From 2e125ece093ef842ca017ffb146cbc5fa33f2f75 Mon Sep 17 00:00:00 2001
From: Andreas Enge <andreas@enge.fr>
Date: Tue, 19 Feb 2019 22:37:02 +0100
Subject: [PATCH] gnu: pplacer: Remove the package, which is affected by a CVE
 on ocaml@4.01.

This makes progress towards fixing <https://bugs.gnu.org/27462>.

* gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): Remove
variables.
---
 gnu/packages/bioinformatics.scm | 124 --------------------------------
 1 file changed, 124 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 69c85563e1..5dc3945035 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4365,130 +4365,6 @@ interrupted by stop codons.  OrfM finds and prints these ORFs.")
     (home-page "https://github.com/wwood/OrfM")
     (license license:lgpl3+)))
 
-(define-public pplacer
-  (let ((commit "807f6f3"))
-    (package
-      (name "pplacer")
-      ;; The commit should be updated with each version change.
-      (version "1.1.alpha19")
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/matsen/pplacer.git")
-               (commit (string-append "v" version))))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn"))))
-      (build-system ocaml-build-system)
-      (arguments
-       `(#:ocaml ,ocaml-4.01
-         #:findlib ,ocaml4.01-findlib
-         #:modules ((guix build ocaml-build-system)
-                    (guix build utils)
-                    (ice-9 ftw))
-         #:phases
-         (modify-phases %standard-phases
-           (delete 'configure)
-           (add-after 'unpack 'replace-bundled-cddlib
-             (lambda* (#:key inputs #:allow-other-keys)
-               (let* ((cddlib-src (assoc-ref inputs "cddlib-src"))
-                      (local-dir "cddlib_guix"))
-                 (mkdir local-dir)
-                 (with-directory-excursion local-dir
-                   (invoke "tar" "xvf" cddlib-src))
-                 (let ((cddlib-src-folder
-                        (string-append local-dir "/"
-                                       (list-ref (scandir local-dir) 2)
-                                       "/lib-src")))
-                   (for-each make-file-writable (find-files "cdd_src" ".*"))
-                   (for-each
-                    (lambda (file)
-                      (copy-file file
-                                 (string-append "cdd_src/" (basename file))))
-                    (find-files cddlib-src-folder ".*[ch]$")))
-                 #t)))
-           (add-after 'unpack 'fix-makefile
-             (lambda _
-               ;; Remove system calls to 'git'.
-               (substitute* "Makefile"
-                 (("^DESCRIPT:=pplacer-.*")
-                  (string-append
-                   "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n")))
-               (substitute* "myocamlbuild.ml"
-                 (("git describe --tags --long .*\\\" with")
-                  (string-append
-                   "echo -n v" ,version "-" ,commit "\" with")))
-               #t))
-           (replace 'install
-             (lambda* (#:key outputs #:allow-other-keys)
-               (let* ((out (assoc-ref outputs "out"))
-                      (bin (string-append out "/bin")))
-                 (copy-recursively "bin" bin))
-               #t)))))
-      (native-inputs
-       `(("zlib" ,zlib)
-         ("gsl" ,gsl)
-         ("ocaml-ounit" ,ocaml4.01-ounit)
-         ("ocaml-batteries" ,ocaml4.01-batteries)
-         ("ocaml-camlzip" ,ocaml4.01-camlzip)
-         ("ocaml-csv" ,ocaml4.01-csv)
-         ("ocaml-sqlite3" ,ocaml4.01-sqlite3)
-         ("ocaml-xmlm" ,ocaml4.01-xmlm)
-         ("ocaml-mcl" ,ocaml4.01-mcl)
-         ("ocaml-gsl" ,ocaml4.01-gsl)
-         ("cddlib-src" ,(package-source cddlib))))
-      (propagated-inputs
-       `(("pplacer-scripts" ,pplacer-scripts)))
-      (synopsis "Phylogenetic placement of biological sequences")
-      (description
-       "Pplacer places query sequences on a fixed reference phylogenetic tree
-to maximize phylogenetic likelihood or posterior probability according to a
-reference alignment.  Pplacer is designed to be fast, to give useful
-information about uncertainty, and to offer advanced visualization and
-downstream analysis.")
-      (home-page "http://matsen.fhcrc.org/pplacer")
-      (license license:gpl3))))
-
-;; This package is installed alongside 'pplacer'.  It is a separate package so
-;; that it can use the python-build-system for the scripts that are
-;; distributed alongside the main OCaml binaries.
-(define pplacer-scripts
-  (package
-    (inherit pplacer)
-    (name "pplacer-scripts")
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'enter-scripts-dir
-           (lambda _ (chdir "scripts") #t))
-         (replace 'check
-           (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t))
-         (add-after 'install 'wrap-executables
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (bin (string-append out "/bin")))
-               (let ((path (string-append
-                            (assoc-ref inputs "hmmer") "/bin:"
-                            (assoc-ref inputs "infernal") "/bin")))
-                 (display path)
-                 (wrap-program (string-append bin "/refpkg_align.py")
-                   `("PATH" ":" prefix (,path))))
-               (let ((path (string-append
-                            (assoc-ref inputs "hmmer") "/bin")))
-                 (wrap-program (string-append bin "/hrefpkg_query.py")
-                   `("PATH" ":" prefix (,path)))))
-             #t)))))
-    (inputs
-     `(("infernal" ,infernal)
-       ("hmmer" ,hmmer)))
-    (propagated-inputs
-     `(("python-biopython" ,python2-biopython)
-       ("taxtastic" ,taxtastic)))
-    (synopsis "Pplacer Python scripts")))
-
 (define-public python2-pbcore
   (package
     (name "python2-pbcore")