From 497fc04d8fe7adfc74646f2e3f3baba0410a3ae3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 20:49:19 +0100
Subject: gnu: mash: Fetch sources from git.

* gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
---
 gnu/packages/bioinformatics.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1fac960eff..625c074349 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3979,14 +3979,14 @@ sequences).")
     (name "mash")
     (version "2.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/marbl/mash/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/marbl/mash.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "00fx14vpmgsijwxd1xql3if934l82v8ckqgjjyyhnr36qb9qrskv"))
+                "13h6v4wzfflb5raxwlqmkl2km54m3izm30f1w9p9scjmfrnfn0wx"))
               (modules '((guix build utils)))
               (snippet
                '(begin
-- 
cgit v1.2.3


From 5c1f35e71ba4176904b1909c7738d43c61eea475 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 20:51:55 +0100
Subject: gnu: mash: Update to 2.1.

* gnu/packages/bioinformatics.scm (mash): Update to 2.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 625c074349..5cd5d744cb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3977,7 +3977,7 @@ sequences).")
 (define-public mash
   (package
     (name "mash")
-    (version "2.0")
+    (version "2.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -3986,7 +3986,7 @@ sequences).")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "13h6v4wzfflb5raxwlqmkl2km54m3izm30f1w9p9scjmfrnfn0wx"))
+                "049hwcc059p2fd9vwndn63laifvvsi0wmv84i6y1fr79k15dxwy6"))
               (modules '((guix build utils)))
               (snippet
                '(begin
-- 
cgit v1.2.3


From b58d9e4aa29d90ae47748c4134e9da53f82c13f6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 20:52:44 +0100
Subject: gnu: metabat: Fetch sources from git.

* gnu/packages/bioinformatics.scm (metabat)[source]: Fetch from git.
---
 gnu/packages/bioinformatics.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5cd5d744cb..e729c173e8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4040,13 +4040,14 @@ form of assemblies or reads.")
     (version "2.12.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://bitbucket.org/berkeleylab/metabat.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73"))
+         "0hyg2smw1nz69mfvjpk45xyyychmda92c80a0cv7baji84ri4iyn"))
        (patches (search-patches "metabat-fix-compilation.patch"))))
     (build-system scons-build-system)
     (arguments
-- 
cgit v1.2.3


From 9d94ca0ebf3d17e3bcf3f9322038e9f29798a9e7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 20:59:28 +0100
Subject: gnu: minced: Fetch sources from git.

* gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git.
---
 gnu/packages/bioinformatics.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e729c173e8..a2eb264a59 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4112,14 +4112,14 @@ probabilistic distances of genome abundance and tetranucleotide frequency.")
     (name "minced")
     (version "0.2.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/ctSkennerton/minced/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/ctSkennerton/minced.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0wxmlsapxfpxfd3ps9636h7i2xy6la8i42mwh0j2lsky63h63jp1"))))
+                "04qp70vawbbp0q5q4hp6vjcgzfhhdrdcaxkn58av9hj79p9gfq2q"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
-- 
cgit v1.2.3


From 6052264b56856a9769cc648ac21c1811934f6211 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 21:01:59 +0100
Subject: gnu: minced: Update to 0.3.2.

* gnu/packages/bioinformatics.scm (minced): Update to 0.3.2.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a2eb264a59..7b50cebd2a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4110,7 +4110,7 @@ probabilistic distances of genome abundance and tetranucleotide frequency.")
 (define-public minced
   (package
     (name "minced")
-    (version "0.2.0")
+    (version "0.3.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -4119,7 +4119,7 @@ probabilistic distances of genome abundance and tetranucleotide frequency.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "04qp70vawbbp0q5q4hp6vjcgzfhhdrdcaxkn58av9hj79p9gfq2q"))))
+                "1f5h9him0gd355cnx7p6pnxpknhckd4g0v62mg8zyhfbx9as25fv"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
-- 
cgit v1.2.3


From a2b9d6a8d05aff0acba2d40ac45790d282c814bf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 21:15:28 +0100
Subject: gnu: pplacer: Fetch sources from git.

* gnu/packages/bioinformatics.scm (pplacer)[source]: Fetch from git.
[arguments]: Make files writable; use INVOKE.
---
 gnu/packages/bioinformatics.scm | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7b50cebd2a..62683ad07f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4310,19 +4310,20 @@ interrupted by stop codons.  OrfM finds and prints these ORFs.")
     (license license:lgpl3+)))
 
 (define-public pplacer
-  (let ((commit "g807f6f3"))
+  (let ((commit "807f6f3"))
     (package
       (name "pplacer")
       ;; The commit should be updated with each version change.
       (version "1.1.alpha19")
       (source
        (origin
-         (method url-fetch)
-         (uri (string-append "https://github.com/matsen/pplacer/archive/v"
-                             version ".tar.gz"))
-         (file-name (string-append name "-" version ".tar.gz"))
+         (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 "0z1lnd2s8sh6kpzg106wzbh2szw7h0hvq8syd5a6wv4rmyyz6x0f"))))
+          (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn"))))
       (build-system ocaml-build-system)
       (arguments
        `(#:ocaml ,ocaml-4.01
@@ -4339,11 +4340,12 @@ interrupted by stop codons.  OrfM finds and prints these ORFs.")
                       (local-dir "cddlib_guix"))
                  (mkdir local-dir)
                  (with-directory-excursion local-dir
-                   (system* "tar" "xvf" cddlib-src))
+                   (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
-- 
cgit v1.2.3


From 1a20bcadf3d75cfce0750c58dee3d5ab23327b99 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 21:25:12 +0100
Subject: gnu: r-seqgl: Fetch sources from git.

* gnu/packages/bioinformatics.scm (r-seqgl)[source]: Fetch from git.
---
 gnu/packages/bioinformatics.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 62683ad07f..c65937ad6c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8877,13 +8877,14 @@ Sequences.")
     (version "1.1.4")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/ManuSetty/SeqGL/"
-                           "archive/" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/ManuSetty/SeqGL.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0pnk1p3sci5yipyc8xnb6jbmydpl80fld927xgnbcv104hy8h8yh"))))
+         "1r6ywvhxl3ffv48lgj7sbd582mcc6dha3ksgc2qjlvjrnkbj3799"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biostrings" ,r-biostrings)
-- 
cgit v1.2.3


From 4257c10ad28bbac98a4ffe86d02c9ef83cfa1a8b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 21:29:40 +0100
Subject: gnu: kentutils: Fetch sources from git.

* gnu/packages/bioinformatics.scm (kentutils)[source]: Fetch from git.
[arguments]: Add phase "fix-permissions".
---
 gnu/packages/bioinformatics.scm | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c65937ad6c..b5523c31fd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11570,13 +11570,14 @@ models.  TADbit is complemented by TADkit for visualizing 3D models.")
     (version "302.0.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/ENCODE-DCC/kentUtils/"
-                           "archive/v" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/ENCODE-DCC/kentUtils.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm"))
+         "0n1wbyjpzii2b9qhyp9r1q76j623cggpg3y8fmw78ld3z4y7ivha"))
        (modules '((guix build utils)
                   (srfi srfi-26)
                   (ice-9 ftw)))
@@ -11627,6 +11628,8 @@ models.  TADbit is complemented by TADkit for visualizing 3D models.")
        #:tests? #f
        #:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'fix-permissions
+           (lambda _ (make-file-writable "src/inc/localEnvironment.mk") #t))
          (add-after 'unpack 'fix-paths
            (lambda _
              (substitute* "Makefile"
-- 
cgit v1.2.3


From 55698df26013bff8646f8c7f1ca135102dad3cb8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 21:37:43 +0100
Subject: gnu: libgff: Fetch sources from git.

* gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git.
---
 gnu/packages/bioinformatics.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b5523c31fd..4682d26279 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11925,14 +11925,14 @@ accurate as existing quantification tools.")
     (name "libgff")
     (version "1.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/Kingsford-Group/"
-                    "libgff/archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/Kingsford-Group/libgff.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0vc4nxyhlm6g9vvmx5l4lfs5pnvixsv1hiiy4kddf2y3p6jna8ls"))))
+                "0n6vfjnq7a2mianipscbshrvbncss8z4zkgkbjw754p9043nfkps"))))
     (build-system cmake-build-system)
     (arguments `(#:tests? #f))          ; no tests included
     (home-page "https://github.com/Kingsford-Group/libgff")
-- 
cgit v1.2.3


From 2b773a9273882b270306154223067a56e1e89e38 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 21:41:20 +0100
Subject: gnu: sra-tools: Fetch sources from git.

* gnu/packages/bioinformatics.scm (sra-tools)[source]: Fetch from git.
---
 gnu/packages/bioinformatics.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4682d26279..0bcfcd4dcf 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5654,14 +5654,14 @@ sequence itself can be retrieved from these databases.")
     (version "2.8.2-1")
     (source
      (origin
-       (method url-fetch)
-       (uri
-        (string-append "https://github.com/ncbi/sra-tools/archive/"
-                       version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/ncbi/sra-tools.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1camsijmvv2s45mb4iyf44ghl4gkd4rl0viphpcgl3ccchy32a0g"))))
+         "12ln0pk8yajhmmj9xsfwa1qgv5m05ji40jsg17wdcls62zz6fwrk"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-build? #f ; not supported
-- 
cgit v1.2.3


From ea68b3f6527cf4a02c554cf3f6f446e30f4940f6 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Wed, 7 Nov 2018 21:53:44 +0100
Subject: pull: Add missing monadic 'return'.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Fixes a regression introduced in
5f7dd092ca577a534067f577b8849ed06cabf970 where, upon completion, 'guix
pull' would fail (instead of printing the new/upgraded packages) with
ugly errors like:

  successfully built /gnu/store/…-profile.drv
  1 package in profile
  Backtrace:
  […]
  In guix/store.scm:
    1605:24  1 (run-with-store _ _ #:guile-for-build _ #:system _ # _)
  In unknown file:
	     0 (_ #<build-daemon 256.97 2476b40>)

  ERROR: Wrong type to apply: #t

Reported by thorwil on #guix.

* guix/scripts/pull.scm (build-and-install): Add missing 'return' when
DRY-RUN? is wrong.
---
 guix/scripts/pull.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/guix/scripts/pull.scm b/guix/scripts/pull.scm
index aff4f378be..dc83729911 100644
--- a/guix/scripts/pull.scm
+++ b/guix/scripts/pull.scm
@@ -177,7 +177,7 @@ true, display what would be built without actually building it."
       (update-profile profile manifest
                       #:dry-run? dry-run?)
       (munless dry-run?
-        (display-profile-news profile)))))
+        (return (display-profile-news profile))))))
 
 (define (honor-lets-encrypt-certificates! store)
   "Tell Guile-Git to use the Let's Encrypt certificates."
-- 
cgit v1.2.3


From b44b1f08f6945ea8370746cfdadb44c7dea9ea3e Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Wed, 7 Nov 2018 23:13:02 +0200
Subject: gnu: hplip: Remove bundled non-free blobs.

This fixes <https://bugs.gnu.org/32184>.

* gnu/packages/cups.scm (hplip)[source]: Add patch. Update snippet to
remove non-free code and binary blobs.
* gnu/packages/patches/hplip-remove-imageprocessor.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
---
 gnu/local.mk                                       |   1 +
 gnu/packages/cups.scm                              |   6 +-
 .../patches/hplip-remove-imageprocessor.patch      | 232 +++++++++++++++++++++
 3 files changed, 238 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/hplip-remove-imageprocessor.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 9a8330aa41..c627577e41 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -808,6 +808,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/higan-remove-march-native-flag.patch	\
   %D%/packages/patches/hubbub-sort-entities.patch		\
   %D%/packages/patches/hurd-fix-eth-multiplexer-dependency.patch        \
+  %D%/packages/patches/hplip-remove-imageprocessor.patch	\
   %D%/packages/patches/hydra-disable-darcs-test.patch		\
   %D%/packages/patches/icecat-avoid-bundled-libraries.patch	\
   %D%/packages/patches/icecat-CVE-2018-12383.patch		\
diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm
index 4259648c69..04a533de02 100644
--- a/gnu/packages/cups.scm
+++ b/gnu/packages/cups.scm
@@ -405,9 +405,13 @@ device-specific programs to convert and print many types of files.")
                (base32
                 "0g3q5mm2crjyc1z4z6gv4lam6sc5d3diz704djrnpqadk4q3h290"))
               (modules '((guix build utils)))
+              (patches (search-patches "hplip-remove-imageprocessor.patch"))
               (snippet
-               ;; Fix type mismatch.
                '(begin
+                  ;; Delete non-free blobs
+                  (for-each delete-file (find-files "." "\\.so$"))
+                  (delete-file "prnt/hpcups/ImageProcessor.h")
+                  ;; Fix type mismatch.
                   (substitute* "prnt/hpcups/genPCLm.cpp"
                     (("boolean") "bool"))
                   #t))))
diff --git a/gnu/packages/patches/hplip-remove-imageprocessor.patch b/gnu/packages/patches/hplip-remove-imageprocessor.patch
new file mode 100644
index 0000000000..cde3ecba2d
--- /dev/null
+++ b/gnu/packages/patches/hplip-remove-imageprocessor.patch
@@ -0,0 +1,232 @@
+This patch is based heavily on the Debian patch.
+
+https://salsa.debian.org/printing-team/hplip/raw/debian/3.18.10+dfsg0-1/debian/patches/0025-Remove-all-ImageProcessor-functionality-which-is-clo.patch
+
+---
+ Makefile.am                  | 22 +++-------------------
+ Makefile.in                  | 33 +++++----------------------------
+ prnt/hpcups/HPCupsFilter.cpp | 21 ---------------------
+ 3 files changed, 8 insertions(+), 68 deletions(-)
+
+diff --git a/Makefile.am b/Makefile.am
+index ef6480f..ecada5c 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -166,7 +166,7 @@ if !HPLIP_CLASS_DRIVER
+ dist_hplip_SCRIPTS = hpssd.py __init__.py hpdio.py
+ endif #HPLIP_CLASS_DRIVER
+ 
+-dist_noinst_DATA += prnt/drv/hpijs.drv.in.template prnt/drv/hpcups.drv.in.template prnt/hpcups/libImageProcessor-x86_64.so prnt/hpcups/libImageProcessor-x86_32.so
++dist_noinst_DATA += prnt/drv/hpijs.drv.in.template prnt/drv/hpcups.drv.in.template
+ dist_noinst_SCRIPTS += dat2drv.py install.py  hplip-install init-suse-firewall init-iptables-firewall class_rpm_build.sh hplipclassdriver.spec createPPD.sh Makefile_dat2drv hpijs-drv
+ 
+ if !HPLIP_CLASS_DRIVER
+@@ -590,11 +590,10 @@ hpcups_SOURCES = prnt/hpcups/HPCupsFilter.cpp prnt/hpcups/HPCupsFilter.h prnt/hp
+ 	prnt/hpcups/flate_colorspace.h prnt/hpcups/RunLenEncoding.h prnt/hpcups/common_defines.h \
+ 	prnt/hpcups/genPCLm.h \
+ 	common/utils.c common/utils.h prnt/hpcups/Hbpl1_Wrapper.cpp prnt/hpcups/genPCLm.cpp \
+-	prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp \
+-	prnt/hpcups/ImageProcessor.h
++	prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp
+ 
+ hpcups_CXXFLAGS = $(APDK_ENDIAN_FLAG) $(DBUS_CFLAGS)
+-hpcups_LDADD = -L./prnt/hpcups/ -ljpeg -ldl -lImageProcessor -lcups -lcupsimage -lz $(DBUS_LIBS)
++hpcups_LDADD = -L./prnt/hpcups/ -ljpeg -ldl -lcups -lcupsimage -lz $(DBUS_LIBS)
+ #else
+ #hpcupsdir = $(cupsfilterdir)
+ #hpcups_PROGRAMS = hpcups
+@@ -679,21 +678,10 @@ printpluginsdir=$(cupsfilterdir)
+ 
+ 
+ dist_filter_DATA = hpcups hpps dat2drv
+-dist_printplugins_DATA = prnt/plugins/hbpl1-arm32.so prnt/plugins/hbpl1-arm64.so prnt/plugins/hbpl1-x86_32.so prnt/plugins/hbpl1-x86_64.so prnt/plugins/lj-arm32.so prnt/plugins/lj-arm64.so prnt/plugins/lj-x86_32.so prnt/plugins/lj-x86_64.so
+ endif #HPLIP_CLASS_DRIVER
+ 
+ install-data-hook:
+ if HPLIP_BUILD
+-	if [ \( "$(UNAME)" = "x86_64" -a  -d "$(libdir)/" \) ]; then \
+-		cp prnt/hpcups/libImageProcessor-x86_64.so $(libdir)/ ; \
+-		chmod 775 $(libdir)/libImageProcessor-x86_64.so ; \
+-		ln -sf $(libdir)/libImageProcessor-x86_64.so $(libdir)/libImageProcessor.so ; \
+-	fi; \
+-	if [ \( \( "$(UNAME)" = "i686" -o "$(UNAME)" = "i386" \) -a -d "$(libdir)/" \) ]; then \
+-		cp prnt/hpcups/libImageProcessor-x86_32.so $(libdir)/ ; \
+-		chmod 775 $(libdir)/libImageProcessor-x86_32.so ; \
+-		ln -sf $(libdir)/libImageProcessor-x86_32.so $(libdir)/libImageProcessor.so ; \
+-	fi
+ if !HPLIP_CLASS_DRIVER
+ #	   If scanner build, add hpaio entry to sane dll.conf.
+ 	if [ "$(scan_build)" = "yes" ]; then \
+@@ -874,10 +862,6 @@ if HPLIP_CLASS_DRIVER
+ 	rm -rf $(distdir)/setup.py
+ 	rm -rf $(distdir)/systray.py
+ 	rm -rf $(distdir)/timedate.py
+-	rm -rf $(distdir)/prnt/plugins/lj-arm32.so
+-	rm -rf $(distdir)/prnt/plugins/lj-arm64.so
+-	rm -rf $(distdir)/prnt/plugins/lj-x86_32.so
+-	rm -rf $(distdir)/prnt/plugins/lj-x86_64.so
+ 	rm -rf $(distdir)/hpijs-drv
+ 	rm -rf $(distdir)/prnt/hpcups/
+ 	rm -rf $(distdir)/prnt/ps/
+diff --git a/Makefile.in b/Makefile.in
+index 910a268..cd44203 100644
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -103,7 +103,7 @@ DIST_COMMON = $(am__configure_deps) \
+ 
+ # ip library
+ @HPLIP_BUILD_TRUE@am__append_12 = libhpip.la
+-@FULL_BUILD_TRUE@@HPLIP_BUILD_TRUE@am__append_13 = prnt/drv/hpijs.drv.in.template prnt/drv/hpcups.drv.in.template prnt/hpcups/libImageProcessor-x86_64.so prnt/hpcups/libImageProcessor-x86_32.so
++@FULL_BUILD_TRUE@@HPLIP_BUILD_TRUE@am__append_13 = prnt/drv/hpijs.drv.in.template prnt/drv/hpcups.drv.in.template
+ @FULL_BUILD_TRUE@@HPLIP_BUILD_TRUE@am__append_14 = dat2drv.py install.py  hplip-install init-suse-firewall init-iptables-firewall class_rpm_build.sh hplipclassdriver.spec createPPD.sh Makefile_dat2drv hpijs-drv
+ @FULL_BUILD_TRUE@@HPLIP_BUILD_TRUE@@HPLIP_CLASS_DRIVER_FALSE@am__append_15 = scan/sane/hpaio.desc \
+ @FULL_BUILD_TRUE@@HPLIP_BUILD_TRUE@@HPLIP_CLASS_DRIVER_FALSE@	installer/text_install.py \
+@@ -500,8 +500,7 @@ am__hpcups_SOURCES_DIST = prnt/hpcups/HPCupsFilter.cpp \
+ 	prnt/hpcups/RunLenEncoding.h prnt/hpcups/common_defines.h \
+ 	prnt/hpcups/genPCLm.h common/utils.c common/utils.h \
+ 	prnt/hpcups/Hbpl1_Wrapper.cpp prnt/hpcups/genPCLm.cpp \
+-	prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp \
+-	prnt/hpcups/ImageProcessor.h
++	prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp
+ @HPCUPS_INSTALL_TRUE@am_hpcups_OBJECTS =  \
+ @HPCUPS_INSTALL_TRUE@	hpcups-HPCupsFilter.$(OBJEXT) \
+ @HPCUPS_INSTALL_TRUE@	hpcups-dbuscomm.$(OBJEXT) \
+@@ -723,8 +722,7 @@ am__dist_locatedriver_DATA_DIST = locatedriver
+ am__dist_models_DATA_DIST = data/models/models.dat
+ am__dist_noinst_DATA_DIST = prnt/drv/hpijs.drv.in.template \
+ 	prnt/drv/hpcups.drv.in.template \
+-	prnt/hpcups/libImageProcessor-x86_64.so \
+-	prnt/hpcups/libImageProcessor-x86_32.so scan/sane/hpaio.desc \
++	scan/sane/hpaio.desc \
+ 	installer/text_install.py data/localization/hplip_de.ts \
+ 	data/localization/hplip_es.ts data/localization/hplip_fr.ts \
+ 	data/localization/hplip_it.ts data/localization/hplip_pt.ts \
+@@ -1932,11 +1930,6 @@ am__dist_ppd_DATA_DIST = prnt/ps/hp-designjet_z6810ps_42in-ps.ppd.gz \
+ 	ppd/classppd/ps/hp-postscript-inkjet.ppd.gz \
+ 	ppd/classppd/ps/hp-postscript-laserjet-pro.ppd.gz \
+ 	ppd/classppd/ps/hp-postscript-laserjet.ppd.gz
+-am__dist_printplugins_DATA_DIST = prnt/plugins/hbpl1-arm32.so \
+-	prnt/plugins/hbpl1-arm64.so prnt/plugins/hbpl1-x86_32.so \
+-	prnt/plugins/hbpl1-x86_64.so prnt/plugins/lj-arm32.so \
+-	prnt/plugins/lj-arm64.so prnt/plugins/lj-x86_32.so \
+-	prnt/plugins/lj-x86_64.so
+ am__dist_prnt_DATA_DIST = prnt/cups.py prnt/__init__.py prnt/ldl.py \
+ 	prnt/pcl.py prnt/colorcal.py
+ am__dist_rules_DATA_DIST = data/rules/56-hpmud.rules \
+@@ -4665,11 +4658,10 @@ libapdk_la_CFLAGS = $(libapdk_la_CXXFLAGS) -Iprnt/hpijs
+ @HPCUPS_INSTALL_TRUE@	prnt/hpcups/flate_colorspace.h prnt/hpcups/RunLenEncoding.h prnt/hpcups/common_defines.h \
+ @HPCUPS_INSTALL_TRUE@	prnt/hpcups/genPCLm.h \
+ @HPCUPS_INSTALL_TRUE@	common/utils.c common/utils.h prnt/hpcups/Hbpl1_Wrapper.cpp prnt/hpcups/genPCLm.cpp \
+-@HPCUPS_INSTALL_TRUE@	prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp \
+-@HPCUPS_INSTALL_TRUE@	prnt/hpcups/ImageProcessor.h
++@HPCUPS_INSTALL_TRUE@	prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp
+ 
+ @HPCUPS_INSTALL_TRUE@hpcups_CXXFLAGS = $(APDK_ENDIAN_FLAG) $(DBUS_CFLAGS)
+-@HPCUPS_INSTALL_TRUE@hpcups_LDADD = -L./prnt/hpcups/ -ljpeg -ldl -lImageProcessor -lcups -lcupsimage -lz $(DBUS_LIBS)
++@HPCUPS_INSTALL_TRUE@hpcups_LDADD = -L./prnt/hpcups/ -ljpeg -ldl -lcups -lcupsimage -lz $(DBUS_LIBS)
+ #else
+ #hpcupsdir = $(cupsfilterdir)
+ #hpcups_PROGRAMS = hpcups
+@@ -4717,7 +4709,6 @@ ppddir = $(hpppddir)
+ @HPLIP_CLASS_DRIVER_TRUE@filterdir = $(cupsfilterdir)
+ @HPLIP_CLASS_DRIVER_TRUE@printpluginsdir = $(cupsfilterdir)
+ @HPLIP_CLASS_DRIVER_TRUE@dist_filter_DATA = hpcups hpps dat2drv
+-@HPLIP_CLASS_DRIVER_TRUE@dist_printplugins_DATA = prnt/plugins/hbpl1-arm32.so prnt/plugins/hbpl1-arm64.so prnt/plugins/hbpl1-x86_32.so prnt/plugins/hbpl1-x86_64.so prnt/plugins/lj-arm32.so prnt/plugins/lj-arm64.so prnt/plugins/lj-x86_32.so prnt/plugins/lj-x86_64.so
+ all: all-am
+ 
+ .SUFFIXES:
+@@ -9380,16 +9371,6 @@ uninstall-am: uninstall-apparmor_abstractionDATA \
+ 
+ 
+ install-data-hook:
+-@HPLIP_BUILD_TRUE@	if [ \( "$(UNAME)" = "x86_64" -a  -d "$(libdir)/" \) ]; then \
+-@HPLIP_BUILD_TRUE@		cp prnt/hpcups/libImageProcessor-x86_64.so $(libdir)/ ; \
+-@HPLIP_BUILD_TRUE@		chmod 775 $(libdir)/libImageProcessor-x86_64.so ; \
+-@HPLIP_BUILD_TRUE@		ln -sf $(libdir)/libImageProcessor-x86_64.so $(libdir)/libImageProcessor.so ; \
+-@HPLIP_BUILD_TRUE@	fi; \
+-@HPLIP_BUILD_TRUE@	if [ \( \( "$(UNAME)" = "i686" -o "$(UNAME)" = "i386" \) -a -d "$(libdir)/" \) ]; then \
+-@HPLIP_BUILD_TRUE@		cp prnt/hpcups/libImageProcessor-x86_32.so $(libdir)/ ; \
+-@HPLIP_BUILD_TRUE@		chmod 775 $(libdir)/libImageProcessor-x86_32.so ; \
+-@HPLIP_BUILD_TRUE@		ln -sf $(libdir)/libImageProcessor-x86_32.so $(libdir)/libImageProcessor.so ; \
+-@HPLIP_BUILD_TRUE@	fi
+ #	   If scanner build, add hpaio entry to sane dll.conf.
+ @HPLIP_BUILD_TRUE@@HPLIP_CLASS_DRIVER_FALSE@	if [ "$(scan_build)" = "yes" ]; then \
+ @HPLIP_BUILD_TRUE@@HPLIP_CLASS_DRIVER_FALSE@	   $(mkinstalldirs) $(DESTDIR)/etc/sane.d; \
+@@ -9556,10 +9537,6 @@ dist-hook:
+ @HPLIP_CLASS_DRIVER_TRUE@	rm -rf $(distdir)/setup.py
+ @HPLIP_CLASS_DRIVER_TRUE@	rm -rf $(distdir)/systray.py
+ @HPLIP_CLASS_DRIVER_TRUE@	rm -rf $(distdir)/timedate.py
+-@HPLIP_CLASS_DRIVER_TRUE@	rm -rf $(distdir)/prnt/plugins/lj-arm32.so
+-@HPLIP_CLASS_DRIVER_TRUE@	rm -rf $(distdir)/prnt/plugins/lj-arm64.so
+-@HPLIP_CLASS_DRIVER_TRUE@	rm -rf $(distdir)/prnt/plugins/lj-x86_32.so
+-@HPLIP_CLASS_DRIVER_TRUE@	rm -rf $(distdir)/prnt/plugins/lj-x86_64.so
+ @HPLIP_CLASS_DRIVER_TRUE@	rm -rf $(distdir)/hpijs-drv
+ @HPLIP_CLASS_DRIVER_TRUE@	rm -rf $(distdir)/prnt/hpcups/
+ @HPLIP_CLASS_DRIVER_TRUE@	rm -rf $(distdir)/prnt/ps/
+diff --git a/prnt/hpcups/HPCupsFilter.cpp b/prnt/hpcups/HPCupsFilter.cpp
+index 5b282d8..0bacfaf 100644
+--- a/prnt/hpcups/HPCupsFilter.cpp
++++ b/prnt/hpcups/HPCupsFilter.cpp
+@@ -31,7 +31,6 @@
+ \*****************************************************************************/
+ 
+ #include "HPCupsFilter.h"
+-#include "ImageProcessor.h"
+ 
+ #include <signal.h>
+ #include <sys/wait.h>
+@@ -637,16 +636,10 @@ int HPCupsFilter::processRasterData(cups_raster_t *cups_raster)
+ 
+ 
+     sprintf(hpPreProcessedRasterFile, "%s/hp_%s_cups_SwapedPagesXXXXXX",CUPS_TMP_DIR, m_JA.user_name);
+-    image_processor_t* imageProcessor = imageProcessorCreate();
+ 
+     while (cupsRasterReadHeader2(cups_raster, &cups_header))
+     {
+ 
+-        IMAGE_PROCESSOR_ERROR result = imageProcessorStartPage(imageProcessor, &cups_header);
+-        if (result != IPE_SUCCESS){
+-            dbglog("DEBUG: imageProcessorStartPage failed result = %d\n", result);
+-        }
+-
+         current_page_number++;
+ 
+         if (current_page_number == 1) {
+@@ -745,12 +738,6 @@ int HPCupsFilter::processRasterData(cups_raster_t *cups_raster)
+             color_raster = rgbRaster;
+             black_raster = kRaster;
+ 
+-            result = imageProcessorProcessLine(imageProcessor, m_pPrinterBuffer, cups_header.cupsBytesPerLine);
+-            if (result != IPE_SUCCESS){
+-                dbglog("DEBUG: imageProcessorProcessLine failed result = %d\n", result);
+-            }
+-
+-
+             if ((y == 0) && !is_ljmono) {
+                 //For ljmono, make sure that first line is not a blankRaster line.Otherwise printer
+                 //may not skip blank lines before actual data
+@@ -780,12 +767,6 @@ int HPCupsFilter::processRasterData(cups_raster_t *cups_raster)
+             }
+         }  // for() loop end
+ 
+-        result = imageProcessorEndPage(imageProcessor);
+-        if (result != IPE_SUCCESS){
+-                dbglog("DEBUG: imageProcessorEndPage failed result = %d\n", result);
+-        }
+-
+-
+         m_Job.NewPage();
+         if (err != NO_ERROR) {
+             break;
+@@ -800,8 +781,6 @@ int HPCupsFilter::processRasterData(cups_raster_t *cups_raster)
+         rgbRaster = NULL;
+     }
+ 
+-    imageProcessorDestroy(imageProcessor);
+-
+     unlink(hpPreProcessedRasterFile);
+     return ret_status;
+ }
+-- 
+2.19.1
+
-- 
cgit v1.2.3


From 5e242b02c37e8c5189a52136a32067bca0767082 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 22:17:58 +0100
Subject: gnu: pyicoteo: Fetch sources from git.

* gnu/packages/bioinformatics.scm (pyicoteo)[source]: Fetch from git.
---
 gnu/packages/bioinformatics.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0bcfcd4dcf..9217a58154 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4670,13 +4670,14 @@ large-scale data and can be applied to hundreds of species at once.")
     (version "2.0.7")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://bitbucket.org/regulatorygenomicsupf/"
-                           "pyicoteo/get/v" version ".tar.bz2"))
-       (file-name (string-append name "-" version ".tar.bz2"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://bitbucket.org/regulatorygenomicsupf/pyicoteo.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa"))))
+         "0hz5g8d25lbjy1wpscr490l0lmyvaix893hhax4fxnh1h9w34w8p"))))
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2 ; does not work with Python 3
-- 
cgit v1.2.3


From 4715d4af171bed48c60dd6d40ea2d4a0688d4f8a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 22:24:34 +0100
Subject: gnu: raxml: Fetch sources from git.

* gnu/packages/bioinformatics.scm (raxml)[source]: Fetch from git.
---
 gnu/packages/bioinformatics.scm | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9217a58154..fa8d873b49 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4856,15 +4856,14 @@ extremely diverse sets of genomes.")
     (version "8.2.10")
     (source
      (origin
-       (method url-fetch)
-       (uri
-        (string-append
-         "https://github.com/stamatak/standard-RAxML/archive/v"
-         version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/stamatak/standard-RAxML.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "13s7aspfdcfr6asynwdg1x6vznys6pzap5f8wsffbnnwpkkg9ya8"))))
+         "1crf5xwchzlals3ypgb9gkm3yzllfp6bn571abdjc21q8c4x7v7k"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; There are no tests.
-- 
cgit v1.2.3


From d9ba126d17b98fbfb5fd68e63375232d2a5120d6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 22:25:13 +0100
Subject: gnu: python2-biom-format: Fix build.

This is a follow-up to commit 239716fb0ba0a7cd81f9d59dcf5a2261b8efe4fa.

* gnu/packages/bioinformatics.scm (python2-biom-format)[arguments]: Modify
phases of base package.
---
 gnu/packages/bioinformatics.scm | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fa8d873b49..d212d2e8b8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -753,15 +753,15 @@ e.g. microbiome samples, genomes, metagenomes.")
     (package
       (inherit base)
       (arguments
-       `(#:phases
-         (modify-phases %standard-phases
-           ;; Do not require the unmaintained pyqi library.
-           (add-after 'unpack 'remove-pyqi
-             (lambda _
-               (substitute* "setup.py"
-                 (("install_requires.append\\(\"pyqi\"\\)") "pass"))
-               #t)))
-         ,@(package-arguments base))))))
+       (substitute-keyword-arguments (package-arguments base)
+         ((#:phases phases)
+          `(modify-phases ,phases
+             ;; Do not require the unmaintained pyqi library.
+             (add-after 'unpack 'remove-pyqi
+               (lambda _
+                 (substitute* "setup.py"
+                   (("install_requires.append\\(\"pyqi\"\\)") "pass"))
+                 #t)))))))))
 
 (define-public bioperl-minimal
   (let* ((inputs `(("perl-module-build" ,perl-module-build)
-- 
cgit v1.2.3


From b9d0c3564b279c6bfbbd3d9bf3f3ffcf5d161440 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 22:26:19 +0100
Subject: gnu: raxml: Update to 8.2.12.

* gnu/packages/bioinformatics.scm (raxml): Update to 8.2.12.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d212d2e8b8..a5554aed7f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4853,7 +4853,7 @@ extremely diverse sets of genomes.")
 (define-public raxml
   (package
     (name "raxml")
-    (version "8.2.10")
+    (version "8.2.12")
     (source
      (origin
        (method git-fetch)
@@ -4863,7 +4863,7 @@ extremely diverse sets of genomes.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1crf5xwchzlals3ypgb9gkm3yzllfp6bn571abdjc21q8c4x7v7k"))))
+         "1jqjzhch0rips0vp04prvb8vmc20c5pdmsqn8knadcf91yy859fh"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; There are no tests.
-- 
cgit v1.2.3


From 019fcdf20af9de5860d7005fe5fb7adef222ce59 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 22:33:06 +0100
Subject: gnu: seqtk: Fetch sources from git.

* gnu/packages/bioinformatics.scm (seqtk)[source]: Fetch from git.
---
 gnu/packages/bioinformatics.scm | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a5554aed7f..b98be8eb51 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5870,15 +5870,15 @@ is one that takes arguments.")
     (name "seqtk")
     (version "1.2")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/lh3/seqtk/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/lh3/seqtk.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0ywdyzpmfiz2wp6ampbzqg4y8bj450nfgqarpamg045b8mk32lxx"))
-                            (modules '((guix build utils)))
+                "1mdkgmzdy734a0na9hxbl4k41jjkm87bvjbm7bdbh50fsra86f93"))
+              (modules '((guix build utils)))
               (snippet
                '(begin
                   ;; Remove extraneous header files, as is done in the seqtk
-- 
cgit v1.2.3


From 63f3255e13be8d1352031c78a37131c2c6644bdb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 22:34:41 +0100
Subject: gnu: seqtk: Update to 1.3.

* gnu/packages/bioinformatics.scm (seqtk): Update to 1.3.
[source]: Remove outdated snippet.
[arguments]: Use INVOKE and return #T unconditionally.
---
 gnu/packages/bioinformatics.scm | 17 +++++------------
 1 file changed, 5 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b98be8eb51..670bea5cd4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5868,7 +5868,7 @@ is one that takes arguments.")
 (define-public seqtk
   (package
     (name "seqtk")
-    (version "1.2")
+    (version "1.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -5877,15 +5877,7 @@ is one that takes arguments.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1mdkgmzdy734a0na9hxbl4k41jjkm87bvjbm7bdbh50fsra86f93"))
-              (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  ;; Remove extraneous header files, as is done in the seqtk
-                  ;; master branch.
-                  (for-each (lambda (file) (delete-file file))
-                            (list "ksort.h" "kstring.h" "kvec.h"))
-                  #t))))
+                "1bfzlqa84b5s1qi22blmmw2s8xdyp9h9ydcq22pfjhh5gab3yz6l"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -5893,11 +5885,12 @@ is one that takes arguments.")
          (delete 'configure)
          (replace 'check
            ;; There are no tests, so we just run a sanity check.
-           (lambda _ (zero? (system* "./seqtk" "seq"))))
+           (lambda _ (invoke "./seqtk" "seq") #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
-               (install-file "seqtk" bin)))))))
+               (install-file "seqtk" bin)
+               #t))))))
     (inputs
      `(("zlib" ,zlib)))
     (home-page "https://github.com/lh3/seqtk")
-- 
cgit v1.2.3


From 37e285be43dcbbb060d07132884b23f597a20b94 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 22:38:53 +0100
Subject: gnu: preseq: Fetch sources from git.

* gnu/packages/bioinformatics.scm (preseq)[source]: Fetch from git.
---
 gnu/packages/bioinformatics.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 670bea5cd4..82a4cbd9ec 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5556,12 +5556,13 @@ structures, classes for genomic regions, mapped sequencing reads, etc.")
     (name "preseq")
     (version "2.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/smithlabcode/"
-                                  "preseq/archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/smithlabcode/preseq.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
-               (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq"))
+               (base32 "09mwj7x3zavnk1j6cax66madxgfaxjpq4c11mf93lsgg7z46znkm"))
               (modules '((guix build utils)))
               (snippet '(begin
                           ;; Remove bundled samtools.
-- 
cgit v1.2.3


From 67caa4b7730da1450d49cbf8b6ac4f87de9ef60f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 22:42:21 +0100
Subject: gnu: preseq: Update to 2.0.3.

* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.3.
---
 gnu/packages/bioinformatics.scm | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 82a4cbd9ec..d761d164b5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5554,15 +5554,14 @@ structures, classes for genomic regions, mapped sequencing reads, etc.")
 (define-public preseq
   (package
     (name "preseq")
-    (version "2.0")
+    (version "2.0.3")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/smithlabcode/preseq.git")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
+              (method url-fetch)
+              (uri (string-append "https://github.com/smithlabcode/preseq/"
+                                  "releases/download/v" version
+                                  "/preseq_v" version ".tar.bz2"))
               (sha256
-               (base32 "09mwj7x3zavnk1j6cax66madxgfaxjpq4c11mf93lsgg7z46znkm"))
+               (base32 "149x9xmk1wy1gff85325yfzqc0qk4sgp1w6gbyj9cnji4x1dszbl"))
               (modules '((guix build utils)))
               (snippet '(begin
                           ;; Remove bundled samtools.
-- 
cgit v1.2.3


From 273df99d7d986c4417940d423c649aec727c744e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 22:46:48 +0100
Subject: gnu: vsearch: Fetch source from git.

* gnu/packages/bioinformatics.scm (vsearch)[source]: Fetch from git.
---
 gnu/packages/bioinformatics.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d761d164b5..744eec571e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6838,14 +6838,14 @@ SELECT or UPDATE queries to an end-point.")
     (version "2.8.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://github.com/torognes/vsearch/archive/v"
-             version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/torognes/vsearch.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "15pbirgzhvflj4pi5n82vybbzjy9mlb0lv5l3qhrmdkfzpbyahw3"))
+         "0lrw6n75gmqkxl053yi2pwwvnzwf1r79ypzxgv6m0kw6df5fwv6r"))
        (patches (search-patches "vsearch-unbundle-cityhash.patch"))
        (snippet
         '(begin
-- 
cgit v1.2.3


From 62365244092576f62931e3178c4ea5598fd91e7b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 23:02:55 +0100
Subject: gnu: sortmerna: Fetch sources from git.

* gnu/packages/bioinformatics.scm (sortmerna)[source]: Fetch from git.
---
 gnu/packages/bioinformatics.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 744eec571e..a571d72bb5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5948,14 +5948,14 @@ of these reads to align data quickly through a hash-based indexing scheme.")
     (version "2.1b")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://github.com/biocore/sortmerna/archive/"
-             version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/biocore/sortmerna.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk"))))
+         "0j3mbz4n25738yijmjbr5r4fyvkgm8v5vn3sshyfvmyqf5q9byqf"))))
     (build-system gnu-build-system)
     (outputs '("out"      ;for binaries
                "db"))     ;for sequence databases
-- 
cgit v1.2.3


From e0a8fc85dd1ee9e9ceef790b311691068a664a28 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 23:06:28 +0100
Subject: gnu: snap-aligner: Fetch sources from git.

* gnu/packages/bioinformatics.scm (snap-aligner)[source]: Fetch from git.
[arguments]: Use INVOKE.
---
 gnu/packages/bioinformatics.scm | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a571d72bb5..3d230a1036 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5906,20 +5906,20 @@ optionally compressed by gzip.")
     (name "snap-aligner")
     (version "1.0beta.18")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/amplab/snap/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/amplab/snap.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly"))))
+                "01w3qq4wm07z73vky0cfwlmrbf50n3w722cxrlzxfi99mnb808d8"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
        (modify-phases %standard-phases
          (delete 'configure)
-         (replace 'check (lambda _ (zero? (system* "./unit_tests"))))
+         (replace 'check (lambda _ (invoke "./unit_tests") #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
-- 
cgit v1.2.3


From 7145f4e519d47ad0a02f320be38d135d96e74792 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 23:10:31 +0100
Subject: gnu: ritornello: Fetch sources from git.

* gnu/packages/bioinformatics.scm (ritornello)[source]: Fetch from git.
---
 gnu/packages/bioinformatics.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3d230a1036..fa455c5125 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11258,14 +11258,14 @@ sort, markdup, and depth.")
     (name "ritornello")
     (version "1.0.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/KlugerLab/"
-                                  "Ritornello/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/KlugerLab/Ritornello.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "02nik86gq9ljjriv6pamwlmqnfky3ads1fpklx6mc3hx6k40pg38"))))
+                "1xpki1pkxwmn7n5n23vv64zvikss4fj53vlzhnp3j34wrmxik3h8"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; there are no tests
-- 
cgit v1.2.3


From 3b888065da0480a9c716929230bd1ffdb82c7e2f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 23:12:08 +0100
Subject: gnu: ritornello: Update to 2.0.1.

* gnu/packages/bioinformatics.scm (ritornello): Update to 2.0.1.
[arguments]: Adjust file patching.
---
 gnu/packages/bioinformatics.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fa455c5125..64b7dd2586 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11256,7 +11256,7 @@ sort, markdup, and depth.")
 (define-public ritornello
   (package
     (name "ritornello")
-    (version "1.0.0")
+    (version "2.0.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -11265,7 +11265,7 @@ sort, markdup, and depth.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1xpki1pkxwmn7n5n23vv64zvikss4fj53vlzhnp3j34wrmxik3h8"))))
+                "1xahvq215qld7x1w8vpa5zbrsj6p9crb9shqa2x89sb0aaxa02jk"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; there are no tests
@@ -11274,7 +11274,7 @@ sort, markdup, and depth.")
          (add-after 'unpack 'patch-samtools-references
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* '("src/SamStream.h"
-                            "src/BufferedGenomeReader.h")
+                            "src/FLD.cpp")
                (("<sam.h>") "<samtools/sam.h>"))
              #t))
          (delete 'configure)
-- 
cgit v1.2.3


From f3f34b132cdbf830e2233f448f0268f3ad529c5f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 23:15:58 +0100
Subject: gnu: filevercmp: Fetch sources from git.

* gnu/packages/bioinformatics.scm (filevercmp)[source]: Fetch from git.
[arguments]: Add #T to the end of the install phase.
---
 gnu/packages/bioinformatics.scm | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 64b7dd2586..0c2e0b50c1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9212,12 +9212,14 @@ group or two ChIP groups run under different conditions.")
       (name "filevercmp")
       (version (string-append "0-1." (string-take commit 7)))
       (source (origin
-        (method url-fetch)
-        (uri (string-append "https://github.com/ekg/filevercmp/archive/"
-                            commit ".tar.gz"))
-        (file-name (string-append name "-" version ".tar.gz"))
-        (sha256
-         (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/ekg/filevercmp.git")
+                      (commit commit)))
+                (file-name (git-file-name name commit))
+                (sha256
+                 (base32
+                  "1j9vxsy0y050v59h0q1d6501fcw1kjvj0d18l1xk2zyg0jzj247c"))))
       (build-system gnu-build-system)
       (arguments
        `(#:tests? #f ; There are no tests to run.
@@ -9227,7 +9229,8 @@ group or two ChIP groups run under different conditions.")
            (replace 'install
              (lambda* (#:key outputs #:allow-other-keys)
                (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
-                 (install-file "filevercmp" bin)))))))
+                 (install-file "filevercmp" bin)
+                 #t))))))
       (home-page "https://github.com/ekg/filevercmp")
       (synopsis "This program compares version strings")
       (description "This program compares version strings.  It intends to be a
-- 
cgit v1.2.3


From e2f36385d3b31086f88a5c1bbb26daddbf70fe64 Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Wed, 7 Nov 2018 10:23:18 -0500
Subject: gnu: Add spread-sheet-widget.

* gnu/packages/gtk.scm (spread-sheet-widget): New public variable.
---
 gnu/packages/gtk.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index 8c25922c9e..640bd75da4 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -1630,6 +1630,33 @@ it does not deal with windowing system surfaces, drawing, scene graphs, or
 input.")
     (license license:expat)))
 
+(define-public spread-sheet-widget
+  (package
+    (name "spread-sheet-widget")
+    (version "0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://alpha.gnu.org/gnu/ssw/"
+                           name "-" version ".tar.gz"))
+       (sha256
+        (base32 "1h93yyh2by6yrmkwqg38nd5knids05k5nqzcihc1hdwgzg3c4b8y"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("glib" ,glib "bin") ; for glib-genmarshal, etc.
+       ("pkg-config" ,pkg-config)))
+    ;; In 'Requires' of spread-sheet-widget.pc.
+    (propagated-inputs
+     `(("glib" ,glib)
+       ("gtk+" ,gtk+)))
+    (home-page "https://www.gnu.org/software/ssw/")
+    (synopsis "Gtk+ widget for dealing with 2-D tabular data")
+    (description
+     "GNU Spread Sheet Widget is a library for Gtk+ which provides a widget for
+viewing and manipulating 2 dimensional tabular data in a manner similar to many
+popular spread sheet programs.")
+    (license license:gpl3+)))
+
 (define-public yad
   (package
     (name "yad")
-- 
cgit v1.2.3


From ed33049cdc4231baa35de4197646a7117d4082df Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Wed, 7 Nov 2018 10:24:53 -0500
Subject: gnu: pspp: Update to 1.2.0.

* gnu/packages/statistics.scm (pspp): Update to 1.2.0.
[inputs]: Add spread-sheet-widget.
[native-inputs]: Add autoconf, python-2, and texinfo.
---
 gnu/packages/statistics.scm | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 258daeac19..642fa2d423 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -39,6 +39,7 @@
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)
+  #:use-module (gnu packages autotools)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
@@ -75,7 +76,7 @@
 (define-public pspp
   (package
     (name "pspp")
-    (version "1.0.1")
+    (version "1.2.0")
     (source
      (origin
       (method url-fetch)
@@ -83,7 +84,7 @@
                           version ".tar.gz"))
       (sha256
        (base32
-        "1r8smr5057993h90nx0mdnff8nxw9x546zzh6qpy4h3xblp1la5s"))))
+        "07pp27zycrb5x927jwaj9r3q7hy915jh51xs85zxby6gfiwl63m5"))))
     (build-system gnu-build-system)
     (inputs
      `(("cairo" ,cairo)
@@ -94,11 +95,15 @@
        ("readline" ,readline)
        ("gtk" ,gtk+)
        ("gtksourceview" ,gtksourceview)
+       ("spread-sheet-widget" ,spread-sheet-widget)
        ("zlib" ,zlib)))
     (native-inputs
-     `(("glib" ,glib "bin")             ;for glib-genmarshal
+     `(("autoconf" ,autoconf)           ;for tests
+       ("glib" ,glib "bin")             ;for glib-genmarshal
        ("perl" ,perl)
-       ("pkg-config" ,pkg-config)))
+       ("pkg-config" ,pkg-config)
+       ("python" ,python-2)             ;for tests
+       ("texinfo" ,texinfo)))
     (home-page "https://www.gnu.org/software/pspp/")
     (synopsis "Statistical analysis")
     (description
-- 
cgit v1.2.3


From e0f1aa2d2b09d9baa69cd6b69735671f694b1f8b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Nov 2018 23:28:10 +0100
Subject: gnu: tadbit: Fetch sources from git.

* gnu/packages/bioinformatics.scm (tadbit)[source]: Fetch from git.
[version]: Use "2.0.0" instead of "2.0".
---
 gnu/packages/bioinformatics.scm | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0c2e0b50c1..bbdecbff43 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11503,15 +11503,16 @@ applications for tackling some common problems in a user-friendly way.")
 (define-public tadbit
   (package
     (name "tadbit")
-    (version "0.2")
+    (version "0.2.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/3DGenomes/TADbit/"
-                                  "archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/3DGenomes/TADbit.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1cnfqrl4685zar4nnw94j94nhvl2h29jm448nadqi1h05z6fdk4f"))))
+                "07g3aj648prmsvxp9caz5yl41k0y0647vxh0f5p3w8376mfiljd0"))))
     (build-system python-build-system)
     (arguments
      `(;; Tests are included and must be run after installation, but
-- 
cgit v1.2.3


From 3398dfb764f309ad4d0cace5c80ae4c6b69b12f6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 08:34:01 +0100
Subject: gnu: ncbi-vdb: Fetch sources from git.

* gnu/packages/bioinformatics.scm (ncbi-vdb)[source]: Fetch from git.
[arguments]: Add phase to make checkout writable.
---
 gnu/packages/bioinformatics.scm | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bbdecbff43..6ef4adb305 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5303,22 +5303,23 @@ simultaneously.")
   (package
     (name "ncbi-vdb")
     (version "2.8.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri
-        (string-append "https://github.com/ncbi/ncbi-vdb/archive/"
-                       version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32
-         "1acn4bv81mfl137qnbn9995mjjhwd36pm0b7qli1iw5skrxa9j8m"))))
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/ncbi/ncbi-vdb.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1ssy5wlqdm86pmbv9mfdjx518lbsk32wfv2qgr7m1z77kaicw7zq"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-build? #f ; not supported
        #:tests? #f ; no "check" target
        #:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'make-files-writable
+           (lambda _ (for-each make-file-writable (find-files "." ".*")) #t))
          (add-before 'configure 'set-perl-search-path
            (lambda _
              ;; Work around "dotless @INC" build failure.
-- 
cgit v1.2.3


From 6a7d9ee39fe58184191f922f8add8c9a99a99caf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 08:34:42 +0100
Subject: gnu: ncbi-vdb: Use INVOKE and end phases on #T.

* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use INVOKE and
unconditionally end phases with #T.
---
 gnu/packages/bioinformatics.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6ef4adb305..0f28dfe37e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5353,8 +5353,7 @@ simultaneously.")
 
                ;; The 'configure' script doesn't recognize things like
                ;; '--enable-fast-install'.
-               (zero? (system*
-                       "./configure"
+               (invoke "./configure"
                        (string-append "--build-prefix=" (getcwd) "/build")
                        (string-append "--prefix=" (assoc-ref outputs "out"))
                        (string-append "--debug")
@@ -5363,7 +5362,8 @@ simultaneously.")
                        (string-append "--with-ngs-sdk-prefix="
                                       (assoc-ref inputs "ngs-sdk"))
                        (string-append "--with-hdf5-prefix="
-                                      (assoc-ref inputs "hdf5")))))))
+                                      (assoc-ref inputs "hdf5")))
+               #t)))
          (add-after 'install 'install-interfaces
            (lambda* (#:key outputs #:allow-other-keys)
              ;; Install interface libraries.  On i686 the interface libraries
-- 
cgit v1.2.3


From 4031e7f1ec1deac8ebf76c047b40b1ac4ffeaab2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 08:35:20 +0100
Subject: gnu: ngs-sdk: Fetch sources from git.

* gnu/packages/bioinformatics.scm (ngs-sdk)[source]: Fetch from git.
---
 gnu/packages/bioinformatics.scm | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0f28dfe37e..065f3adc11 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5237,16 +5237,15 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
   (package
     (name "ngs-sdk")
     (version "1.3.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri
-        (string-append "https://github.com/ncbi/ngs/archive/"
-                       version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32
-         "1wiyf4c6nm2j87pv015cbi0qny5byf3pbvcw3likifz5dl56ag40"))))
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/ncbi/ngs.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1l8p81azb9p6nsdfai0hvyai33z6nsgy7hj30arh9b5kb6m443dx"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-build? #f ; not supported
-- 
cgit v1.2.3


From c098c49b3e249011bfd81b3623608ee85fef879f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 08:42:15 +0100
Subject: gnu: sailfish: Fetch sources from git.

* gnu/packages/bioinformatics.scm (sailfish)[source]: Fetch from git.
---
 gnu/packages/bioinformatics.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 065f3adc11..aa2ae6c449 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11974,14 +11974,14 @@ bytes of memory space, where n is the length of the string.")
     (name "sailfish")
     (version "0.10.1")
     (source (origin
-              (method url-fetch)
-              (uri
-               (string-append "https://github.com/kingsfordgroup/"
-                              "sailfish/archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/kingsfordgroup/sailfish.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1inn60dxiwsz8g9w7kvfhjxj4bwfb0r12dyhpzzhfbig712dkmm0"))
+                "1amcc5hqvsl42hg4x19bi9vy47cl874s0lw1fmi0hwsdk9i8c03v"))
               (modules '((guix build utils)))
               (snippet
                '(begin
-- 
cgit v1.2.3


From e438c9655808c0c3f1a56b7c5a17954670fd365d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 08:58:46 +0100
Subject: gnu: fraggenescan: Use INVOKE.

* gnu/packages/bioinformatics.scm (fraggenescan)[arguments]: Use INVOKE in
build phases and return #T unconditionally.
---
 gnu/packages/bioinformatics.scm | 39 ++++++++++++++++++++++-----------------
 1 file changed, 22 insertions(+), 17 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index aa2ae6c449..e1ed7117f2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2716,8 +2716,10 @@ Illumina, Roche 454, and the SOLiD platform.")
                   (string-append "  strcpy(train_dir, \"" share "/train/\");"))))
              #t))
          (replace 'build
-           (lambda _ (and (zero? (system* "make" "clean"))
-                          (zero? (system* "make" "fgs")))))
+           (lambda _
+             (invoke "make" "clean")
+             (invoke "make" "fgs")
+             #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (string-append (assoc-ref outputs "out")))
@@ -2734,21 +2736,24 @@ Illumina, Roche 454, and the SOLiD platform.")
              (let* ((out (string-append (assoc-ref outputs "out")))
                     (bin (string-append out "/bin/"))
                     (frag (string-append bin "run_FragGeneScan.pl")))
-               (and (zero? (system* frag ; Test complete genome.
-                             "-genome=./example/NC_000913.fna"
-                             "-out=./test2"
-                             "-complete=1"
-                             "-train=complete"))
-                    (file-exists? "test2.faa")
-                    (file-exists? "test2.ffn")
-                    (file-exists? "test2.gff")
-                    (file-exists? "test2.out")
-                    (zero? (system* ; Test incomplete sequences.
-                            frag
-                            "-genome=./example/NC_000913-fgs.ffn"
-                            "-out=out"
-                            "-complete=0"
-                            "-train=454_30")))))))))
+               ;; Test complete genome.
+               (invoke frag
+                       "-genome=./example/NC_000913.fna"
+                       "-out=./test2"
+                       "-complete=1"
+                       "-train=complete")
+               (unless (and (file-exists? "test2.faa")
+                            (file-exists? "test2.ffn")
+                            (file-exists? "test2.gff")
+                            (file-exists? "test2.out"))
+                 (error "Expected files do not exist."))
+               ;; Test incomplete sequences.
+               (invoke frag
+                       "-genome=./example/NC_000913-fgs.ffn"
+                       "-out=out"
+                       "-complete=0"
+                       "-train=454_30")
+               #t))))))
     (inputs
      `(("perl" ,perl)
        ("python" ,python-2))) ;not compatible with python 3.
-- 
cgit v1.2.3


From c527d36f0250b9815507e4ac28c3d7cfb6b87b20 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 09:02:34 +0100
Subject: gnu: java-picard-1.113: Use INVOKE.

* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use INVOKE
and return #T unconditionally.
---
 gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++-----------------
 1 file changed, 19 insertions(+), 17 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e1ed7117f2..70597e2bcb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3476,26 +3476,28 @@ VCF.")
            (lambda* (#:key inputs #:allow-other-keys)
              (mkdir-p "lib/jni")
              (mkdir-p "jdk-src")
-             (and (zero? (system* "tar" "--strip-components=1" "-C" "jdk-src"
-                                  "-xf" (assoc-ref inputs "jdk-src")))
-                  (zero? (system* "javah" "-jni"
-                                  "-classpath" "classes"
-                                  "-d" "lib/"
-                                  "net.sf.samtools.util.zip.IntelDeflater"))
-                  (with-directory-excursion "src/c/inteldeflater"
-                    (zero? (system* "gcc" "-I../../../lib" "-I."
-                                    (string-append "-I" (assoc-ref inputs "jdk")
-                                                   "/include/linux")
-                                    "-I../../../jdk-src/src/share/native/common/"
-                                    "-I../../../jdk-src/src/solaris/native/common/"
-                                    "-c" "-O3" "-fPIC" "IntelDeflater.c"))
-                    (zero? (system* "gcc" "-shared"
-                                    "-o" "../../../lib/jni/libIntelDeflater.so"
-                                    "IntelDeflater.o" "-lz" "-lstdc++"))))))
+             (invoke "tar" "--strip-components=1" "-C" "jdk-src"
+                     "-xf" (assoc-ref inputs "jdk-src"))
+             (invoke "javah" "-jni"
+                     "-classpath" "classes"
+                     "-d" "lib/"
+                     "net.sf.samtools.util.zip.IntelDeflater")
+             (with-directory-excursion "src/c/inteldeflater"
+               (invoke "gcc" "-I../../../lib" "-I."
+                       (string-append "-I" (assoc-ref inputs "jdk")
+                                      "/include/linux")
+                       "-I../../../jdk-src/src/share/native/common/"
+                       "-I../../../jdk-src/src/solaris/native/common/"
+                       "-c" "-O3" "-fPIC" "IntelDeflater.c")
+               (invoke "gcc" "-shared"
+                       "-o" "../../../lib/jni/libIntelDeflater.so"
+                       "IntelDeflater.o" "-lz" "-lstdc++"))
+             #t))
          ;; We can only build everything else after building the JNI library.
          (add-after 'build-jni 'build-rest
            (lambda* (#:key make-flags #:allow-other-keys)
-             (zero? (apply system* `("ant" "all" ,@make-flags)))))
+             (apply invoke `("ant" "all" ,@make-flags))
+             #t))
          (add-before 'build 'set-JAVA6_HOME
            (lambda _
              (setenv "JAVA6_HOME" (getenv "JAVA_HOME"))
-- 
cgit v1.2.3


From 31c41a8cfeb6c488cb60139ab809f6332a52679c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 09:04:34 +0100
Subject: gnu: vsearch: Remove custom autogen phase.

* gnu/packages/bioinformatics.scm (vsearch)[arguments]: Remove.
---
 gnu/packages/bioinformatics.scm | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 70597e2bcb..ff6cd03b21 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6863,11 +6863,6 @@ SELECT or UPDATE queries to an end-point.")
            (delete-file "src/city.cc")
            #t))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autogen
-           (lambda _ (zero? (system* "autoreconf" "-vif")))))))
     (inputs
      `(("zlib" ,zlib)
        ("bzip2" ,bzip2)
-- 
cgit v1.2.3


From e35dce017090685d07aedf10c9899c0cdcc70d9e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 09:10:20 +0100
Subject: gnu: mash: Remove custom autoconf phase.

* gnu/packages/bioinformatics.scm (mash)[arguments]: Remove autoconf phase.
---
 gnu/packages/bioinformatics.scm | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ff6cd03b21..91f87a759e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4018,9 +4018,7 @@ sequences).")
                             "src/mash/CommandScreen.cpp")
                (("^#include \"kseq\\.h\"")
                 "#include \"htslib/kseq.h\""))
-             #t))
-         (add-after 'fix-includes 'autoconf
-           (lambda _ (zero? (system* "autoconf")))))))
+             #t)))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ;; Capnproto and htslib are statically embedded in the final
-- 
cgit v1.2.3


From 0881d62f2528187420ea049200138d15984d6c05 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 09:10:58 +0100
Subject: gnu: newick-utils: Remove custom autoconf phase.

* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Remove.
---
 gnu/packages/bioinformatics.scm | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 91f87a759e..8b1170fd47 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4266,11 +4266,6 @@ program for nucleotide and protein sequences.")
                  (base32
                   "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb"))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoconf
-           (lambda _ (zero? (system* "autoreconf" "-vif")))))))
     (inputs
      ;; XXX: TODO: Enable Lua and Guile bindings.
      ;; https://github.com/tjunier/newick_utils/issues/13
-- 
cgit v1.2.3


From 179416467fce3b66fa4746e3ed92795b27e1f192 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 09:11:38 +0100
Subject: gnu: muscle: Use INVOKE.

* gnu/packages/bioinformatics.scm (muscle)[arguments]: Use INVOKE and
return #T unconditionally.
---
 gnu/packages/bioinformatics.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8b1170fd47..b453b46873 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4236,12 +4236,13 @@ that a read originated from a particular isoform.")
          (delete 'configure)
          (replace 'check
            ;; There are no tests, so just test if it runs.
-           (lambda _ (zero? (system* "./muscle" "-version"))))
+           (lambda _ (invoke "./muscle" "-version") #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
                     (bin (string-append out "/bin")))
-               (install-file "muscle" bin)))))))
+               (install-file "muscle" bin)
+               #t))))))
     (home-page "http://www.drive5.com/muscle")
     (synopsis "Multiple sequence alignment program")
     (description
-- 
cgit v1.2.3


From 2e2d88539ceb52369c0f20566786603f4d368c94 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 09:12:43 +0100
Subject: gnu: sra-tools: Use INVOKE.

* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use INVOKE and
return #T unconditionally.
---
 gnu/packages/bioinformatics.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b453b46873..2947b51d03 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5712,8 +5712,7 @@ sequence itself can be retrieved from these databases.")
 
              ;; The 'configure' script doesn't recognize things like
              ;; '--enable-fast-install'.
-             (zero? (system*
-                     "./configure"
+             (invoke "./configure"
                      (string-append "--build-prefix=" (getcwd) "/build")
                      (string-append "--prefix=" (assoc-ref outputs "out"))
                      (string-append "--debug")
@@ -5731,7 +5730,8 @@ sequence itself can be retrieved from these databases.")
                      (string-append "--with-ngs-sdk-prefix="
                                     (assoc-ref inputs "ngs-sdk"))
                      (string-append "--with-hdf5-prefix="
-                                    (assoc-ref inputs "hdf5"))))))
+                                    (assoc-ref inputs "hdf5")))
+             #t))
          ;; This version of sra-tools fails to build with glibc because of a
          ;; naming conflict.  glibc-2.25/include/bits/mathcalls.h already
          ;; contains a definition of "canonicalize", so we rename it.
-- 
cgit v1.2.3


From 8b685c47200ad146632cb452aea2dc9f077d882b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 09:13:35 +0100
Subject: gnu: taxtastic: Use INVOKE.

* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Use INVOKE and
return #T unconditionally.
---
 gnu/packages/bioinformatics.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2947b51d03..a3d37af78a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6202,8 +6202,7 @@ Cuffdiff or Ballgown programs.")
        #:phases
        (modify-phases %standard-phases
          (replace 'check
-           (lambda _
-             (zero? (system* "python" "-m" "unittest" "discover" "-v")))))))
+           (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t)))))
     (propagated-inputs
      `(("python-sqlalchemy" ,python2-sqlalchemy)
        ("python-decorator" ,python2-decorator)
-- 
cgit v1.2.3


From e78e54d029869f82fd13958b959ed549f73b7aa9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 09:14:09 +0100
Subject: gnu: emboss: Use INVOKE.

* gnu/packages/bioinformatics.scm (emboss)[arguments]: Use INVOKE and
return #T unconditionally.
---
 gnu/packages/bioinformatics.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a3d37af78a..eef42bc0f9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9034,7 +9034,7 @@ AM_CONDITIONAL(AMPNG, true)"))
                (("\\$\\(bindir\\)/embossupdate") ""))
              #t))
          (add-after 'disable-update-check 'autogen
-           (lambda _ (zero? (system* "autoreconf" "-vif")))))))
+           (lambda _ (invoke "autoreconf" "-vif") #t)))))
     (inputs
      `(("perl" ,perl)
        ("libpng" ,libpng)
-- 
cgit v1.2.3


From 3da3cedf76b4f19af5db5a6122a6d98f6fa7fa67 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 09:15:05 +0100
Subject: gnu: ngs-sdk: Use INVOKE.

* gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Use INVOKE and
return #T unconditionally.
---
 gnu/packages/bioinformatics.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index eef42bc0f9..c501736c4b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5262,9 +5262,10 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
 
                ;; The 'configure' script doesn't recognize things like
                ;; '--enable-fast-install'.
-               (zero? (system* "./configure"
-                               (string-append "--build-prefix=" (getcwd) "/build")
-                               (string-append "--prefix=" out))))))
+               (invoke "./configure"
+                       (string-append "--build-prefix=" (getcwd) "/build")
+                       (string-append "--prefix=" out))
+               #t)))
          (add-after 'unpack 'enter-dir
            (lambda _ (chdir "ngs-sdk") #t)))))
     (native-inputs `(("perl" ,perl)))
-- 
cgit v1.2.3


From 8d3eaa92623efab8af21bbf3002406c46197590f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 09:29:58 +0100
Subject: gnu: ngs-sdk: Update to 2.9.3.

* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.3.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c501736c4b..493f11f943 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5237,7 +5237,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
 (define-public ngs-sdk
   (package
     (name "ngs-sdk")
-    (version "1.3.0")
+    (version "2.9.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -5246,7 +5246,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1l8p81azb9p6nsdfai0hvyai33z6nsgy7hj30arh9b5kb6m443dx"))))
+                "17c0v1nah3g3d2ib5bbi0vhma1ghd6vb9xycavqsh64lhp840rk3"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-build? #f ; not supported
-- 
cgit v1.2.3


From 87408854ecd4e89961539d7091c72fd53ca59a20 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 09:30:16 +0100
Subject: gnu: ncbi-vdb: Update to 2.9.3.

* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.3.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 493f11f943..924b671712 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5303,7 +5303,7 @@ simultaneously.")
 (define-public ncbi-vdb
   (package
     (name "ncbi-vdb")
-    (version "2.8.2")
+    (version "2.9.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -5312,7 +5312,7 @@ simultaneously.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1ssy5wlqdm86pmbv9mfdjx518lbsk32wfv2qgr7m1z77kaicw7zq"))))
+                "1l4ny67nxwv1lagk9wwjbrgm7ln7adci6dnpc7k1yaln6shj0qpm"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-build? #f ; not supported
-- 
cgit v1.2.3


From b17333414ff75db6e909533b383171721d60702e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 09:30:59 +0100
Subject: gnu: plink-ng: Fetch sources from git.

* gnu/packages/bioinformatics.scm (plink-ng)[source]: Fetch from git.
---
 gnu/packages/bioinformatics.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 924b671712..057151be05 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5469,12 +5469,13 @@ subsequent visualization, annotation and storage of results.")
     (version "1.90b4")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/chrchang/plink-ng/archive/v"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/chrchang/plink-ng.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "09ixrds009aczjswxr2alcb774mksq5g0v78dgjjn1h4dky0kf9a"))))
+        (base32 "02npdwgkpfkdnhw819rhj5kw02a5k5m90b14zq9zzya4hyg929c0"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f ;no "check" target
-- 
cgit v1.2.3


From 15c9609482aa26bd179d1316dcf62f6292223c96 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 09:46:05 +0100
Subject: gnu: sra-tools: Update to 2.9.3.

* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.3.
[arguments]: Remove build phase patch-away-glibc-conflict.
---
 gnu/packages/bioinformatics.scm | 16 ++--------------
 1 file changed, 2 insertions(+), 14 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 057151be05..9954fcf20b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5654,7 +5654,7 @@ sequence itself can be retrieved from these databases.")
 (define-public sra-tools
   (package
     (name "sra-tools")
-    (version "2.8.2-1")
+    (version "2.9.3")
     (source
      (origin
        (method git-fetch)
@@ -5664,7 +5664,7 @@ sequence itself can be retrieved from these databases.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "12ln0pk8yajhmmj9xsfwa1qgv5m05ji40jsg17wdcls62zz6fwrk"))))
+         "0663gcdxkziwsmlznjxysb00621rllpbz6jwsfifq7z3dj3lwm8b"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-build? #f ; not supported
@@ -5733,18 +5733,6 @@ sequence itself can be retrieved from these databases.")
                                     (assoc-ref inputs "ngs-sdk"))
                      (string-append "--with-hdf5-prefix="
                                     (assoc-ref inputs "hdf5")))
-             #t))
-         ;; This version of sra-tools fails to build with glibc because of a
-         ;; naming conflict.  glibc-2.25/include/bits/mathcalls.h already
-         ;; contains a definition of "canonicalize", so we rename it.
-         ;;
-         ;; See upstream bug report:
-         ;; https://github.com/ncbi/sra-tools/issues/67
-         (add-after 'unpack 'patch-away-glibc-conflict
-           (lambda _
-             (substitute* "tools/bam-loader/bam.c"
-               (("canonicalize\\(" line)
-                (string-append "sra_tools_" line)))
              #t)))))
     (native-inputs `(("perl" ,perl)))
     (inputs
-- 
cgit v1.2.3


From 86c6928ea39aff622124030c20404ce94dae9b49 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 09:46:42 +0100
Subject: gnu: vsearch: Update to 2.9.1.

* gnu/packages/bioinformatics.scm (vsearch): Update to 2.9.1.
* gnu/packages/patches/vsearch-unbundle-cityhash.patch: Update.
---
 gnu/packages/bioinformatics.scm                      | 4 ++--
 gnu/packages/patches/vsearch-unbundle-cityhash.patch | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9954fcf20b..d9362ea4c6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6825,7 +6825,7 @@ SELECT or UPDATE queries to an end-point.")
 (define-public vsearch
   (package
     (name "vsearch")
-    (version "2.8.0")
+    (version "2.9.1")
     (source
      (origin
        (method git-fetch)
@@ -6835,7 +6835,7 @@ SELECT or UPDATE queries to an end-point.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0lrw6n75gmqkxl053yi2pwwvnzwf1r79ypzxgv6m0kw6df5fwv6r"))
+         "0vhrpjfdf75ba04b24xknp41790cvcgwl0vgpy7qbzj5xh2521ss"))
        (patches (search-patches "vsearch-unbundle-cityhash.patch"))
        (snippet
         '(begin
diff --git a/gnu/packages/patches/vsearch-unbundle-cityhash.patch b/gnu/packages/patches/vsearch-unbundle-cityhash.patch
index b1ecb1f063..2a2ab13a73 100644
--- a/gnu/packages/patches/vsearch-unbundle-cityhash.patch
+++ b/gnu/packages/patches/vsearch-unbundle-cityhash.patch
@@ -6,7 +6,7 @@ index e56a8a2..4adcc48 100644
  if TARGET_PPC
  AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=power8
  else
--AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g
+-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=x86-64 -mtune=generic
 +AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -lcityhash
  endif
  
@@ -39,7 +39,7 @@ index e56a8a2..4adcc48 100644
 -
  if TARGET_WIN
  
--libcityhash_a_CXXFLAGS = -Wall -Wno-sign-compare -O3 -g -D_MSC_VER
+-libcityhash_a_CXXFLAGS = $(AM_CXXFLAGS) -Wno-sign-compare -D_MSC_VER
 -__top_builddir__bin_vsearch_LDFLAGS = -static
 -__top_builddir__bin_vsearch_LDADD = libregex.a libcityhash.a libcpu_ssse3.a libcpu_sse2.a
 +__top_builddir__bin_vsearch_LDFLAGS = -static -lcityhash
@@ -47,7 +47,7 @@ index e56a8a2..4adcc48 100644
  
  else
  
--libcityhash_a_CXXFLAGS = -Wall -Wno-sign-compare -O3 -g
+-libcityhash_a_CXXFLAGS = $(AM_CXXFLAGS) -Wno-sign-compare
 -
  if TARGET_PPC
 -__top_builddir__bin_vsearch_LDADD = libcityhash.a libcpu.a
-- 
cgit v1.2.3


From 9f527c91990c4f620c88bb609e95589809a1354c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 09:52:46 +0100
Subject: gnu: sailfish: Use INVOKE.

* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use INVOKE instead of
SYSTEM*.
---
 gnu/packages/bioinformatics.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d9362ea4c6..c175227997 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12014,10 +12014,10 @@ bytes of memory space, where n is the length of the string.")
                    (include "external/install/include/rapmap/")
                    (rapmap (assoc-ref inputs "rapmap")))
                (mkdir-p "/tmp/rapmap")
-               (system* "tar" "xf"
-                        (assoc-ref inputs "rapmap")
-                        "-C" "/tmp/rapmap"
-                        "--strip-components=1")
+               (invoke "tar" "xf"
+                       (assoc-ref inputs "rapmap")
+                       "-C" "/tmp/rapmap"
+                       "--strip-components=1")
                (mkdir-p src)
                (mkdir-p include)
                (for-each (lambda (file)
-- 
cgit v1.2.3


From a9542937c8361b3aabda482bfdb40b07d92fba86 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 09:54:22 +0100
Subject: gnu: seek: Use INVOKE.

* gnu/packages/bioinformatics.scm (seek)[arguments]: Use INVOKE and return #T
unconditionally; patch "gen_tools_am" shebang in "bootstrap" phase.
---
 gnu/packages/bioinformatics.scm | 25 ++++++++++++++-----------
 1 file changed, 14 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c175227997..1ceb40cb95 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5057,21 +5057,24 @@ distribution, coverage uniformity, strand specificity, etc.")
            (modify-phases %standard-phases
              (replace 'bootstrap
                (lambda _
-                 (invoke "bash" "gen_auto")))
+                 (substitute* "gen_tools_am"
+                   (("/usr/bin/env.*") (which "perl")))
+                 (invoke "bash" "gen_auto")
+                 #t))
              (add-after 'build 'build-additional-tools
                (lambda* (#:key make-flags #:allow-other-keys)
-                 (every (lambda (dir)
-                          (with-directory-excursion (string-append "tools/" dir)
-                            (zero? (apply system* "make" make-flags))))
-                        dirs)))
+                 (for-each (lambda (dir)
+                             (with-directory-excursion (string-append "tools/" dir)
+                               (apply invoke "make" make-flags)))
+                           dirs)
+                 #t))
              (add-after 'install 'install-additional-tools
                (lambda* (#:key make-flags #:allow-other-keys)
-                 (fold (lambda (dir result)
-                         (with-directory-excursion (string-append "tools/" dir)
-                           (and result
-                                (zero? (apply system*
-                                              `("make" ,@make-flags "install"))))))
-                       #t dirs)))))))
+                 (for-each (lambda (dir)
+                             (with-directory-excursion (string-append "tools/" dir)
+                               (apply invoke `("make" ,@make-flags "install"))))
+                           dirs)
+                 #t))))))
       (inputs
        `(("gsl" ,gsl)
          ("boost" ,boost)
-- 
cgit v1.2.3


From ce49fdcce91803c873b899b088f9ed2ce22f1cd3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 09:58:05 +0100
Subject: gnu: roary: Use INVOKE.

* gnu/packages/bioinformatics.scm (roary)[arguments]: Use INVOKE and return #T
unconditionally.
---
 gnu/packages/bioinformatics.scm | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1ceb40cb95..94b82660c9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4762,10 +4762,11 @@ partial genes, and identifies translation initiation sites.")
                                            (getenv "PATH")))
              (setenv "PERL5LIB" (string-append (getcwd) "/lib" ":"
                                                (getenv "PERL5LIB")))
-             (zero? (length (filter (lambda (file)
-                                      (display file)(display "\n")
-                                      (not (zero? (system* "perl" file))))
-                                    (find-files "t" ".*\\.t$"))))))
+             (for-each (lambda (file)
+                         (display file)(display "\n")
+                         (invoke "perl" file))
+                       (find-files "t" ".*\\.t$"))
+             #t))
          (replace 'install
            ;; There is no 'install' target in the Makefile.
            (lambda* (#:key outputs #:allow-other-keys)
-- 
cgit v1.2.3


From a1e83a9856100b7d1993ad7917e11d8bb37c2646 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 10:06:35 +0100
Subject: gnu: pplacer-scripts: Use INVOKE.

* gnu/packages/bioinformatics.scm (pplacer-scripts)[arguments]: Use INVOKE and
return #T unconditionally.
---
 gnu/packages/bioinformatics.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 94b82660c9..8820ba0d8e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4410,8 +4410,7 @@ downstream analysis.")
          (add-after 'unpack 'enter-scripts-dir
            (lambda _ (chdir "scripts")))
          (replace 'check
-           (lambda _
-             (zero? (system* "python" "-m" "unittest" "discover" "-v"))))
+           (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"))
-- 
cgit v1.2.3


From 9c30cba431ccc36462f91652b624ae0068d77491 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 10:08:09 +0100
Subject: gnu: pcc: Use INVOKE.

* gnu/packages/c.scm (pcc)[arguments]: Use INVOKE and return #T
unconditionally.
---
 gnu/packages/c.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/c.scm b/gnu/packages/c.scm
index 83268e871c..d89b6ea00d 100644
--- a/gnu/packages/c.scm
+++ b/gnu/packages/c.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016, 2018 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
@@ -160,8 +160,7 @@ standard.")
      `(#:phases
        (modify-phases %standard-phases
          (replace 'check
-           (lambda _
-             (zero? (system* "make" "-C" "cc/cpp" "test")))))))
+           (lambda _ (invoke "make" "-C" "cc/cpp" "test") #t)))))
     (native-inputs
      `(("bison" ,bison)
        ("flex" ,flex)))
-- 
cgit v1.2.3


From ec618c2005a1dc5e5154d25e9599313cea1ce6e9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 10:09:32 +0100
Subject: gnu: cmus: Use INVOKE.

* gnu/packages/music.scm (cmus)[arguments]: Use INVOKE and return #T
unconditionally.
---
 gnu/packages/music.scm | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 7f1d124233..af7589c23d 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -322,16 +322,14 @@ playing your music.")
      `(#:tests? #f ; cmus does not include tests
        #:phases
        (modify-phases %standard-phases
-         (replace
-          'configure
-          (lambda* (#:key outputs #:allow-other-keys)
-            (let ((out (assoc-ref outputs "out")))
-
-              ;; It's an idiosyncratic configure script that doesn't
-              ;; understand --prefix=..; it wants prefix=.. instead.
-              (zero?
-               (system* "./configure"
-                        (string-append "prefix=" out)))))))))
+         (replace 'configure
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               ;; It's an idiosyncratic configure script that doesn't
+               ;; understand --prefix=..; it wants prefix=.. instead.
+               (invoke "./configure"
+                       (string-append "prefix=" out))
+               #t))))))
     ;; TODO: cmus optionally supports the following formats, which haven't yet
     ;; been added to Guix:
     ;;
-- 
cgit v1.2.3


From 4e8294688877ebe2c312b0939421f895755ae52f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 10:10:06 +0100
Subject: gnu: cmus: Fetch sources from git.

* gnu/packages/music.scm (cmus)[source]: Fetch from git.
---
 gnu/packages/music.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index af7589c23d..fe4d9df085 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -309,14 +309,14 @@ playing your music.")
     (name "cmus")
     (version "2.7.1")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/" name "/" name "/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/cmus/cmus.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0raixgjavkm7hxppzsc5zqbfbh2bhjcmbiplhnsxsmyj8flafyc1"))))
+                "0xd96py21bl869qlv1353zw7xsgq6v5s8szr0ldr63zj5fgc2ps5"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; cmus does not include tests
-- 
cgit v1.2.3


From 9ab90ead36af854950c420b53ee9202d802da09d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 10:14:08 +0100
Subject: gnu: pd: Remove custom autoconf phase.

* gnu/packages/music.scm (pd)[arguments]: Remove custom autoconf phase.
---
 gnu/packages/music.scm | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index fe4d9df085..ad6ace1f3f 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -1748,9 +1748,7 @@ export.")
            (lambda _
              (substitute* "tcl/pd-gui.tcl"
                (("exec wish ") (string-append "exec " (which "wish8.6") " ")))
-             #t))
-         (add-after 'unpack 'autoconf
-           (lambda _ (zero? (system* "bash" "./autogen.sh")))))))
+             #t)))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
-- 
cgit v1.2.3


From 69cb939ee756eb81659371be49152b4e5d510c95 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Nov 2018 10:17:15 +0100
Subject: gnu: libmusicbrainz: Use INVOKE.

* gnu/packages/music.scm (libmusicbrainz)[arguments]: Use INVOKE and return #T
unconditionally.
---
 gnu/packages/music.scm | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index ad6ace1f3f..25928d2cdd 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -4066,14 +4066,15 @@ ISRCs and the MCN (=UPC/EAN) from disc.")
         (base32
          "0ikb9igyyk28jm34raxfzkw2qyn4nzzwsymdyprp7cmvi6g2ajb7"))))
     (build-system cmake-build-system)
-    (arguments `(#:phases
-                 (modify-phases %standard-phases
-                   (replace 'check
-                     (lambda _
-                       (and
-                        ;; requires network connections
-                        ;; (zero? (system* "tests/mbtest"))
-                        (zero? (system* "tests/ctest"))))))))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             ;; requires network connections
+             ;; (invoke "tests/mbtest")
+             (invoke "tests/ctest")
+             #t)))))
     (inputs `(("neon" ,neon)
               ("libxml2" ,libxml2)))
     (native-inputs `(("pkg-config" ,pkg-config)))
-- 
cgit v1.2.3


From 195e081b43f2a9469e426bd7b3938a7e741faa0d Mon Sep 17 00:00:00 2001
From: Vagrant Cascadian <vagrant@debian.org>
Date: Mon, 5 Nov 2018 19:36:57 +0000
Subject: gnu: Add python-pyelftools.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/python.scm (python-pyelftools):
  New public variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/python.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 54ea0caac3..ea439b7ac3 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -10578,6 +10578,31 @@ useful as a validator for JSON data.")
 (define-public python2-validictory
   (package-with-python2 python-validictory))
 
+(define-public python-pyelftools
+  (package
+    (name "python-pyelftools")
+    (version "0.25")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pyelftools" version))
+       (sha256
+        (base32
+         "090vdksbz341f7ljvr0zswblw4lspa8qaiikzyjkf318arpxmil9"))))
+    (build-system python-build-system)
+    ;; Test suite requires python-setuptools
+    (native-inputs
+     `(("python-setuptools" ,python-setuptools)))
+    (home-page
+     "https://github.com/eliben/pyelftools")
+    (synopsis
+     "Analyze binary and library file information")
+    (description "This Python library provides interfaces for parsing and
+analyzing two binary and library file formats; the Executable and Linking
+Format (ELF), and debugging information in the Debugging With Attributed
+Record Format (DWARF).")
+    (license license:public-domain)))
+
 (define-public python-pyev
   (package
     (name "python-pyev")
-- 
cgit v1.2.3


From 9870b9f7f8a10192ad960f898d967bacd7ad0422 Mon Sep 17 00:00:00 2001
From: Luther Thompson <lutheroto@gmail.com>
Date: Tue, 6 Nov 2018 17:40:51 -0500
Subject: gnu: python-ilinkedlist: Update to 0.3.1.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/python.scm (python-ilinkedlist): Update to 0.3.1.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index ea439b7ac3..5f81c428ff 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -14537,14 +14537,14 @@ run on top of the dynamic task schedulers. ")
 (define-public python-ilinkedlist
   (package
     (name "python-ilinkedlist")
-    (version "0.2.0")
+    (version "0.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ilinkedlist" version))
        (sha256
         (base32
-         "0klb846q5vs62d8f89my7wan1sji4yjj6pjhjch9dha3p8vlncd2"))))
+         "04wpv7km8jggrngc4bjg3nm615czd3bjdvpsy2icg6c1c8162zyg"))))
     (build-system python-build-system)
     (native-inputs `(("python-pytest" ,python-pytest)))
     (inputs `(("python" ,python)))
-- 
cgit v1.2.3


From ec868631136d19ca3748e2f6f82d157f943cd7ee Mon Sep 17 00:00:00 2001
From: Stefan Stefanović <stefanx2ovic@gmail.com>
Date: Wed, 7 Nov 2018 16:37:34 +0100
Subject: services: elogind: Fix spelling errors of left value fields in
 elogind config file.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/services/desktop.scm (elogind-configuration-file)[ini-file]:
    Fix spelling of left value fields:
    InhibitDelayMaxSecs, HoldoffTimeoutSecs, IdleActionSeconds, RemoveIpc.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/services/desktop.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/services/desktop.scm b/gnu/services/desktop.scm
index e038f97683..47d1096c6d 100644
--- a/gnu/services/desktop.scm
+++ b/gnu/services/desktop.scm
@@ -672,7 +672,7 @@ include the @command{udisksctl} command, part of UDisks, and GNOME Disks."
    ("KillUserProcesses" (yesno elogind-kill-user-processes?))
    ("KillOnlyUsers" (user-name-list elogind-kill-only-users))
    ("KillExcludeUsers" (user-name-list elogind-kill-exclude-users))
-   ("InhibitDelayMaxSecs" (non-negative-integer elogind-inhibit-delay-max-seconds))
+   ("InhibitDelayMaxSec" (non-negative-integer elogind-inhibit-delay-max-seconds))
    ("HandlePowerKey" (handle-action elogind-handle-power-key))
    ("HandleSuspendKey" (handle-action elogind-handle-suspend-key))
    ("HandleHibernateKey" (handle-action elogind-handle-hibernate-key))
@@ -682,16 +682,16 @@ include the @command{udisksctl} command, part of UDisks, and GNOME Disks."
    ("SuspendKeyIgnoreInhibited" (yesno elogind-suspend-key-ignore-inhibited?))
    ("HibernateKeyIgnoreInhibited" (yesno elogind-hibernate-key-ignore-inhibited?))
    ("LidSwitchIgnoreInhibited" (yesno elogind-lid-switch-ignore-inhibited?))
-   ("HoldoffTimeoutSecs" (non-negative-integer elogind-holdoff-timeout-seconds))
+   ("HoldoffTimeoutSec" (non-negative-integer elogind-holdoff-timeout-seconds))
    ("IdleAction" (handle-action elogind-idle-action))
-   ("IdleActionSeconds" (non-negative-integer elogind-idle-action-seconds))
+   ("IdleActionSec" (non-negative-integer elogind-idle-action-seconds))
    ("RuntimeDirectorySize"
     (identity
      (lambda (config)
        (match (elogind-runtime-directory-size-percent config)
          (#f (non-negative-integer (elogind-runtime-directory-size config)))
          (percent (string-append (non-negative-integer percent) "%"))))))
-   ("RemoveIpc" (yesno elogind-remove-ipc?))
+   ("RemoveIPC" (yesno elogind-remove-ipc?))
    "[Sleep]"
    ("SuspendState" (sleep-list elogind-suspend-state))
    ("SuspendMode" (sleep-list elogind-suspend-mode))
-- 
cgit v1.2.3


From 8fa9ace1d6022ff2dca4618d1c7b22dc4be28b86 Mon Sep 17 00:00:00 2001
From: Laura Lazzati <laura.lazzati.15@gmail.com>
Date: Wed, 7 Nov 2018 14:51:21 -0300
Subject: doc: Add index entries.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* doc/guix.texi: Added various cindex tags to assist readers.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 doc/guix.texi | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/doc/guix.texi b/doc/guix.texi
index d021875bbf..441b65bcaf 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -51,6 +51,7 @@ Copyright @copyright{} 2018 Mike Gerwitz@*
 Copyright @copyright{} 2018 Pierre-Antoine Rouby@*
 Copyright @copyright{} 2018 Gábor Boskovits@*
 Copyright @copyright{} 2018 Florian Pelz@*
+Copyright @copyright{} 2018 Laura Lazzati@*
 
 Permission is granted to copy, distribute and/or modify this document
 under the terms of the GNU Free Documentation License, Version 1.3 or
@@ -354,6 +355,7 @@ configuration in a transactional, reproducible, and stateless fashion
 (@pxref{System Configuration}).
 
 @cindex functional package management
+@cindex isolation
 Under the hood, Guix implements the @dfn{functional package management}
 discipline pioneered by Nix (@pxref{Acknowledgments}).
 In Guix, the package build and installation process is seen
@@ -387,6 +389,7 @@ garbage collection of packages (@pxref{Features}).
 @chapter Installation
 
 @cindex installing Guix
+@cindex official website
 GNU Guix is available for download from its website at
 @url{http://www.gnu.org/software/guix/}.  This section describes the
 software requirements of Guix, as well as how to install it and get
@@ -398,6 +401,8 @@ instead, you want to install the complete GNU operating system,
 @pxref{System Installation}.
 
 @cindex foreign distro
+@cindex directories related to foreign distro
+
 When installed on a running GNU/Linux system---thereafter called a
 @dfn{foreign distro}---GNU@tie{}Guix complements the available tools
 without interference.  Its data lives exclusively in two directories,
@@ -420,6 +425,7 @@ Once installed, Guix can be updated by running @command{guix pull}
 @section Binary Installation
 
 @cindex installing Guix from binaries
+@cindex installer script
 This section describes how to install Guix on an arbitrary system from a
 self-contained tarball providing binaries for Guix and for all its
 dependencies.  This is often quicker than installing from source, which
-- 
cgit v1.2.3


From 988b78ba28b5104407ec14e6f07ab80df31d17d8 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 8 Nov 2018 11:53:03 +0200
Subject: gnu: Add fstrcmp.

* gnu/packages/kodi.scm (fstrcmp): New variable.
---
 gnu/packages/kodi.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/kodi.scm b/gnu/packages/kodi.scm
index 6729f1f322..f0aa3bd476 100644
--- a/gnu/packages/kodi.scm
+++ b/gnu/packages/kodi.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -48,6 +49,7 @@
   #:use-module (gnu packages gl)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gperf)
+  #:use-module (gnu packages groff)
   #:use-module (gnu packages gnunet)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages image)
@@ -233,6 +235,35 @@ generator library for C++.")
       (description (package-description libdvdcss))
       (license license:gpl2+))))
 
+(define-public fstrcmp
+  (package
+    (name "fstrcmp")
+    (version "0.7.D001")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "http://fstrcmp.sourceforge.net/fstrcmp-"
+                            version ".tar.gz"))
+        (sha256
+         (base32
+          "0xilghiy3mz78bjmfldi39qyy7jvw5b6wafsx370lw401y2qw0g4"))))
+    (build-system gnu-build-system)
+    (home-page "http://fstrcmp.sourceforge.net/")
+    (arguments
+     '(#:configure-flags '("SH=sh")))
+    (native-inputs
+     `(("ghostscript" ,ghostscript) ; ps2pdf
+       ("groff" ,groff)
+       ("libtool" ,libtool)
+       ("which" ,which)))
+    (synopsis "fuzzy comparison of strings")
+    (description
+     "The fstrcmp project provides a library that is used to make fuzzy
+comparisons of strings and byte arrays, including multi-byte character strings.
+This can be useful in error messages, enabling the suggestion of likely valid
+alternatives. In compilers, this can reduce the cascade of secondary errors.")
+    (license license:gpl3+)))
+
 (define-public kodi
   ;; We package the git version because the current released
   ;; version was cut while the cmake transition was in turmoil.
-- 
cgit v1.2.3


From e3407254d5e23cfd2741b51d48297bad01864311 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 8 Nov 2018 11:55:38 +0200
Subject: gnu: kodi: Update to 18.0b5.

* gnu/packages/kodi.scm (kodi): Update to 18.0b5.
[source]: Update snippet.
[inputs]: Add flatbuffers, fstrcmp.
(crossguid): Update to commit fef89a4174a7bf8cd99fa9154864ce9e8e3bf989.
(libdvdnav/kodi, libdvdread/kodi): Update to 6.0.0-Leia-Alpha-3.
(libdvdcss/kodi): Update to 1.4.2-Leia-Beta-5.
---
 gnu/packages/kodi.scm | 39 +++++++++++++++++++--------------------
 1 file changed, 19 insertions(+), 20 deletions(-)

diff --git a/gnu/packages/kodi.scm b/gnu/packages/kodi.scm
index f0aa3bd476..fe7f93fa53 100644
--- a/gnu/packages/kodi.scm
+++ b/gnu/packages/kodi.scm
@@ -64,6 +64,7 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages samba)
   #:use-module (gnu packages sdl)
+  #:use-module (gnu packages serialization)
   #:use-module (gnu packages ssh)
   #:use-module (gnu packages swig)
   #:use-module (gnu packages textutils)
@@ -77,11 +78,12 @@
   #:use-module (gnu packages assembly))
 
 (define-public crossguid
-  (let ((commit "8f399e8bd4252be9952f3dfa8199924cc8487ca4"))
+  (let ((commit "fef89a4174a7bf8cd99fa9154864ce9e8e3bf989")
+        (revision "2"))
     (package
       (name "crossguid")
-      (version (string-append "0.0-1." (string-take commit 7)))
-      ;; There's no official release.  Just a Git repository.
+      (version (string-append "0.0-" revision "." (string-take commit 7)))
+      ;; This is the commit that Kodi wants.
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
@@ -90,13 +92,12 @@
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "1i29y207qqddvaxbn39pk2fbh3gx8zvdprfp35wasj9rw2wjk3s9"))))
+                  "1blrkc7zcqrqcr5msvhyhm98s2jvm9hr0isqs4288q2r4mdnrfq0"))))
       (build-system gnu-build-system)
       (arguments
        '(#:phases
          (modify-phases %standard-phases
            (delete 'configure)          ; no configure script
-           ;; There's no build system here, so we have to do it ourselves.
            (replace 'build
              (lambda _
                (invoke "g++" "-c" "guid.cpp" "-o" "guid.o"
@@ -131,7 +132,7 @@ generator library for C++.")
 ;; of the standard build process. To make things easier, we bootstrap
 ;; and patch shebangs here, so we don't have to worry about it later.
 (define libdvdnav/kodi
-  (let ((commit "6.0.0-Leia-Alpha-1"))
+  (let ((commit "6.0.0-Leia-Alpha-3"))
     (package
       (name "libdvdnav-bootstrapped")
       (version commit)
@@ -143,7 +144,7 @@ generator library for C++.")
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "1xiyfgf8v8aknlxlzsvk6pbzkhclz0hbh3s1b0w6ivkng2k310j9"))))
+                  "0qwlf4lgahxqxk1r2pzl866mi03pbp7l1fc0rk522sc0ak2s9jhb"))))
       (build-system gnu-build-system)
       (arguments
        '(#:tests? #f
@@ -166,7 +167,7 @@ generator library for C++.")
       (license license:gpl2+))))
 
 (define libdvdread/kodi
-  (let ((commit "6.0.0-Leia-Alpha-1"))
+  (let ((commit "6.0.0-Leia-Alpha-3"))
     (package
       (name "libdvdread-bootstrapped")
       (version commit)
@@ -178,7 +179,7 @@ generator library for C++.")
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "1c3g18n2vwhgcfz3dka1pmw58bnv2ram7xjvizfiykb3sgi9zfwp"))))
+                  "1xxn01mhkdnp10cqdr357wx77vyzfb5glqpqyg8m0skyi75aii59"))))
       (build-system gnu-build-system)
       (arguments
        '(#:tests? #f
@@ -201,7 +202,7 @@ generator library for C++.")
       (license (list license:gpl2+ license:lgpl2.1+)))))
 
 (define libdvdcss/kodi
-  (let ((commit "1.4.1-Leia-Alpha-1"))
+  (let ((commit "1.4.2-Leia-Beta-5"))
     (package
       (name "libdvdcss-bootstrapped")
       (version commit)
@@ -213,7 +214,7 @@ generator library for C++.")
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "0adafwsawxssj3nilkql447v0l4a2584rdpmy5rfjmznh91lykgh"))))
+                  "0j41ydzx0imaix069s3z07xqw9q95k7llh06fc27dcn6f7b8ydyl"))))
       (build-system gnu-build-system)
       (arguments
        '(#:tests? #f
@@ -265,27 +266,23 @@ alternatives. In compilers, this can reduce the cascade of secondary errors.")
     (license license:gpl3+)))
 
 (define-public kodi
-  ;; We package the git version because the current released
-  ;; version was cut while the cmake transition was in turmoil.
-  (let ((commit "ec16dbca4dcf2923f53f819695a6d47c52e68d74")
-        (revision "8"))
   (package
     (name "kodi")
-    (version (git-version "18.0_alpha" revision commit))
+    (version "18.0b5")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/xbmc/xbmc.git")
-                    (commit commit)))
+                    (commit (string-append version "-Leia"))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1rxg752cl59124cfpfwmyjldn6qpq5jginxddpzvgagfadf10i4d"))
+                "042qzvhys3sajby6ywgmrsymhji37qk0iqgppznrvm53vrizwsam"))
               (snippet
                '(begin
                   (use-modules (guix build utils))
                   (for-each delete-file-recursively
-                            '("project/BuildDependencies/bin/"
+                            '("project/BuildDependencies/"
                               ;; TODO: Purge these jars.
                               ;;"tools/codegenerator/groovy"
                               ;; And these sources:
@@ -401,10 +398,12 @@ alternatives. In compilers, this can reduce the cascade of secondary errors.")
        ("eudev" ,eudev)
        ("ffmpeg" ,ffmpeg)
        ("flac" ,flac)
+       ("flatbuffers" ,flatbuffers)
        ("fmt" ,fmt)
        ("fontconfig" ,fontconfig)
        ("freetype" ,freetype)
        ("fribidi" ,fribidi)
+       ("fstrcmp" ,fstrcmp)
        ("giflib" ,giflib)
        ("glew" ,glew)
        ("gnutls" ,gnutls)
@@ -458,7 +457,7 @@ plug-in system.")
                    license:expat                  ;cpluff, dbwrappers
                    license:public-domain          ;cpluff/examples
                    license:bsd-3                  ;misc, gtest
-                   license:bsd-2)))))             ;xbmc/freebsd
+                   license:bsd-2))))              ;xbmc/freebsd
 
 (define-public kodi-cli
   (let ((commit "104dc23b2a993c8e6db8c46f4f8bec24b146549b") ; Add support for
-- 
cgit v1.2.3


From 2705780f3f4d15740cbd9d54a5133aced15a7200 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Thu, 8 Nov 2018 13:08:26 +0100
Subject: gnu: Add emacs-clang-format.

* gnu/packages/emacs.scm (emacs-clang-format): New variable.
---
 gnu/packages/emacs.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 4821c18f6e..3c7d902e11 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -12463,3 +12463,40 @@ correctly.")
 @item helm-slime-repl-history: Select an input from the SLIME REPL history and insert it.
 @end itemize\n")
       (license license:gpl3+))))
+
+(define-public emacs-clang-format
+  (let ((commit "5556c31528af2661bed3011bd63ffc0ed44e18a0"))
+    (package
+      (name "emacs-clang-format")
+      (version (git-version "0.0.0" "1" commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/emacsorphanage/clang-format")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0ynvnp3vrcpngmwakb23xv4xn7jbkg43s196q7pg9nkl13x4n2nq"))))
+      (build-system emacs-build-system)
+      (inputs
+       `(("clang" ,clang)))
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'configure
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((clang (assoc-ref inputs "clang")))
+                 ;; Repo is read-only.
+                 (chmod "clang-format.el" #o644)
+                 (emacs-substitute-variables "clang-format.el"
+                   ("clang-format-executable"
+                    (string-append clang "/bin/clang-format"))))
+               #t)))))
+      (home-page "https://github.com/emacsorphanage/clang-format")
+      (synopsis "Format code using clang-format")
+      (description "This package allows to filter code through clang-format to
+fix its formatting.  @command{clang-format} is a tool that formats C/C++/Obj-C
+code according to a set of style options, see
+@url{http://clang.llvm.org/docs/ClangFormatStyleOptions.html}.")
+      (license license:gpl3+))))
-- 
cgit v1.2.3


From 41d2b7f50b82469177c0ae2429571db6a5c1c3f0 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Thu, 8 Nov 2018 13:24:35 -0500
Subject: gnu: PostgreSQL 9: Update to 9.6.11 [fixes CVE-2018-16850].

* gnu/packages/databases.scm (postgresql-9.6): Update to 9.6.11.
---
 gnu/packages/databases.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 87fb170e5d..dc7e2aa53d 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -849,14 +849,14 @@ pictures, sounds, or video.")
   (package
     (inherit postgresql)
     (name "postgresql")
-    (version "9.6.9")
+    (version "9.6.11")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "0biy8j69dbvdmrag55pdszpc0702agzqhhcwdx21xp02mzim4ydr"))))))
+                "0c55akrkzqd6p6a8hr0338wk246hl76r9j16p4zn3s51d7f0l99q"))))))
 
 (define-public python-pymysql
   (package
-- 
cgit v1.2.3


From e4b62e229e9dfb7da158a3a5c7a26b149b41c8ab Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Fri, 9 Nov 2018 01:06:21 -0500
Subject: gnu: wxmaxima: Update to 18.10.1.

* gnu/packages/maths.scm (wxmaxima): Update to 18.10.1.
[source]: Update URL and remove patch.
* gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch: Remove
file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
---
 gnu/local.mk                                       |  1 -
 gnu/packages/maths.scm                             | 10 ++++-----
 ...xmaxima-do-not-use-old-gnuplot-parameters.patch | 26 ----------------------
 3 files changed, 4 insertions(+), 33 deletions(-)
 delete mode 100644 gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index c627577e41..68a87b1255 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1228,7 +1228,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/wpa-supplicant-fix-zeroed-keys.patch	\
   %D%/packages/patches/wpa-supplicant-fix-nonce-reuse.patch	\
   %D%/packages/patches/wpa-supplicant-krack-followups.patch	\
-  %D%/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch	\
   %D%/packages/patches/x265-detect512-all-arches.patch		\
   %D%/packages/patches/xboing-CVE-2004-0149.patch		\
   %D%/packages/patches/xf86-video-ark-remove-mibstore.patch	\
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 808ab5345b..0d040bf296 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2763,18 +2763,16 @@ point numbers.")
 (define-public wxmaxima
   (package
     (name "wxmaxima")
-    (version "18.02.0")
+    (version "18.10.1")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://github.com/andrejv/" name "/archive"
-                           "/Version-" version ".tar.gz"))
+       (uri (string-append "https://github.com/wxMaxima-developers/" name
+                           "/archive/Version-" version ".tar.gz"))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "03kr2rgfp4hcf3is8m8d8f9hj660c3xgrc50vrrfpixx4syh6wvj"))
-       (patches
-        (search-patches "wxmaxima-do-not-use-old-gnuplot-parameters.patch"))))
+         "0c2blq65r0am509p3rjqpwqk6vl5r2yg1p9nh2jczf80vhi3ldas"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("gettext" ,gettext-minimal)))
diff --git a/gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch b/gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch
deleted file mode 100644
index 345101bd3a..0000000000
--- a/gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-This fixes the wxplot2d plotting issue found at
-https://github.com/andrejv/wxmaxima/issues/973.
-
-From 5a0693c97ceaa4935b908f1e478126896952f399 Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Gunter=20K=C3=B6nigsmann?= <gunter@peterpall.de>
-Date: Mon, 19 Feb 2018 05:37:35 +0100
-Subject: [PATCH] Seems I accidentally made wxMaxima to default to parameters
- for old gnuplots. Resolves #973
-
----
- data/wxmathml.lisp.in | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/data/wxmathml.lisp.in b/data/wxmathml.lisp.in
-index a32e3fc3..4e19acaf 100644
---- a/data/wxmathml.lisp.in
-+++ b/data/wxmathml.lisp.in
-@@ -43,7 +43,7 @@
- (defvar $wxsubscripts t
-   "Recognize TeX-style subscripts")
- (defvar $wxplot_pngcairo nil "Use gnuplot's pngcairo terminal for new plots?")
--(defmvar $wxplot_old_gnuplot t)
-+(defmvar $wxplot_old_gnuplot nil)
- 
- (defun $wxstatusbar (status)
-   (format t "<statusbar>~a</statusbar>~%" status))
-- 
cgit v1.2.3


From b1b82aed5d5947eaa1ebf300f8c592e660555a3c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 9 Nov 2018 08:36:42 +0100
Subject: gnu: powertabeditor: Use INVOKE.

* gnu/packages/music.scm (powertabeditor)[arguments]: Use INVOKE and return #T
unconditionally.
---
 gnu/packages/music.scm | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 25928d2cdd..7df29deabd 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -1182,14 +1182,14 @@ add_library( rapidjson INTERFACE IMPORTED )"))
        (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             (zero? (system* "bin/pte_tests"
-                             ;; FIXME: these tests fail
-                             "exclude:Actions/EditStaff"
-                             "exclude:Formats/PowerTabOldImport/MergeMultiBarRests"
-                             "exclude:Score/ViewFilter/FilterRule"
-                             "exclude:Score/ViewFilter/ViewFilter"
-                             "exclude:Formats/PowerTabOldImport/Directions"
-                             ))))
+             (invoke "bin/pte_tests"
+                     ;; FIXME: these tests fail
+                     "exclude:Actions/EditStaff"
+                     "exclude:Formats/PowerTabOldImport/MergeMultiBarRests"
+                     "exclude:Score/ViewFilter/FilterRule"
+                     "exclude:Score/ViewFilter/ViewFilter"
+                     "exclude:Formats/PowerTabOldImport/Directions")
+             #t))
          ;; FIXME: This bug has been fixed upstream, but no release has been
          ;; made yet.  See https://github.com/powertab/powertabeditor/issues/257
          (add-after 'unpack 'fix-boost-bug
-- 
cgit v1.2.3


From 1b12b572a5df2b8c6f67ad0515a87543da098a09 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 9 Nov 2018 08:37:12 +0100
Subject: gnu: powertabeditor: Fetch sources from git.

* gnu/packages/music.scm (powertabeditor)[source]: Fetch from git.
---
 gnu/packages/music.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 7df29deabd..3f0498ee53 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -1141,14 +1141,14 @@ your own lessons.")
     (name "powertabeditor")
     (version "2.0.0-alpha10")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/powertab/powertabeditor/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/powertab/powertabeditor.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1fr14ql0yhlqvh6y08yaanszm2nvca5i50rqym396kfvga3ky18x"))
+                "1z4fhdp71ck9synr12rg1p6365xnypd8ih40c5icj4si36khvksk"))
               (modules '((guix build utils)))
               (snippet
                '(begin
-- 
cgit v1.2.3


From 97f33b05ec90deecaf43587467ed3fbbcb36bd2a Mon Sep 17 00:00:00 2001
From: Mathieu Othacehe <m.othacehe@gmail.com>
Date: Fri, 9 Nov 2018 19:33:00 +0900
Subject: gnu: guile-newt: Update to revision 1.

* gnu/packages/guile.scm (guile-newt): Update to revision 1.
---
 gnu/packages/guile.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 3c8d2e58f9..8c55c749d8 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -2289,8 +2289,8 @@ tracker's SOAP service, such as @url{https://bugs.gnu.org}.")
 
 ;; There has not been any release yet.
 (define-public guile-newt
-  (let ((commit "596ad760bee1be419d71271732f0f30eaee55143")
-        (revision "0"))
+  (let ((commit "4eaa3cf84b9b426cc0ff7bec48b76cca6ca3ec83")
+        (revision "1"))
     (package
       (name "guile-newt")
       (version (string-append "0-" revision "." (string-take commit 9)))
@@ -2302,7 +2302,7 @@ tracker's SOAP service, such as @url{https://bugs.gnu.org}.")
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "18qqbi0bc7vp2vlrhib3p3wwgn7wrlv5728dn0avirhw4fxxivnf"))))
+                  "0ww7jbdsmjlsxm60ym6cb5s5kc4ljz8bn4y2lvcqnap0aihqfk10"))))
       (build-system gnu-build-system)
       (arguments
        '(#:make-flags
-- 
cgit v1.2.3


From 2cce23bfb8fbb57c3f11780a939d74b5bd9ed3a2 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Fri, 9 Nov 2018 11:31:17 +0100
Subject: gnu: Add xmlrpc-c.

* gnu/packages/xml.scm (xmlrpc-c): New variable.
---
 gnu/packages/xml.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index c1f14d720e..347ac878a3 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -19,6 +19,7 @@
 ;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2017 Petter <petter@mykolab.ch>
 ;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -39,6 +40,7 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages curl)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages java)
   #:use-module (gnu packages gnuzilla)
@@ -2095,3 +2097,39 @@ derivations of regular expressions.")
      "The Haskell XML Toolbox bases on the ideas of HaXml and HXML, but
 introduces a more general approach for processing XML with Haskell.")
     (license license:expat)))
+
+(define-public xmlrpc-c
+  (package
+    (name "xmlrpc-c")
+    (version "1.43.08")
+    (source (origin
+             (method url-fetch)
+             (uri (string-append "mirror://sourceforge/xmlrpc-c/Xmlrpc-c%20Super%20Stable/"
+                                 version "/xmlrpc-c-" version ".tgz"))
+             (sha256
+              (base32
+               "18zwbj6i2hpcn5riiyp8i6rml0sfv60dd7phw1x8g4r4lj2bbxf9"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("curl" ,curl)))
+    (native-inputs
+     `(;; For tools, if ever needed.
+       ("perl" ,perl)))
+    (arguments
+     `(#:make-flags ; Add $libdir to the RUNPATH of all the executables.
+       (list (string-append "LDFLAGS_PERSONAL=-Wl,-rpath=" %output "/lib"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-/bin/sh-in-tests
+           (lambda _
+             (substitute* "GNUmakefile"
+               (("#! /bin/sh") (which "sh")))
+             #t)))))
+    (home-page "http://xmlrpc-c.sourceforge.net/")
+    (synopsis "Lightweight RPC library based on XML and HTTP")
+    (description
+     "XML-RPC is a quick-and-easy way to make procedure calls over the Internet.
+It converts the procedure call into an XML document, sends it to a remote
+server using HTTP, and gets back the response as XML.  This library provides a
+modular implementation of XML-RPC for C and C++.")
+    (license (list license:psfl license:expat))))
-- 
cgit v1.2.3


From ddd925f608bf7bf9af367447ef937e92d531a941 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Fri, 9 Nov 2018 11:32:25 +0100
Subject: gnu: Add emacs-gtk-look.

* gnu/packages/emacs.scm (emacs-gtk-look): New variable.
---
 gnu/packages/emacs.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 3c7d902e11..c6008e6a94 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -12500,3 +12500,41 @@ fix its formatting.  @command{clang-format} is a tool that formats C/C++/Obj-C
 code according to a set of style options, see
 @url{http://clang.llvm.org/docs/ClangFormatStyleOptions.html}.")
       (license license:gpl3+))))
+
+(define-public emacs-gtk-look
+  (package
+    (name "emacs-gtk-look")
+    (version "29")
+    (source (origin
+              (method url-fetch)
+              (uri "https://download.tuxfamily.org/user42/gtk-look.el")
+              (sha256
+               (base32
+                "14p2nwrd51cr1v06fxbjjn6jdrkf9d6vcxhmscm0kl677s25ypsp"))))
+    (build-system emacs-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'configure
+           (lambda _
+             ;; File is read-only.
+             (chmod "gtk-look.el" #o644)
+             (emacs-substitute-variables "gtk-look.el"
+               ("gtk-lookup-devhelp-indices"
+                '(list (expand-file-name "~/.guix-profile/share/gtk-doc/html/*/*.devhelp*"))))
+             #t)))))
+    (home-page "http://user42.tuxfamily.org/gtk-look/index.html")
+    (synopsis "Find and display HTML documentation for GTK, GNOME and Glib")
+    (description "@command{gtk-look} finds and displays HTML documentation for
+GTK, GNOME and Glib functions and variables in Emacs, similar to what
+info-lookup-symbol does for info files (C-h S).  The documentation is expected
+to be devhelp indexes with HTML files.  The location of the indexes can be
+customized.  In addition to C code development @command{gtk-look} is good for
+
+@itemize
+@item @command{perl-gtk2}, recognising class funcs like
+@command{Gtk2::Label->new} and bare method names like @command{set_text}.
+@item @command{guile-gnome}, recognising methods like @command{set-text} and
+classes like @command{<gtk-window>}.
+@end itemize\n")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From 2eaaadb4d67977773d7f39ab0025acdffc135cc0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 9 Nov 2018 10:47:05 +0100
Subject: gnu: r-with-tests: Use INVOKE.

* gnu/packages/statistics.scm (r-with-tests)[arguments]: Use INVOKE and
return #T unconditionally.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 642fa2d423..e76bc7cfc7 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -218,9 +218,9 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
                                     "/share/zoneinfo"))
              #t))
          (add-after 'build 'make-info
-          (lambda _ (zero? (system* "make" "info"))))
+           (lambda _ (invoke "make" "info") #t))
          (add-after 'build 'install-info
-          (lambda _ (zero? (system* "make" "install-info")))))
+           (lambda _ (invoke "make" "install-info") #t)))
        #:configure-flags
        `(;; We build the recommended packages here, because they are needed in
          ;; order to run the test suite.  We disable them in the r-minimal
-- 
cgit v1.2.3


From cee9ab244f9ba9f3156b6aa50927418bae951096 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 9 Nov 2018 10:47:34 +0100
Subject: gnu: r-with-tests: Update to 3.5.1.

* gnu/packages/statistics.scm (r-with-tests): Update to 3.5.1.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index e76bc7cfc7..5b494c4829 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -121,7 +121,7 @@ be output in text, PostScript, PDF or HTML.")
 (define r-with-tests
   (package
     (name "r-with-tests")
-    (version "3.5.0")
+    (version "3.5.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cran/src/base/R-"
@@ -129,7 +129,7 @@ be output in text, PostScript, PDF or HTML.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0w38865laqg28cdhikxdxhx4rfp0kgcn72gakwypsy91br9ja5zx"))))
+                "1vap2k8kj5icy9naw61f9zyphf4rs0c9rxvil0zxkwx0xvsvyqq4"))))
     (build-system gnu-build-system)
     (arguments
      `(#:disallowed-references (,tzdata-for-tests)
-- 
cgit v1.2.3