Hello,
I am attempting to install phylocsf through both means introduced in their github. The first is through installing ocaml and opam, and later on running
git clone git://github.com/mlin/PhyloCSF.git cd PhyloCSF make
When running the make command, I get the following error:
/Library/Developer/CommandLineTools/usr/bin/make -C lib/CamlPaml reinstall make uninstall ocamlfind remove CamlPaml ocamlfind: [WARNING] No such file: /Users/dr/.opam/default/lib/CamlPaml/META make install ocamlbuild -use-ocamlfind CamlPaml.cma CamlPaml.cmxa
- ocamlfind ocamlc -c -g -package gsl -pp ocaml+twt -o PhyloLik.cmo PhyloLik.ml
File "PhyloLik.ml", line 7, characters 16-29:
7 | pe leaf = [
Certain of int |Distribution of float array | `Marginalize]
Error: Modules do not match:^^^^^^^^^^^^^
is not included in Set.OrderedType Values do not match:sig type t = int val compare : ('a -> 'a -> int) -> 'a list -> 'a list -> int end
is not included inval compare : ('a -> 'a -> int) -> 'a list -> 'a list -> int
The type ('a -> 'a -> int) -> 'a list -> 'a list -> int is not compatible with the type t -> t -> int Type 'a -> 'a -> int is not compatible with type t = int File "set.mli", line 55, characters 4-31: Expected declaration File "PhyloLik.ml", line 6, characters 5-12: Actual declaration Command exited with code 2. Compilation unsuccessful after building 51 targets (50 cached) in 00:00:00. make[2]: [lib] Error 10 make[1]: [reinstall] Error 2 make: *** [CamlPaml] Error 2.val compare : t -> t -> int
I then tried installing through docker by running:
docker build -t mlin:PhyloCSF https://gist.githubusercontent.com/mlin/31c0a7623f99d3bf3222/raw/Dockerfile
and get:
[+] Building 67.7s (8/14) => [internal] load remote build context 0.0s => [internal] load metadata for docker.io/library/ubuntu:trusty 2.8s => [ 1/12] FROM docker.io/library/ubuntu:trusty@sha256:64483f3496c1373b 10.8s => => resolve docker.io/library/ubuntu:trusty@sha256:64483f3496c1373bfd5 0.0s => => sha256:75f8eea31a63686c11aa74b7df6da0f6450afbee2 59.10kB / 59.10kB 0.6s => => sha256:a72d031efbfb01751d5de3b287566e7d7f33697674a6c47 187B / 187B 0.7s => => sha256:64483f3496c1373bfd55348e88694d1c4d0c9b660de 1.20kB / 1.20kB 0.0s => => sha256:5ed16aa332467821529d451800e6fe599d83e30471e91b0 945B / 945B 0.0s => => sha256:55b7b4f7c5d6a56a3ccb5e93538311838599b65e746 3.33kB / 3.33kB 0.0s => => sha256:d1a5a1e51f251c3431dec02e2cc8d157e92d1b469 66.47MB / 66.47MB 9.6s => => extracting sha256:d1a5a1e51f251c3431dec02e2cc8d157e92d1b46913708ce 1.0s => => extracting sha256:75f8eea31a63686c11aa74b7df6da0f6450afbee2c9e1e3a 0.0s => => extracting sha256:a72d031efbfb01751d5de3b287566e7d7f33697674a6c477 0.0s => [ 2/12] RUN apt-get update 12.9s => [ 3/12] RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-i 31.4s => [ 4/12] RUN add-apt-repository ppa:avsm/ppa 3.6s => [ 5/12] RUN apt-get update 5.3s
=> ERROR [ 6/12] RUN DEBIAN_FRONTEND=noninteractive apt-get install --no 0.9s
[ 6/12] RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-suggests --no-install-recommends -y ocaml camlp4 camlp4-extra opam libgsl0-dev m4 pkg-config:
8 0.283 Reading package lists...
8 0.791 Building dependency tree...
8 0.848 Reading state information...
8 0.874 Some packages could not be installed. This may mean that you have
8 0.874 requested an impossible situation or if you are using the unstable
8 0.874 distribution that some required packages have not yet been created
8 0.874 or been moved out of Incoming.
8 0.874 The following information may help to resolve the situation:
8 0.874
8 0.874 The following packages have unmet dependencies:
8 0.874 opam : Depends: opam-docs (= 1.1.1-1) but 1.2.2-1ppa2~trusty is to be installed
8 0.880 E: Unable to correct problems, you have held broken packages.
executor failed running [/bin/sh -c DEBIAN_FRONTEND=noninteractive apt-get install --no-install-suggests --no-install-recommends -y ocaml camlp4 camlp4-extra opam libgsl0-dev m4 pkg-config]: exit code: 100
Would appreciate any help troubleshooting! Thank you for your time.
