gravatar for nikitavlassenko

3 hours ago by

I am trying to install PhyloCSF:

github.com/mlin/PhyloCSF

Since it is needed for new VEP99. In order to do that I needed to install ocaml, bubblewrap, opam. Second bullet point:

opam install batteries ocaml+twt gsl

Did not work, but I found that this one works:

opam install ocaml-twt

As can be found in this thread: github.com/mlin/PhyloCSF/issues/16

Then I tried the actual compilation of PhyloCSF by running make in the cloned repo folder and got the following error:

(py37) -bash-4.2$ make
make -C lib/CamlPaml  reinstall
make[1]: Entering directory `/vep/PhyloCSF/lib/CamlPaml'
make uninstall
make[2]: Entering directory `/vep/PhyloCSF/lib/CamlPaml'
ocamlfind remove CamlPaml
ocamlfind: [WARNING] No such file: /usr/lib64/ocaml/CamlPaml/META
make[2]: Leaving directory `/vep/PhyloCSF/lib/CamlPaml'
make install
make[2]: Entering directory `/vep/PhyloCSF/lib/CamlPaml'
ocamlbuild -use-ocamlfind CamlPaml.cma CamlPaml.cmxa
make[2]: ocamlbuild: Command not found
make[2]: *** [lib] Error 127
make[2]: Leaving directory `/vep/PhyloCSF/lib/CamlPaml'
make[1]: *** [reinstall] Error 2
make[1]: Leaving directory `/vep/PhyloCSF/lib/CamlPaml'
make: *** [CamlPaml] Error 2

Meaning that there is no ocamlbuild. Ok, so I tried installing it:

opam install ocamlbuild

And got the error:

The following actions will be performed:
  ∗ install ocamlbuild 0.14.0

<><> Gathering sources ><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
[ocamlbuild.0.14.0] found in cache

<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
[ERROR] The compilation of ocamlbuild failed at "/opt/seqr/.opam/opam-init/hooks/sandbox.sh build make
        check-if-preinstalled all opam-install".

#=== ERROR while compiling ocamlbuild.0.14.0 ==================================#
# context     2.0.6 | linux/x86_64 | ocaml-system.4.05.0 | https://opam.ocaml.org#d74ac435
# path        ~/.opam/default/.opam-switch/build/ocamlbuild.0.14.0
# command     ~/.opam/opam-init/hooks/sandbox.sh build make check-if-preinstalled all opam-install
# exit-code   2
# env-file    ~/.opam/log/ocamlbuild-19788-6d07ae.env
# output-file ~/.opam/log/ocamlbuild-19788-6d07ae.out
### output ###
# if test -d /usr/lib64/ocaml/ocamlbuild; then
#   >&2 echo "ERROR: Preinstalled ocamlbuild detected at"
#        "/usr/lib64/ocaml/ocamlbuild";
#   >&2 echo "Installation aborted; if you want to bypass this"
#         "safety check, pass CHECK_IF_PREINSTALLED=false to make";
#   exit 2;
# fi
# ERROR: Preinstalled ocamlbuild detected at /usr/lib64/ocaml/ocamlbuild
# Installation aborted; if you want to bypass this safety check, pass CHECK_IF_PREINSTALLED=false to make
# make: *** [check-if-preinstalled] Error 2



<><> Error report <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
┌─ The following actions failed
│ λ build ocamlbuild 0.14.0
└─ 
╶─ No changes have been performed

So, I tried installing it though yum install ocambuild but there is no such package. I tried putting folder /usr/lib64/ocaml in PATH and got a permission denied error that is not resolved by chomd 777 -R /usr/lib64/ocaml and chmod 777 -R PhyloCSF or running as a root:

(base) [[email protected] PhyloCSF]# make
make -C lib/CamlPaml  reinstall
make[1]: Entering directory `/vep/PhyloCSF/lib/CamlPaml'
make uninstall
make[2]: Entering directory `/vep/PhyloCSF/lib/CamlPaml'
ocamlfind remove CamlPaml
ocamlfind: [WARNING] No such file: /usr/lib64/ocaml/CamlPaml/META
make[2]: Leaving directory `/vep/PhyloCSF/lib/CamlPaml'
make install
make[2]: Entering directory `/vep/PhyloCSF/lib/CamlPaml'
ocamlbuild -use-ocamlfind CamlPaml.cma CamlPaml.cmxa
make[2]: execvp: ocamlbuild: Permission denied
make[2]: *** [lib] Error 127
make[2]: Leaving directory `/vep/PhyloCSF/lib/CamlPaml'
make[1]: *** [reinstall] Error 2
make[1]: Leaving directory `/vep/PhyloCSF/lib/CamlPaml'
make: *** [CamlPaml] Error 2

I followed this thread and tried the accepted solution but it did not fix anything in my case:

stackoverflow.com/questions/9106536/why-do-i-get-permission-denied-when-i-try-use-make-to-install-something

Instead giving an error:

(base) [[email protected] PhyloCSF]# make install DESTDIR=/var/lib/spark/vep/PhyloCSF/
make: *** No rule to make target `install'.  Stop.



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