class `Arbitrary'

Bio/Util/TestBase.hs:109:4:
`coarbitrary' is not a (visible) method of class `Arbitrary'

Bio/Util/TestBase.hs:117:4:
`coarbitrary' is not a (visible) method of class `Arbitrary'

Bio/Util/TestBase.hs:125:4:
`coarbitrary' is not a (visible) method of class `Arbitrary'

Bio/Util/TestBase.hs:132:4:
`coarbitrary' is not a (visible) method of class `Arbitrary'

you will need to edit bio.cabal, find Bio.Util.TestBase and delete it then save file.

runhaskell Setup install
Installing library in $HOME/.cabal/lib/bio-0.4/ghc-6.12.1
Registering bio-0.4…

ls $HOME/.cabal/lib/bio-0.4/ghc-6.12.1/
Bio HSbio-0.4.o libHSbio-0.4.a

ready, that's all

ketil, what's is your opinion ?

Ciao

Configuring bio-0.4.4...
Dependency QuickCheck >=2: using QuickCheck-2.1.0.2
Dependency array -any: using array-0.3.0.0
Dependency base ==4.*: using base-4.2.0.0
Dependency binary -any: using binary-0.5.0.2
Dependency bytestring >=0.9.1: using bytestring-0.9.1.5
Dependency containers -any: using containers-0.3.0.0
Dependency mtl -any: using mtl-1.1.0.2
Dependency old-time -any: using old-time-1.0.0.3
Dependency parallel -any: using parallel-1.1.0.1
Dependency parsec -any: using parsec-2.1.0.1
Dependency random -any: using random-1.0.0.2
Dependency tagsoup >=0.4: using tagsoup-0.6


Bio/Alignment/BlastXML.hs:41:12:
`Tag’ is not applied to enough type arguments
Expected kind `*’, but `Tag’ has kind `* -> *’
In the type signature for `getFrom’:
getFrom :: [Tag] -> String -> String

Could you please perhaps state clearly which combination of the complier/libraries is recommended?

cabal install bio
Resolving dependencies…
cabal: cannot configure tagsoup-0.8. It requires QuickCheck ==2.1.*
For the dependency on QuickCheck ==2.1.* there are these packages:
QuickCheck-2.1, QuickCheck-2.1.0.1, QuickCheck-2.1.0.2 and QuickCheck-2.1.0.3.
However none of them are available.
QuickCheck-2.1 was excluded because bio-0.4 requires QuickCheck <2

Is there anything to be done to fix this?
j131