Failing build

[CosteaPaul]

Hello,

I am unable to build pplacer. After installing all the dependencies and running make i get: File "pplacer_src/pquery.ml", line 98, characters 31-37: Error: Unbound value second

Since i am unfamiliar with ocaml i find it hard to debug this. Any help would be greatly appreciated.

[cmccoy]

It sounds like you might have a different version of batteries than pplacer requires. Did you install the OCaml dependencies via the installation script here?

Alternatively, there are binaries available for OS X and 64-bit Linux at at http://matsen.fhcrc.org/pplacer.

[CosteaPaul]

Binaries work fine, but i was trying to get things running on a 32bit machine. I have used the installation script, but that fails at some point: Installing findlib library 'oUnit'

ocamlfind: Package oUnit is already installed

• (file /home/paul/Work/Software/test/godi/lib/ocaml/site-lib/oUnit/META already exists)

E: Command '/home/paul/Work/Software/test/godi/bin/ocamlfind install oUnit src/META /home/paul/.odb/install-ounit/ounit-1.1.0/_build/src/oUnit.cmi /home/paul/.odb/install-ounit/ounit-1.1.0/_build/src/oUnitDiff.cmi /home/paul/.odb/install-ounit/ounit-1.1.0/_build/src/oUnit.a /home/paul/.odb/install-ounit/ounit-1.1.0/_build/src/oUnit.cmxa /home/paul/.odb/install-ounit/ounit-1.1.0/_build/src/oUnit.cma src/oUnitDiff.mli src/oUnit.mli' terminated with error code 2

Exception: Failure "Could not install package ounit".

The last "Command" fails because it cannot find src/META. For now i will use the 64bit build.

[CosteaPaul]

Cleaned everything up and now running the script hangs as originally mentioned: File "pplacer_src/pquery.ml", line 98, characters 31-37: Error: Unbound value second

[matsen]

Hello there Paul---

I apologize for the delay in getting this fixed for you. @habnabit, the primary developer for pplacer and the author of this build script, has just moved on to another position. I'm going to take some time tomorrow to see if I can get it running. The previous build system was built the GODI system, which was relatively fragile.

We may drop GODI and move on to https://github.com/OCamlPro/opam.

Thank you for your patience,

Erick

On Fri, Jan 11, 2013 at 5:37 AM, Paul Costea notifications@github.comwrote:

Cleaned everything up and now running the script hangs as originally mentioned:

File "pplacer_src/pquery.ml", line 98, characters 31-37: Error: Unbound value second

—

Reply to this email directly or view it on GitHubhttps://github.com/matsen/pplacer/issues/292#issuecomment-12144438.

Frederick "Erick" Matsen, Assistant Member Fred Hutchinson Cancer Research Center http://matsen.fhcrc.org/

[cmccoy]

Hello Paul,

I've updated the pplacer build process and instructions to use OPAM: http://matsen.github.com/pplacer/compiling.html

Would you mind trying those? They worked for me on a fresh install of 32-bit Ubuntu 12.04. Alternatively, I can send you 32-bit binaries.

[CosteaPaul]

Hello,

I tried the new approach and i get stuck at adding the opam requirements: cat opam-requirements.txt | xargs opam install -y fails with: Version 2.0beta1 of "batteries" is incompatible with your compiler or your OS.

I'm running DISTRIB_DESCRIPTION="Ubuntu 12.04.1 LTS" opam 0.9.2 oCaml 3.12.1

Thanks, -Paul

[cmccoy]

I believe that's actually a misleading error message - I've seen it when the package and/or version is unknown. Did the opam repo add step complete successfully?

Anyway, I uploaded 32-bit binaries to https://www.dropbox.com/s/6xfag3pqiv35gyl/pplacer-v1.1.alpha13r2-5-g5a86d8c-linux32.tar.bz2

Connor

On Wed, Jan 16, 2013 at 12:40 AM, Paul Costea notifications@github.comwrote:

Hello,

I tried the new approach and i get stuck at adding the opam requirements: cat opam-requirements.txt | xargs opam install -y fails with: Version 2.0beta1 of "batteries" is incompatible with your compiler or your OS.

I'm running DISTRIB_DESCRIPTION="Ubuntu 12.04.1 LTS" opam 0.9.2 oCaml 3.12.1

Thanks, -Paul

— Reply to this email directly or view it on GitHubhttps://github.com/matsen/pplacer/issues/292#issuecomment-12309177.

[cmccoy]

Closing - feel free to reopen if you're still having trouble.

[michelia]

Thanks cmccoy. You provided 32-bit binaries that is very good!