gnu: ocaml: Switch to ocaml 4.09 by default.

Bap and earley cannot be updated as they do not support 4.09 yet. Bap requires
the janestreet packages, which cannot be upgraded as no version supports
4.09 and 4.07 at the same time. Moreover, newer versions of the
janestreet packages have a different dependency graph, which will
require a whole new set of packages. We cannot simply use
package-with-ocaml4.07 on them.

* gnu/packages/ocaml.scm (ocaml-sqlite3, ocaml-ppx-tools, ocaml-gen)
(ocaml-sedlex, ocaml-pcre, ocaml-expect, ocaml-ezjsonm, ocaml-uri)
(ocaml-piqilib, ocaml-piqi, ocaml-charinfo-width, ocaml-zed)
(ocaml-lambda-term, ocaml-utop, ocaml-ppx-inline-test, ocaml-earley)
(ocaml-merlin, ocaml-gsl, ocaml-gsl-1, ocaml-sexplib0, ocaml-parsexp)
(ocaml-sexplib, ocaml-base, ocaml-stdio, ocaml-ppxlib, ocaml-ppx-compare)
(ocaml-fieldslib, ocaml-variantslib, ocaml-ppx-fields-conv)
(ocaml-ppx-sexp-conv, ocaml-ppx-variants-conv, ocaml-ppx-custom-printf)
(ocaml-bin-prot, ocaml-ppx-hash, ocaml-ppx-enumerate, ocaml-ppx-bench)
(ocaml-ppx-here, ocaml-ppx-typerep, ocaml-ppx-sexp-value)
(ocaml-ppx-sexp-message, ocaml-ppx-pipebang, ocaml-ppx-optional)
(ocaml-ppx-optcomp, ocaml-ppx-fail, ocaml-ppx-let, ocaml-ppx-assert)
(ocaml-ppx-expect, ocaml-ppx-js-style, ocaml-ppx-typerep-conv)
(ocaml-ppx-base, ocaml-ppx-bin-prot, ocaml-ppx-jane)
(ocaml-splittable-random, ocaml-configurator, ocaml-spawn, ocaml-core)
(ocaml-core-kernel, ocaml-odoc, ocaml-fftw3, ocaml-lacaml): Rename to ...
(ocaml4.07-sqlite3, ocaml4.07-ppx-tools, ocaml4.07-gen, ocaml4.07-sedlex)
(ocaml4.07-pcre, ocaml4.07-expect, ocaml4.07-ezjsonm, ocaml4.07-uri)
(ocaml4.07-piqilib, ocaml4.07-piqi, ocaml4.07-charinfo-width)
(ocaml4.07-zed, ocaml4.07-lambda-term, ocaml4.07-utop)
(ocaml4.07-ppx-inline-test, ocaml4.07-earley, ocaml4.07-merlin)
(ocaml4.07-gsl, ocaml4.07-gsl-1, ocaml4.07-sexplib0, ocaml4.07-parsexp)
(ocaml4.07-sexplib, ocaml4.07-base, ocaml4.07-stdio, ocaml4.07-ppxlib)
(ocaml4.07-ppx-compare, ocaml4.07-fieldslib, ocaml4.07-variantslib)
(ocaml4.07-ppx-fields-conv, ocaml4.07-ppx-sexp-conv)
(ocaml4.07-ppx-variants-conv, ocaml4.07-ppx-custom-printf)
(ocaml4.07-bin-prot, ocaml4.07-ppx-hash, ocaml4.07-ppx-enumerate)
(ocaml4.07-ppx-bench, ocaml4.07-ppx-here, ocaml4.07-ppx-typerep)
(ocaml4.07-ppx-sexp-value, ocaml4.07-ppx-sexp-message)
(ocaml4.07-ppx-pipebang, ocaml4.07-ppx-optional, ocaml4.07-ppx-optcomp)
(ocaml4.07-ppx-fail, ocaml4.07-ppx-let, ocaml4.07-ppx-assert)
(ocaml4.07-ppx-expect, ocaml4.07-ppx-js-style)
(ocaml4.07-ppx-typerep-conv, ocaml4.07-ppx-base, ocaml4.07-ppx-bin-prot)
(ocaml4.07-ppx-jane, ocaml4.07-splittable-random)
(ocaml4.07-configurator, ocaml4.07-spawn, ocaml4.07-core)
(ocaml4.07-core-kernel, ocaml4.07-odoc, ocaml4.07-fftw3)
(ocaml4.07-lacaml): ... to this and use ocaml 4.07.
(bap, unison): Use ocaml-4.07.
* gnu/packages/bioinformatics.scm (pplacer): Use ocaml-4.07.

1 files changed, 12 insertions, 10 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e8dac2a12b..c71adbe98c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14626,21 +14626,23 @@ let before_space s =
                (let* ((out (assoc-ref outputs "out"))
                       (bin (string-append out "/bin")))
                  (copy-recursively "bin" bin))
-               #t)))))
+               #t)))
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
       (inputs
        `(("zlib" ,zlib "static")
          ("gsl" ,gsl)
-         ("ocaml-ounit" ,ocaml-ounit)
-         ("ocaml-batteries" ,ocaml-batteries)
-         ("ocaml-camlzip" ,camlzip)
-         ("ocaml-csv" ,ocaml-csv)
-         ("ocaml-sqlite3" ,ocaml-sqlite3)
-         ("ocaml-xmlm" ,ocaml-xmlm)
-         ("ocaml-mcl" ,ocaml-mcl)
-         ("ocaml-gsl" ,ocaml-gsl-1)))
+         ("ocaml-ounit" ,(package-with-ocaml4.07 ocaml-ounit))
+         ("ocaml-batteries" ,(package-with-ocaml4.07 ocaml-batteries))
+         ("ocaml-camlzip" ,(package-with-ocaml4.07 camlzip))
+         ("ocaml-csv" ,(package-with-ocaml4.07 ocaml-csv))
+         ("ocaml-sqlite3" ,ocaml4.07-sqlite3)
+         ("ocaml-xmlm" ,(package-with-ocaml4.07 ocaml-xmlm))
+         ("ocaml-mcl" ,(package-with-ocaml4.07 ocaml-mcl))
+         ("ocaml-gsl" ,ocaml4.07-gsl-1)))
       (native-inputs
        `(("cddlib-src" ,(package-source cddlib))
-         ("ocamlbuild" ,ocamlbuild)
+         ("ocamlbuild" ,(package-with-ocaml4.07 ocamlbuild))
          ("pkg-config" ,pkg-config)))
       (propagated-inputs
        `(("pplacer-scripts" ,pplacer-scripts)))