From 4722330d68581d9ac20c419b1a4d2c8bf5137506 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 6 Oct 2019 22:07:03 +0200
Subject: gnu: nss-pam-ldapd: Update to 0.9.11.

* gnu/packages/openldap.scm (nss-pam-ldapd): Update to 0.9.11.
[inputs]: Replace python-2 with python.
---
 gnu/packages/openldap.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/openldap.scm b/gnu/packages/openldap.scm
index b84a417ff5..b355665da0 100644
--- a/gnu/packages/openldap.scm
+++ b/gnu/packages/openldap.scm
@@ -112,14 +112,14 @@
 (define-public nss-pam-ldapd
   (package
     (name "nss-pam-ldapd")
-    (version "0.9.10")
+    (version "0.9.11")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://arthurdejong.org/nss-pam-ldapd/"
                                   "nss-pam-ldapd-" version ".tar.gz"))
               (sha256
                (base32
-                "1cqamcr6qpgwxijlr6kg7jspjamjra8w0haan0qssn0yxn95d7c0"))))
+                "1dna3r0q6sjhhlkhcp8x2zkslrd4y7701kk6fl5r940sdph1pmyh"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -146,7 +146,7 @@
      `(("linux-pam" ,linux-pam)
        ("openldap" ,openldap)
        ("mit-krb5" ,mit-krb5)
-       ("python" ,python-2)))
+       ("python" ,python)))
     (home-page "https://arthurdejong.org/nss-pam-ldapd")
     (synopsis "NSS and PAM modules for LDAP")
     (description "nss-pam-ldapd provides a @dfn{Name Service Switch} (NSS)
-- 
cgit v1.2.3


From 45d04b2a7d01f693020149853e1d810cf92205a4 Mon Sep 17 00:00:00 2001
From: Brian Leung <leungbk@mailfence.com>
Date: Sun, 6 Oct 2019 22:02:25 +0200
Subject: gnu: emacs-helm: Update to 3.5.0.

* gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.5.0.
---
 gnu/packages/emacs-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 442115882d..bfcfb98d1e 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -6621,7 +6621,7 @@ ack, ag, helm and pt.")
 (define-public emacs-helm
   (package
     (name "emacs-helm")
-    (version "3.3")
+    (version "3.5.0")
     (source
      (origin
        (method git-fetch)
@@ -6630,7 +6630,7 @@ ack, ag, helm and pt.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0fqhw7r9fcsja5d3pgbipw7pkw9nj534faav6hi45413hc3gyv92"))))
+        (base32 "07bijcnfkv60l3swasxv53x32l6glds05mxnbb3xbnmkgm1pm9if"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-async" ,emacs-async)
-- 
cgit v1.2.3


From cb2197508a62210b8bdb132b6f96aebba637e6b3 Mon Sep 17 00:00:00 2001
From: Brian Leung <leungbk@mailfence.com>
Date: Sun, 6 Oct 2019 22:02:46 +0200
Subject: gnu: Add emacs-helm-org.

* gnu/packages/emacs-xyz.scm (emacs-helm-org): New variable.
---
 gnu/packages/emacs-xyz.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

(limited to 'gnu')

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index bfcfb98d1e..cc16a5d04f 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -6647,6 +6647,31 @@ considered to be its successor.  Helm sets out to clean up the legacy code in
 not tied in the trap of backward compatibility.")
     (license license:gpl3+)))
 
+(define-public emacs-helm-org
+  (let ((commit "542dda7bc9a3b9dfb439e4f8a1e5f60cfb6cc256")
+        (revision "1"))
+    (package
+      (name "emacs-helm-org")
+      (version (git-version "1.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/emacs-helm/helm-org.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1xa32w80icrykpyfb89fhb0s4l7ysi0sc7f7lfwqz5najwbgqipl"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-helm" ,emacs-helm)))
+      (home-page "https://github.com/emacs-helm/helm-org")
+      (synopsis "Helm interface to the Silver Searcher")
+      (description
+       "This package provides a frontend for grepping tools like ag and ack,
+as well as features for editing search results.")
+      (license license:gpl3+))))
+
 (define-public emacs-helm-swoop
   (package
     (name "emacs-helm-swoop")
-- 
cgit v1.2.3


From d050fdf4c6309cf5e0bfad3806cac51e3fefaa1b Mon Sep 17 00:00:00 2001
From: Brian Leung <leungbk@mailfence.com>
Date: Sun, 6 Oct 2019 22:02:56 +0200
Subject: gnu: emacs-helm-ag: Fix version.

* gnu/packages/emacs-xyz.scm (emacs-helm-ag): Fix version.
---
 gnu/packages/emacs-xyz.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu')

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index cc16a5d04f..5be5b4be45 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -6700,7 +6700,7 @@ for search-based navigation of buffers.")
         (revision "1"))
     (package
       (name "emacs-helm-ag")
-      (version "0.58")
+      (version (git-version "0.58" revision commit))
       (source
        (origin
          (method git-fetch)
-- 
cgit v1.2.3


From 122c1b3ce7718e956db0c6ce7e1058362dd7bb1c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 6 Oct 2019 23:03:27 +0200
Subject: gnu: r-biomart: Update to 2.40.5.

* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.5.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5ec600598b..93a458b133 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7658,13 +7658,13 @@ annotation data packages using SQLite data storage.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.40.4")
+    (version "2.40.5")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "0dj51qkxm7bh24b3bs1di7lic6zgi7g5gf9iqkqhrwkbm7sqvn0v"))))
+                "1kjvxnkpsx3j2hji3cg3ka2gv8a9mg117lzzxyqjb7qa4zw7dipx"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 94638cbe77f070645dbbeb983e1e8db8917c1be9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 6 Oct 2019 23:03:39 +0200
Subject: gnu: r-rsamtools: Update to 2.0.2.

* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.2.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 93a458b133..e4cfa0cad3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7742,13 +7742,13 @@ biological sequences or sets of sequences.")
 (define-public r-rsamtools
   (package
     (name "r-rsamtools")
-    (version "2.0.1")
+    (version "2.0.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Rsamtools" version))
               (sha256
                (base32
-                "0wzp5vsmqs7h44r7lcw8fnz5x9bcdcfiqq8d3h62wwibyk2lg0w1"))))
+                "188k5g40lbli7dxr96hldyvg9r9hmlbh2fp0qs5nnd12b8zbf338"))))
     (properties
      `((upstream-name . "Rsamtools")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 33651044c6e4989d2e3546a772963b2b3a8b0703 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 6 Oct 2019 23:03:49 +0200
Subject: gnu: r-seurat: Update to 3.1.1.

* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.1.
[propagated-inputs]: Add r-httr.
---
 gnu/packages/bioinformatics.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e4cfa0cad3..f2f67f36b0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9465,13 +9465,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "3.1.0")
+    (version "3.1.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "0icxndnnkkmmr9hhd01dv3w8pih7x9r0rlp3fq9pk3qajp9gmlyq"))))
+                "084lr2fjdksshsmv1ww82bgn3a9mml7kswsidjrs89snabgvn360"))))
     (properties `((upstream-name . "Seurat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9484,6 +9484,7 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
        ("r-ggplot2" ,r-ggplot2)
        ("r-ggrepel" ,r-ggrepel)
        ("r-ggridges" ,r-ggridges)
+       ("r-httr" ,r-httr)
        ("r-ica" ,r-ica)
        ("r-igraph" ,r-igraph)
        ("r-irlba" ,r-irlba)
-- 
cgit v1.2.3


From 82acc94fbfc5cfb1257f0a75ae9997262d90fef6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 6 Oct 2019 23:04:11 +0200
Subject: gnu: r-htmltools: Update to 0.4.0.

* gnu/packages/cran.scm (r-htmltools): Update to 0.4.0.
[arguments]: Remove field.
[propagated-inputs]: Add r-rlang.
---
 gnu/packages/cran.scm | 21 ++++-----------------
 1 file changed, 4 insertions(+), 17 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1f35356e05..1e153b1284 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -525,31 +525,18 @@ directory.")
 (define-public r-htmltools
   (package
     (name "r-htmltools")
-    (version "0.3.6")
+    (version "0.4.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "htmltools" version))
               (sha256
                (base32
-                "18k8r1s8sz1jy7dkz35n69wj20xhmllr53xmwb4pdzf2z61gpbs4"))))
+                "06l17d8jkf438yk2mchpsp4j90bynnapz3nabh5vkcc324p5a62v"))))
     (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         ;; See https://github.com/rstudio/htmltools/pull/68
-         ;; The resource files are in the store and have mode 444.  After
-         ;; copying the files R fails to remove them again because it doesn't
-         ;; have write access to them.
-         (add-after 'unpack 'copy-files-without-mode
-           (lambda _
-             (substitute* "R/html_dependency.R"
-               (("file.copy\\(from, to, " prefix)
-                (string-append prefix
-                               "copy.mode = FALSE, ")))
-             #t)))))
     (propagated-inputs
      `(("r-digest" ,r-digest)
-       ("r-rcpp" ,r-rcpp)))
+       ("r-rcpp" ,r-rcpp)
+       ("r-rlang" ,r-rlang)))
     (home-page "https://cran.r-project.org/web/packages/htmltools")
     (synopsis "R tools for HTML")
     (description
-- 
cgit v1.2.3


From ff743445975ba67fc827c415e686b0ec2a0a7baf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 6 Oct 2019 23:06:20 +0200
Subject: gnu: r-htmlwidgets: Update to 1.5.

* gnu/packages/cran.scm (r-htmlwidgets): Update to 1.5.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1e153b1284..902a9975a8 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -546,13 +546,13 @@ directory.")
 (define-public r-htmlwidgets
   (package
     (name "r-htmlwidgets")
-    (version "1.3")
+    (version "1.5")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "htmlwidgets" version))
               (sha256
                (base32
-                "04jsdh14l2zifbjpbbh23w7bxz1wpsas0zb2gy2zwv4yqamzzr7i"))))
+                "1h2sj5h9vcssb73nz63gmw5bajs73m9q807fsypvr621gb1s124i"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-htmltools" ,r-htmltools)
-- 
cgit v1.2.3


From b7e7c320a27e013cd0bfd949f1825924c005278e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 6 Oct 2019 23:06:26 +0200
Subject: gnu: r-maptools: Update to 0.9-8.

* gnu/packages/cran.scm (r-maptools): Update to 0.9-8.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 902a9975a8..500379bdae 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -5326,14 +5326,14 @@ simple method for converting between file types.")
 (define-public r-maptools
   (package
     (name "r-maptools")
-    (version "0.9-5")
+    (version "0.9-8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "maptools" version))
        (sha256
         (base32
-         "1pbvcn9xfx0hxq1ppbfg9xm5j04q4c15nj983yjmg7dlkzq135ax"))))
+         "1ix3cg74w0w6cj8nwi0r9n3y5q9ljc21hm8xq6yqqngs57prvn2x"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-foreign" ,r-foreign)
-- 
cgit v1.2.3


From ab99236eba6d7f932b50652c80eb41946c0a92ef Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 6 Oct 2019 23:06:31 +0200
Subject: gnu: r-later: Update to 1.0.0.

* gnu/packages/cran.scm (r-later): Update to 1.0.0.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 500379bdae..384a0afa5c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -5354,14 +5354,14 @@ exchanging spatial objects with other R packages.")
 (define-public r-later
   (package
     (name "r-later")
-    (version "0.8.0")
+    (version "1.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "later" version))
        (sha256
         (base32
-         "08g503xjxrfxvrzj0cavsrz4m8ykbha64344j1w2r6v17js2hakb"))))
+         "11xjavj7siz0xv2ffq1ld4bwl35jyrcfpvvs4p3ilpifxx49hyr7"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bh" ,r-bh)
-- 
cgit v1.2.3


From 2e6ccd6c2d94313ba37c6d48042a052ff9b0f829 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 6 Oct 2019 23:06:37 +0200
Subject: gnu: r-promises: Update to 1.1.0.

* gnu/packages/cran.scm (r-promises): Update to 1.1.0.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 384a0afa5c..b1e0847622 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -5377,14 +5377,14 @@ time after the current time, after the R execution stack has emptied.")
 (define-public r-promises
   (package
     (name "r-promises")
-    (version "1.0.1")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "promises" version))
        (sha256
         (base32
-         "0n2mlv6bvfb4yhgcml696l9vkbw21pz0smqylivr606z99rwgny2"))))
+         "01l0ydjvvy6afcg5d6pzvk1ikd3djq8n2flv8c831ksn68z0zsn8"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-later" ,r-later)
-- 
cgit v1.2.3


From 770321180fda2e9359842761699a5439047bdf94 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 6 Oct 2019 23:06:42 +0200
Subject: gnu: r-hdf5r: Update to 1.3.0.

* gnu/packages/cran.scm (r-hdf5r): Update to 1.3.0.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b1e0847622..6073804398 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -5847,14 +5847,14 @@ results to the user.")
 (define-public r-hdf5r
   (package
     (name "r-hdf5r")
-    (version "1.2.0")
+    (version "1.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "hdf5r" version))
        (sha256
         (base32
-         "10gynjwaaxks8y9c2fl8k040j0nbwn372nil70009yfk9wrkx0aq"))))
+         "1pq12vkfqxvcaznwaxvjdg3acimk5a20m8h18sixvxc34vnqxw8f"))))
     (build-system r-build-system)
     (inputs
      `(("hdf5" ,hdf5)
-- 
cgit v1.2.3


From 9b112f403059aadb268b8844c84fe08a5747f8c7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 6 Oct 2019 23:06:49 +0200
Subject: gnu: r-rcppparallel: Update to 4.4.4.

* gnu/packages/cran.scm (r-rcppparallel): Update to 4.4.4.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 6073804398..7a856df734 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8947,14 +8947,14 @@ package provides a minimal R interface by relying on the Rcpp package.")
 (define-public r-rcppparallel
   (package
     (name "r-rcppparallel")
-    (version "4.4.3")
+    (version "4.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RcppParallel" version))
        (sha256
         (base32
-         "1ym0bzs9g6bsg2lz24fisxxa3gypr6xcvrczn304czmrrag9413s"))))
+         "0p13f2mywjr7gmskf8ri4y8p5yr1bvr4xrpw2w11vdvafwz1vcia"))))
     (properties `((upstream-name . "RcppParallel")))
     (build-system r-build-system)
     (home-page "http://rcppcore.github.io/RcppParallel")
-- 
cgit v1.2.3


From f817005bfeb904810e102c3f675036ff34857229 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 6 Oct 2019 23:06:54 +0200
Subject: gnu: r-gargle: Update to 0.4.0.

* gnu/packages/cran.scm (r-gargle): Update to 0.4.0.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 7a856df734..8754f83f72 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -10304,14 +10304,14 @@ and manipulating sets of ontological terms.")
 (define-public r-gargle
   (package
     (name "r-gargle")
-    (version "0.3.1")
+    (version "0.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gargle" version))
        (sha256
         (base32
-         "0vqgp4w03sdyj0q96gxkybqflzzbaw84zifsbi7pxk5y08fimj2v"))))
+         "08zhfk2sl342w35i5n2c93ayypg3z0kbl0020l3y9adqka1vazgx"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-fs" ,r-fs)
-- 
cgit v1.2.3


From 07d0645b6bc0d191dcf3d635159a8951ad395e0b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 6 Oct 2019 23:06:59 +0200
Subject: gnu: r-backports: Update to 1.1.5.

* gnu/packages/statistics.scm (r-backports): Update to 1.1.5.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 0c98e61cbc..3c69901a0a 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2119,14 +2119,14 @@ limited to R.")
 (define-public r-backports
   (package
     (name "r-backports")
-    (version "1.1.4")
+    (version "1.1.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "backports" version))
        (sha256
         (base32
-         "00zz969vc2gfi5p9q65pzghq2bxm3p9zqgwqswkyz9rgybz5wjzf"))))
+         "0k19w68b2aihyj5mflw3732gkkzs78sssqdns960pdw3yfnkiv33"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/backports")
     (synopsis "Reimplementations of functions introduced since R 3.0.0")
-- 
cgit v1.2.3


From 1c2e573302421bf7c130afcac4c9207f63222333 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 6 Oct 2019 23:07:04 +0200
Subject: gnu: r-regioner: Update to 1.16.5.

* gnu/packages/bioconductor.scm (r-regioner): Update to 1.16.5.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7ca6788dd8..9d6f5bb2ad 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1192,14 +1192,14 @@ the Human Protein Atlas project.")
 (define-public r-regioner
   (package
     (name "r-regioner")
-    (version "1.16.4")
+    (version "1.16.5")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "regioneR" version))
        (sha256
         (base32
-         "0xzk057h6nkr3rvd412prxgnkpq625b90laj1kwb0i5q8j5ch760"))))
+         "12x7sh5d8y549hqz4qjb2j3ak22l79w9l0vdbv4gn0bwi5206k8h"))))
     (properties `((upstream-name . "regioneR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From eb796f53efd5332b401a5756429b8710664ee930 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 6 Oct 2019 23:07:09 +0200
Subject: gnu: r-mixomics: Update to 6.8.5.

* gnu/packages/bioconductor.scm (r-mixomics): Update to 6.8.5.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9d6f5bb2ad..9de3deedea 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5343,14 +5343,14 @@ self-organizing map clustering and minimal spanning trees.")
 (define-public r-mixomics
   (package
     (name "r-mixomics")
-    (version "6.8.4")
+    (version "6.8.5")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mixOmics" version))
        (sha256
         (base32
-         "0lw4c9lxcm83xrvl4y120i1z710qjbdqginhrw738azpr1f82hcg"))))
+         "0s93ai5d7li8pnxd87n12j9gypvac5zfahsk68j7zjv68dglj8s7"))))
     (properties `((upstream-name . "mixOmics")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 326746e14ce792710d41c24ad6994d1ac432d1b3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 6 Oct 2019 23:07:16 +0200
Subject: gnu: r-variancepartition: Update to 1.14.1.

* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.14.1.
[propagated-inputs]: Add r-biocparallel.
---
 gnu/packages/bioconductor.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9de3deedea..7b0405427c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6010,19 +6010,20 @@ arrays based on fast wavelet-based functional models.")
 (define-public r-variancepartition
   (package
     (name "r-variancepartition")
-    (version "1.14.0")
+    (version "1.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "variancePartition" version))
        (sha256
         (base32
-         "1ycapwb2mq57xibrzzjz9zwxqz4nwz9f3n5gskhlr5vcs7irkjd6"))))
+         "0w4kri2389x1082xppx7l6xl1a5g74fyp02iwb4938x3gzwqwbjd"))))
     (properties
      `((upstream-name . "variancePartition")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
+       ("r-biocparallel" ,r-biocparallel)
        ("r-colorramps" ,r-colorramps)
        ("r-doparallel" ,r-doparallel)
        ("r-foreach" ,r-foreach)
-- 
cgit v1.2.3


From b44271350b897aff8cd90b5e77b3c40b0bf6e3dc Mon Sep 17 00:00:00 2001
From: Brian Leung <leungbk@mailfence.com>
Date: Mon, 7 Oct 2019 01:43:37 +0200
Subject: gnu: emacs-deadgrep: Update to 0.8-2.3fc7ca1.

* gnu/packages/emacs-xyz.scm (emacs-deadgrep): Update to 0.8-2.3fc7ca1.
---
 gnu/packages/emacs-xyz.scm | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 5be5b4be45..85931912d4 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -15107,10 +15107,8 @@ accept and reject GitHub pull requests.")
       (license license:gpl3+))))
 
 (define-public emacs-deadgrep
-  ;; We prefer a newer commit (four commits newer than release) because of a
-  ;; bugfix for globbing.
-  (let ((commit "329119c65126f7917d3910bc584f4191ba8f21ac")
-        (revision "1"))
+  (let ((commit "3fc7ca1f58e190f0c80da455a0e40187e673020e")
+        (revision "2"))
     (package
       (name "emacs-deadgrep")
       (version (git-version "0.8" revision commit))
@@ -15123,7 +15121,7 @@ accept and reject GitHub pull requests.")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "0fxf7gq9sjfkgpdfqx10w3l3nd4rwa8kv9plyxk1fqacb3s5m6ai"))))
+           "016gwqxd9aqzjw3hqv3vdf8cs6la8r65g6azg5rlmjqwfx3vsaha"))))
       (build-system emacs-build-system)
       (inputs
        `(("emacs-dash" ,emacs-dash)
-- 
cgit v1.2.3


From 47467ce75ab8c4ea24b9c8bf21d7e1041b8e603e Mon Sep 17 00:00:00 2001
From: Brian Leung <leungbk@mailfence.com>
Date: Sun, 6 Oct 2019 07:31:25 +0200
Subject: gnu: Add emacs-peg.

* gnu/packages/emacs-xyz.scm (emacs-peg): New variable.
---
 gnu/packages/emacs-xyz.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

(limited to 'gnu')

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 85931912d4..95cb9951de 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -11715,6 +11715,26 @@ tables of contents.")
 timestamps by providing a @code{ts} struct.")
       (license license:gpl3+))))
 
+(define-public emacs-peg
+  (package
+    (name "emacs-peg")
+    (version "0.6")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/emacsmirror/peg")
+                    (commit version)))
+              (sha256
+               (base32
+                "0kjz7ch4bn0m4v9zgqyqcrsasnqc5c5drv2hp22j7rnbb7ny0q3n"))
+              (file-name (git-file-name name version))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/emacsmirror/peg/")
+    (synopsis "Parsing Expression Grammars in Elisp")
+    (description "This package provides a macro that parses the current buffer
+according to a parsing expression grammar.")
+    (license license:gpl3+)))
+
 (define-public emacs-org-ql
   (package
     (name "emacs-org-ql")
-- 
cgit v1.2.3


From 3f68853557ba57918c99cca5aad1c2d3daee8f54 Mon Sep 17 00:00:00 2001
From: Brian Leung <leungbk@mailfence.com>
Date: Mon, 7 Oct 2019 05:15:55 +0200
Subject: gnu: emacs-evil-traces: Update to 0.0.1-2.1931e3e.

* gnu/packages/emacs-xyz.scm (emacs-evil-traces): Update to 0.0.1-2.1931e3e.
---
 gnu/packages/emacs-xyz.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 95cb9951de..7959f283f7 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -18204,8 +18204,8 @@ corresponding Evil keys.")
       (license license:expat))))
 
 (define-public emacs-evil-traces
-  (let ((commit "b41b7432b8110378c199a3d25af464083777f453")
-        (revision "1"))
+  (let ((commit "1931e3ea2c64b4aec393a9c25063c330deff55e3")
+        (revision "2"))
     (package
       (name "emacs-evil-traces")
       (version (git-version "0.0.1" revision commit))
@@ -18217,7 +18217,7 @@ corresponding Evil keys.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0a15f2saynz9fws1h5s7py3cshsk4xs1kwgwj1m5rsin36g0j6hc"))))
+                  "12p9lfxscs182vbd4dy0m5gacs3d4kyprbz5yndpwvl8g2qsqplz"))))
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-evil" ,emacs-evil)))
-- 
cgit v1.2.3


From 4f2a3fbe8872f02e5186d354444da2dbee6b7c5f Mon Sep 17 00:00:00 2001
From: Brian Leung <leungbk@mailfence.com>
Date: Mon, 7 Oct 2019 08:20:50 +0200
Subject: gnu: emacs-evil-nerd-commenter: Update to 3.3.8.

* gnu/packages/emacs-xyz.scm (emacs-evil-nerd-commenter): Update to 3.3.8.
---
 gnu/packages/emacs-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 7959f283f7..5f8b3952fd 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -7292,7 +7292,7 @@ pasting into and from @code{tmux} paste buffers.")
 (define-public emacs-evil-nerd-commenter
   (package
     (name "emacs-evil-nerd-commenter")
-    (version "3.3.7")
+    (version "3.3.8")
     (source
      (origin
        (method git-fetch)
@@ -7302,7 +7302,7 @@ pasting into and from @code{tmux} paste buffers.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1r8shfdddys9vqvrxf7s6z83ydqx9xhqs9sa7klbsajryqcp50b7"))))
+         "0qd5a89mzvdyhd8lm13iwp220vzpd6dajwx54frlc5bzsxdmg6vc"))))
     (build-system emacs-build-system)
     (propagated-inputs `(("emacs-evil" ,emacs-evil)))
     (arguments
-- 
cgit v1.2.3


From 4261a9d162f723347981dfc6e72c8938343681a5 Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Mon, 7 Oct 2019 10:21:19 +0300
Subject: gnu: emacs-mbsync: Update to 0.1.2-4.b62491c.

* gnu/packages/emacs-xyz.scm (emacs-mbsync): Update to 0.1.2-4.b62491c.
---
 gnu/packages/emacs-xyz.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 5f8b3952fd..e87fa2ad11 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -12654,8 +12654,8 @@ key again.")
     (license license:gpl3+)))
 
 (define-public emacs-mbsync
-  (let ((commit "8f80c267cab1acb0d5bdd5b0059f5d1790d499ff")
-        (revision "3"))
+  (let ((commit "b62491c0e0d89eb9c66261a16d7ac81231c9c453")
+        (revision "4"))
     (package
       (name "emacs-mbsync")
       (version (git-version "0.1.2" revision commit))
@@ -12668,7 +12668,7 @@ key again.")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "1dwlpcczsa6b7bwv5149by0qmk8v2y7bjad02k4fy25yxznqzci9"))))
+           "1zlih37mkqjn2czl12zn7lgxxljvrwhqqpbksj9c91zn0f0rm3mz"))))
       (build-system emacs-build-system)
       (home-page "https://github.com/dimitri/mbsync-el")
       (synopsis "Interface to mbsync for Emacs")
-- 
cgit v1.2.3


From d3e22bcc1141cd33dde7017f51058f18d428917c Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Mon, 7 Oct 2019 09:50:51 +0200
Subject: gnu: icedtea-7: Support non-Intel systems.

This is a followup to 1b6f99ea538d767099596860017e67755c1ac42f.

* gnu/packages/java.scm (icedtea-7)[arguments]: In 'install-libjvm'
phase, match armhf and aarch64.
[supported-systems]: New field.
---
 gnu/packages/java.scm | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

(limited to 'gnu')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 3b7404973a..452180eead 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -1377,11 +1377,17 @@ bootstrapping purposes.")
              (lambda* (#:key inputs outputs #:allow-other-keys)
                (let* ((lib-path (string-append (assoc-ref outputs "out")
                                                "/lib/"
+                                               ;; See 'INSTALL_ARCH_DIR' in
+                                               ;; 'configure'.
                                                ,(match (%current-system)
                                                   ("i686-linux"
                                                    "i386")
                                                   ("x86_64-linux"
-                                                   "amd64")))))
+                                                   "amd64")
+                                                  ("armhf-linux"
+                                                   "arm")
+                                                  ("aarch64-linux"
+                                                   "aarch64")))))
                  (symlink (string-append lib-path "/server/libjvm.so")
                           (string-append lib-path "/libjvm.so")))
                #t))
@@ -1529,6 +1535,10 @@ bootstrapping purposes.")
       (description
        "This package provides the Java development kit OpenJDK built with the
 IcedTea build harness.")
+
+      ;; 'configure' lists "mips" and "mipsel", but not "mips64el'.
+      (supported-systems (delete "mips64el-linux" %supported-systems))
+
       ;; IcedTea is released under the GPL2 + Classpath exception, which is the
       ;; same license as both GNU Classpath and OpenJDK.
       (license license:gpl2+))))
-- 
cgit v1.2.3


From 7b6a8e23b0de18262a42e44432f955517d71d796 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 7 Oct 2019 11:18:45 +0300
Subject: gnu: aria2: Update to 1.35.0.

* gnu/packages/bittorrent.scm (aria2): Update to 1.35.0.
[source]: Use new upstream uri. Remove patch.
* gnu/packages/patches/aria2-CVE-2019-3500.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                   |  1 -
 gnu/packages/bittorrent.scm                    | 13 +++---
 gnu/packages/patches/aria2-CVE-2019-3500.patch | 55 --------------------------
 3 files changed, 6 insertions(+), 63 deletions(-)
 delete mode 100644 gnu/packages/patches/aria2-CVE-2019-3500.patch

(limited to 'gnu')

diff --git a/gnu/local.mk b/gnu/local.mk
index 54ae09f619..ffe697c2e1 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -695,7 +695,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/antlr3-3_1-fix-java8-compilation.patch	\
   %D%/packages/patches/antlr3-3_3-fix-java8-compilation.patch	\
   %D%/packages/patches/apr-skip-getservbyname-test.patch	\
-  %D%/packages/patches/aria2-CVE-2019-3500.patch		\
   %D%/packages/patches/aspell-default-dict-dir.patch		\
   %D%/packages/patches/ath9k-htc-firmware-binutils.patch	\
   %D%/packages/patches/ath9k-htc-firmware-gcc.patch		\
diff --git a/gnu/packages/bittorrent.scm b/gnu/packages/bittorrent.scm
index 50b63048e4..da01848ec7 100644
--- a/gnu/packages/bittorrent.scm
+++ b/gnu/packages/bittorrent.scm
@@ -2,7 +2,7 @@
 ;;; Copyright © 2014 Taylan Ulrich Bayirli/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2017, 2018, 2019 Leo Famulari <leo@famulari.name>
-;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Tomáš Čech <sleep_walker@gnu.org>
 ;;; Copyright © 2016, 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Jelle Licht <jlicht@fsfe.org>
@@ -262,16 +262,15 @@ maintained upstream.")
 (define-public aria2
   (package
     (name "aria2")
-    (version "1.34.0")
+    (version "1.35.0")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://github.com/tatsuhiro-t/aria2/"
-                                  "releases/download/release-" version "/"
-                                  name "-" version ".tar.xz"))
-              (patches (search-patches "aria2-CVE-2019-3500.patch"))
+              (uri (string-append "https://github.com/aria2/aria2/releases/"
+                                  "download/release-" version
+                                  "/aria2-" version ".tar.xz"))
               (sha256
                (base32
-                "18vpgr430vxlwbcc3598rr1srfmwypls6wp1m4wf21hncc1ahi1s"))))
+                "1zbxc517d97lb96f15xcy4l7b66grxrp3h2ids2jiwkaip87yaqy"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags (list "--enable-libaria2"
diff --git a/gnu/packages/patches/aria2-CVE-2019-3500.patch b/gnu/packages/patches/aria2-CVE-2019-3500.patch
deleted file mode 100644
index 891c9047ba..0000000000
--- a/gnu/packages/patches/aria2-CVE-2019-3500.patch
+++ /dev/null
@@ -1,55 +0,0 @@
-Fix CVE-2019-3500:
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2019-3500
-https://github.com/aria2/aria2/issues/1329
-
-Patch copied from upstream source repository:
-
-https://github.com/aria2/aria2/commit/37368130ca7de5491a75fd18a20c5c5cc641824a
-
-From 37368130ca7de5491a75fd18a20c5c5cc641824a Mon Sep 17 00:00:00 2001
-From: Tatsuhiro Tsujikawa <tatsuhiro.t@gmail.com>
-Date: Sat, 5 Jan 2019 09:32:40 +0900
-Subject: [PATCH] Mask headers
-
----
- src/HttpConnection.cc | 18 ++++++++++++------
- 1 file changed, 12 insertions(+), 6 deletions(-)
-
-diff --git a/src/HttpConnection.cc b/src/HttpConnection.cc
-index 77cb9d27a..be5b97723 100644
---- a/src/HttpConnection.cc
-+++ b/src/HttpConnection.cc
-@@ -102,11 +102,17 @@ std::string HttpConnection::eraseConfidentialInfo(const std::string& request)
-   std::string result;
-   std::string line;
-   while (getline(istr, line)) {
--    if (util::startsWith(line, "Authorization: Basic")) {
--      result += "Authorization: Basic ********\n";
-+    if (util::istartsWith(line, "Authorization: ")) {
-+      result += "Authorization: <snip>\n";
-     }
--    else if (util::startsWith(line, "Proxy-Authorization: Basic")) {
--      result += "Proxy-Authorization: Basic ********\n";
-+    else if (util::istartsWith(line, "Proxy-Authorization: ")) {
-+      result += "Proxy-Authorization: <snip>\n";
-+    }
-+    else if (util::istartsWith(line, "Cookie: ")) {
-+      result += "Cookie: <snip>\n";
-+    }
-+    else if (util::istartsWith(line, "Set-Cookie: ")) {
-+      result += "Set-Cookie: <snip>\n";
-     }
-     else {
-       result += line;
-@@ -154,8 +160,8 @@ std::unique_ptr<HttpResponse> HttpConnection::receiveResponse()
-   const auto& proc = outstandingHttpRequests_.front()->getHttpHeaderProcessor();
-   if (proc->parse(socketRecvBuffer_->getBuffer(),
-                   socketRecvBuffer_->getBufferLength())) {
--    A2_LOG_INFO(
--        fmt(MSG_RECEIVE_RESPONSE, cuid_, proc->getHeaderString().c_str()));
-+    A2_LOG_INFO(fmt(MSG_RECEIVE_RESPONSE, cuid_,
-+                    eraseConfidentialInfo(proc->getHeaderString()).c_str()));
-     auto result = proc->getResult();
-     if (result->getStatusCode() / 100 == 1) {
-       socketRecvBuffer_->drain(proc->getLastBytesProcessed());
-- 
cgit v1.2.3


From 048d21a8733f4173705ed59a22a03caddb876fe1 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Mon, 7 Oct 2019 10:38:22 +0200
Subject: gnu: icedtea-7: Avoid massive rebuild.

Reported by Efraim Flashner.

* gnu/packages/java.scm (icedtea-7)[arguments]: Change 'lib-path'
definition in 'install-libjvm' to avoid the rebuilds that commit
1b6f99ea538d767099596860017e67755c1ac42f would otherwise entail.
---
 gnu/packages/java.scm | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 452180eead..1f5e39d9c6 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -1376,18 +1376,17 @@ bootstrapping purposes.")
            (add-after 'install 'install-libjvm
              (lambda* (#:key inputs outputs #:allow-other-keys)
                (let* ((lib-path (string-append (assoc-ref outputs "out")
-                                               "/lib/"
                                                ;; See 'INSTALL_ARCH_DIR' in
                                                ;; 'configure'.
                                                ,(match (%current-system)
                                                   ("i686-linux"
-                                                   "i386")
+                                                   "/lib/i386")
                                                   ("x86_64-linux"
-                                                   "amd64")
+                                                   "/lib/amd64")
                                                   ("armhf-linux"
-                                                   "arm")
+                                                   "/lib/arm")
                                                   ("aarch64-linux"
-                                                   "aarch64")))))
+                                                   "/lib/aarch64")))))
                  (symlink (string-append lib-path "/server/libjvm.so")
                           (string-append lib-path "/libjvm.so")))
                #t))
-- 
cgit v1.2.3


From 7d82e920717f08bceb42bb570d786dff233171e1 Mon Sep 17 00:00:00 2001
From: Vagrant Cascadian <vagrant@debian.org>
Date: Sun, 6 Oct 2019 06:07:15 +0000
Subject: gnu: linux-libre: Update to 5.3.4.

* gnu/packages/linux (linux-libre-5.3-version): Update to 5.3.4.
  (deblob-scripts-5.3): Update to 5.3.4.
---
 gnu/packages/linux.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 21cd4a205f..910aeed6ff 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -184,9 +184,9 @@ defconfig.  Return the appropriate make target if applicable, otherwise return
 
 (define deblob-scripts-5.3
   (linux-libre-deblob-scripts
-   "5.3.1"
+   "5.3.4"
    (base32 "15n09zq38d69y1wl28s3nasf3377qp2yil5b887zpqrm00dif7i4")
-   (base32 "1av9ykv714cnl0clls8rhwa8rwflz6ivg17gharj1x650qp6vnw3")))
+   (base32 "0nrimraf46nf6y1hwkg29fyl0a83wnj0mwq54ggxvffn9gk5h9pa")))
 
 (define deblob-scripts-5.2
   (linux-libre-deblob-scripts
@@ -358,10 +358,10 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
                         "linux-" version ".tar.xz"))
     (sha256 hash)))
 
-(define-public linux-libre-5.3-version "5.3.2")
+(define-public linux-libre-5.3-version "5.3.4")
 (define-public linux-libre-5.3-pristine-source
   (let ((version linux-libre-5.3-version)
-        (hash (base32 "0szw21mpp94gp3zn2fgllbv6fdjjf20njgrcjay7vjmm7farq7rn")))
+        (hash (base32 "0vi4bgcr921z5l6fbcrcgmhaji5gl2avpmp7njna6v0f7sxism0r")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.3)))
-- 
cgit v1.2.3


From 85747bab82f529a476a5468f0c0f48b8ba047594 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 7 Oct 2019 13:45:53 +0200
Subject: gnu: sbcl-optima: Fix version number

* gnu/packages/lisp.scm (sbcl-optima)[version]: It's actually 1.0.
---
 gnu/packages/lisp.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu')

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index ed3efc7bdb..c358aa6465 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -6388,7 +6388,7 @@ the return type of a function.")
     (package
       (name "sbcl-optima")
       (build-system asdf-build-system/sbcl)
-      (version (git-version "0.1" revision commit))
+      (version (git-version "1.0" revision commit))
       (home-page "https://github.com/m2ym/optima")
       (source
        (origin
-- 
cgit v1.2.3


From 7baaf7f3587961255d429087e5d18d35275a176d Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 7 Oct 2019 13:46:36 +0200
Subject: gnu: Add cl-fare-quasiquote.

* gnu/packages/lisp.scm (cl-fare-quasiquote): New variable.
---
 gnu/packages/lisp.scm | 3 +++
 1 file changed, 3 insertions(+)

(limited to 'gnu')

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index c358aa6465..c1ea8cc37b 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -6451,6 +6451,9 @@ quasiquote is enable matching of quasiquoted patterns, using Optima or
 Trivia.")
     (license license:expat)))
 
+(define-public cl-fare-quasiquote
+  (sbcl-package->cl-source-package sbcl-fare-quasiquote))
+
 (define-public sbcl-fare-quasiquote-readtable
   (package
     (inherit sbcl-fare-quasiquote)
-- 
cgit v1.2.3


From 06e2da719ea95a9d48ad86002ab183c5114ff2b1 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 7 Oct 2019 13:46:55 +0200
Subject: gnu: Add fare-quasiquote-optima.

* gnu/packages/lisp.scm (cl-fare-quasiquote-optima,
  sbcl-fare-quasiquote-optima): New variables.
---
 gnu/packages/lisp.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

(limited to 'gnu')

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index c1ea8cc37b..4d3b4fbcbc 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -6454,6 +6454,26 @@ Trivia.")
 (define-public cl-fare-quasiquote
   (sbcl-package->cl-source-package sbcl-fare-quasiquote))
 
+(define-public sbcl-fare-quasiquote-optima
+  (package
+    (inherit sbcl-fare-quasiquote)
+    (name "sbcl-fare-quasiquote-optima")
+    (inputs
+     `(("optima" ,sbcl-optima)
+       ("fare-quasiquote" ,sbcl-fare-quasiquote)))
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-requirement
+           (lambda _
+             (substitute* "fare-quasiquote-optima.asd"
+               (("\\(:version \"optima\" \"1\\.0\"\\)")
+                "\"optima\""))
+             #t)))))))
+
+(define-public cl-fare-quasiquote-optima
+  (sbcl-package->cl-source-package sbcl-fare-quasiquote-optima))
+
 (define-public sbcl-fare-quasiquote-readtable
   (package
     (inherit sbcl-fare-quasiquote)
-- 
cgit v1.2.3


From 7b9cb9c01c097f66c0b617ad4e7462ee72a349c9 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 7 Oct 2019 13:47:46 +0200
Subject: gnu: Add cl-fare-quasiquote-readtable.

* gnu/packages/lisp.scm (cl-fare-quasiquote-readtable): New variable.
---
 gnu/packages/lisp.scm | 3 +++
 1 file changed, 3 insertions(+)

(limited to 'gnu')

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 4d3b4fbcbc..b2cd4dd352 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -6487,6 +6487,9 @@ Trivia.
 
 This package uses fare-quasiquote with named-readtable.")))
 
+(define-public cl-fare-quasiquote-readtable
+  (sbcl-package->cl-source-package sbcl-fare-quasiquote-readtable))
+
 (define-public sbcl-trivia.level0
   (let ((commit "902e0c65602bbfe96ae82e679330b3771ddc7603")
         (revision "1"))
-- 
cgit v1.2.3


From 6fdb5b79478d0c6087a1b05cd092ec87f7435c72 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 7 Oct 2019 13:48:00 +0200
Subject: gnu: Add cl-fare-quasiquote-extras.

* gnu/packages/lisp.scm (cl-fare-quasiquote-extras): New variable.
---
 gnu/packages/lisp.scm | 13 +++++++++++++
 1 file changed, 13 insertions(+)

(limited to 'gnu')

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index b2cd4dd352..0ca815fb2e 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -6490,6 +6490,19 @@ This package uses fare-quasiquote with named-readtable.")))
 (define-public cl-fare-quasiquote-readtable
   (sbcl-package->cl-source-package sbcl-fare-quasiquote-readtable))
 
+;; TODO: Add support for component-less system in asdf-build-system/sbcl.
+(define-public cl-fare-quasiquote-extras
+  (package
+    (inherit cl-fare-quasiquote)
+    (name "cl-fare-quasiquote-extras")
+    (build-system asdf-build-system/source)
+    (propagated-inputs
+     `(("fare-quasiquote" ,cl-fare-quasiquote)
+       ("fare-quasiquote-optima" ,cl-fare-quasiquote-optima)
+       ("fare-quasiquote-readtable" ,cl-fare-quasiquote-readtable)))
+    (description "This library combines @code{fare-quasiquote-readtable} and
+@code{fare-quasiquote-optima}.")))
+
 (define-public sbcl-trivia.level0
   (let ((commit "902e0c65602bbfe96ae82e679330b3771ddc7603")
         (revision "1"))
-- 
cgit v1.2.3


From 3658db3fd73d3e04e81e5a3b03d2c395312e833a Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 7 Oct 2019 13:48:23 +0200
Subject: gnu: Add string-case.

* gnu/packages/lisp.scm (cl-string-case, ecl-string-case, sbcl-string-case):
  New variables.
---
 gnu/packages/lisp.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

(limited to 'gnu')

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 0ca815fb2e..debe568347 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -7527,3 +7527,33 @@ of C+GObject libraries without the need of writing dedicated bindings.")
 
 (define-public cl-gobject-introspection
   (sbcl-package->cl-source-package sbcl-cl-gobject-introspection))
+
+(define-public sbcl-string-case
+  (let ((commit "718c761e33749e297cd2809c7ba3ade1985c49f7")
+        (revision "0"))
+    (package
+      (name "sbcl-string-case")
+      (version (git-version "0.0.2" revision commit))
+      (home-page "https://github.com/pkhuong/string-case")
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url home-page)
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "1n5i3yh0h5s636rcnwn7jwqy3rjflikra04lymimhpcshhjsk0md"))))
+      (build-system asdf-build-system/sbcl)
+      (synopsis "Efficient string= case in Common Lisp")
+      (description
+       "@code{string-case} is a Common Lisp macro that generates specialised decision
+trees to dispatch on string equality.")
+      (license license:bsd-3))))
+
+(define-public cl-string-case
+  (sbcl-package->cl-source-package sbcl-string-case))
+
+(define-public ecl-string-case
+  (sbcl-package->ecl-package sbcl-string-case))
-- 
cgit v1.2.3


From 003a714e7e1f458b84e60b7480149a59b034312c Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 7 Oct 2019 13:48:52 +0200
Subject: gnu: Add global-vars.

* gnu/packages/lisp.scm (cl-global-vars, ecl-global-vars, sbcl-global-vars):
  New variables.
---
 gnu/packages/lisp.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

(limited to 'gnu')

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index debe568347..88261d5f8e 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -7557,3 +7557,40 @@ trees to dispatch on string equality.")
 
 (define-public ecl-string-case
   (sbcl-package->ecl-package sbcl-string-case))
+
+(define-public sbcl-global-vars
+  (let ((commit "c749f32c9b606a1457daa47d59630708ac0c266e")
+        (revision "0"))
+    (package
+      (name "sbcl-global-vars")
+      (version (git-version "1.0.0" revision commit))
+      (home-page "https://github.com/lmj/global-vars")
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url home-page)
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "06m3xc8l3pgsapl8fvsi9wf6y46zs75cp9zn7zh6dc65v4s5wz3d"))))
+      (build-system asdf-build-system/sbcl)
+      (synopsis "Efficient global variables in Common Lisp")
+      (description
+       "In Common Lisp, a special variable that is never dynamically bound
+typically serves as a stand-in for a global variable.  The @code{global-vars}
+library provides true global variables that are implemented by some compilers.
+An attempt to rebind a global variable properly results in a compiler error.
+That is, a global variable cannot be dynamically bound.
+
+Global variables therefore allow us to communicate an intended usage that
+differs from special variables.  Global variables are also more efficient than
+special variables, especially in the presence of threads.")
+      (license license:expat))))
+
+(define-public cl-global-vars
+  (sbcl-package->cl-source-package sbcl-global-vars))
+
+(define-public ecl-global-vars
+  (sbcl-package->ecl-package sbcl-global-vars))
-- 
cgit v1.2.3


From c6dd9cf7ffd968520e78c438f7064935c40e139d Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 7 Oct 2019 13:49:42 +0200
Subject: gnu: Add trivial-file-size.

* gnu/packages/lisp.scm (cl-trivial-file-size, ecl-trivial-file-size,
  sbcl-trivial-file-size): New variables.
---
 gnu/packages/lisp.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

(limited to 'gnu')

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 88261d5f8e..031d172c39 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -7594,3 +7594,41 @@ special variables, especially in the presence of threads.")
 
 (define-public ecl-global-vars
   (sbcl-package->ecl-package sbcl-global-vars))
+
+(define-public sbcl-trivial-file-size
+  (let ((commit "1c1d672a01a446ba0391dbb4ffc40be3b0476f23")
+        (revision "0"))
+    (package
+      (name "sbcl-trivial-file-size")
+      (version (git-version "0.0.0" revision commit))
+      (home-page "https://github.com/ruricolist/trivial-file-size")
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url home-page)
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "17pp86c9zs4y7i1sh7q9gbfw9iqv6655k7fz8qbj9ly1ypgxp4qs"))))
+      (build-system asdf-build-system/sbcl)
+      (native-inputs
+       `(("fiveam" ,sbcl-fiveam)))
+      (synopsis "Size of a file in bytes in Common Lisp")
+      (description
+       "The canonical way to determine the size of a file in bytes, using Common Lisp,
+is to open the file with an element type of (unsigned-byte 8) and then
+calculate the length of the stream.  This is less than ideal.  In most cases
+it is better to get the size of the file from its metadata, using a system
+call.
+
+This library exports a single function, file-size-in-octets.  It returns the
+size of a file in bytes, using system calls when possible.")
+      (license license:expat))))
+
+(define-public cl-trivial-file-size
+  (sbcl-package->cl-source-package sbcl-trivial-file-size))
+
+(define-public ecl-trivial-file-size
+  (sbcl-package->ecl-package sbcl-trivial-file-size))
-- 
cgit v1.2.3


From fa4bbd9f3427994b3041ec6834500a864dbbe238 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 7 Oct 2019 13:50:07 +0200
Subject: gnu: Add trivial-macroexpand-all.

* gnu/packages/lisp.scm (cl-trivial-macroexpand-all,
  ecl-trivial-macroexpand-all, sbcl-trivial-macroexpand-all): New variables.
---
 gnu/packages/lisp.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

(limited to 'gnu')

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 031d172c39..84597e4e73 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -7632,3 +7632,35 @@ size of a file in bytes, using system calls when possible.")
 
 (define-public ecl-trivial-file-size
   (sbcl-package->ecl-package sbcl-trivial-file-size))
+
+(define-public sbcl-trivial-macroexpand-all
+  (let ((commit "933270ac7107477de1bc92c1fd641fe646a7a8a9")
+        (revision "0"))
+    (package
+      (name "sbcl-trivial-macroexpand-all")
+      (version (git-version "0.0.0" revision commit))
+      (home-page "https://github.com/cbaggers/trivial-macroexpand-all")
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url home-page)
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "191hnn4b5j4i3crydmlzbm231kj0h7l8zj6mzj69r1npbzkas4bd"))))
+      (build-system asdf-build-system/sbcl)
+      (native-inputs
+       `(("fiveam" ,sbcl-fiveam)))
+      (synopsis "Portable macroexpand-all for Common Lisp")
+      (description
+       "This library provides a macroexpand-all function that calls the
+implementation specific equivalent.")
+      (license license:unlicense))))
+
+(define-public cl-trivial-macroexpand-all
+  (sbcl-package->cl-source-package sbcl-trivial-macroexpand-all))
+
+(define-public ecl-trivial-macroexpand-all
+  (sbcl-package->ecl-package sbcl-trivial-macroexpand-all))
-- 
cgit v1.2.3


From fa984fa678f98ddc72cc89c6f6dc50ba4aff2487 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 7 Oct 2019 16:32:03 +0200
Subject: gnu: jack-2: Update to 1.9.13.

* gnu/packages/audio.scm (jack-2): Update to 1.9.13.
[arguments]: Don't build with python-2.
[inputs]: Replace python2-dbus with python-dbus.
---
 gnu/packages/audio.scm | 42 ++++++++++++++++++++----------------------
 1 file changed, 20 insertions(+), 22 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 6eb61583f7..afa02c1239 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -1532,7 +1532,7 @@ synchronous execution of all clients, and low latency operation.")
 (define-public jack-2
   (package (inherit jack-1)
     (name "jack2")
-    (version "1.9.12")
+    (version "1.9.13")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/jackaudio/jack2/releases/"
@@ -1541,40 +1541,38 @@ synchronous execution of all clients, and low latency operation.")
              (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
-               "0crf4y9a5j9miw8r5ji4l3w5w0y2frrf7xyfsfdgacnw6vwy5vyy"))))
+               "1d1d403jn4366mqig6g8ghr8057b3rn7gs26b5p3rkal34j20qw2"))))
     (build-system waf-build-system)
     (arguments
-     `(#:python ,python-2
-       #:tests? #f  ; no check target
+     `(#:tests? #f  ; no check target
        #:configure-flags '("--dbus"
                            "--alsa")
        #:phases
        (modify-phases %standard-phases
-         (add-before
-          'configure 'set-linkflags
-          (lambda _
-            ;; Add $libdir to the RUNPATH of all the binaries.
-            (substitute* "wscript"
-              ((".*CFLAGS.*-Wall.*" m)
-               (string-append m
-                              "    conf.env.append_unique('LINKFLAGS',"
-                              "'-Wl,-rpath=" %output "/lib')\n")))
-            #t))
+         (add-before 'configure 'set-linkflags
+           (lambda _
+             ;; Add $libdir to the RUNPATH of all the binaries.
+             (substitute* "wscript"
+               ((".*CFLAGS.*-Wall.*" m)
+                (string-append m
+                               "    conf.env.append_unique('LINKFLAGS',"
+                               "'-Wl,-rpath=" %output "/lib')\n")))
+             #t))
          (add-after 'install 'wrap-python-scripts
-          (lambda* (#:key inputs outputs #:allow-other-keys)
-            ;; Make sure 'jack_control' runs with the correct PYTHONPATH.
-            (let* ((out (assoc-ref outputs "out"))
-                   (path (getenv "PYTHONPATH")))
-              (wrap-program (string-append out "/bin/jack_control")
-                `("PYTHONPATH" ":" prefix (,path))))
-            #t)))))
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             ;; Make sure 'jack_control' runs with the correct PYTHONPATH.
+             (let* ((out (assoc-ref outputs "out"))
+                    (path (getenv "PYTHONPATH")))
+               (wrap-program (string-append out "/bin/jack_control")
+                 `("PYTHONPATH" ":" prefix (,path))))
+             #t)))))
     (inputs
      `(("alsa-lib" ,alsa-lib)
        ("dbus" ,dbus)
        ("expat" ,expat)
        ("libsamplerate" ,libsamplerate)
        ("opus" ,opus)
-       ("python2-dbus" ,python2-dbus)
+       ("python-dbus" ,python-dbus)
        ("readline" ,readline)))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
-- 
cgit v1.2.3