Merge branch 'master' into staging

26 files changed, 197 insertions, 108 deletions

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 05aa746f29..f6be0d387b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -977,7 +977,7 @@ supports interactive trees, to enable rich, editable trees in Shiny.")
        ("r-shiny" ,r-shiny)))
     (native-inputs
      `(("uglify-js" ,uglify-js)))
-    (home-page "http://rstudio.github.io/shinydashboard/")
+    (home-page "https://rstudio.github.io/shinydashboard/")
     (synopsis "Create dashboards with shiny")
     (description "This package provides an extension to the Shiny web
 application framework for R, making it easy to create attractive dashboards.")
@@ -1028,7 +1028,7 @@ well as file saving is available.")
     (properties `((upstream-name . "shinythemes")))
     (build-system r-build-system)
     (propagated-inputs `(("r-shiny" ,r-shiny)))
-    (home-page "http://rstudio.github.io/shinythemes/")
+    (home-page "https://rstudio.github.io/shinythemes/")
     (synopsis "Themes for Shiny")
     (description
      "This package provides themes for use with Shiny.  It includes several
@@ -9534,7 +9534,7 @@ circular variables).")
          "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-subplex" ,r-subplex)))
-    (home-page "http://kingaa.github.io/ouch/")
+    (home-page "https://kingaa.github.io/ouch/")
     (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
     (description
      "This package provides tools to fit and compare Ornstein-Uhlenbeck models
@@ -11584,7 +11584,7 @@ lasso, adaptive lasso and Ridge regression based on cross-validation.")
         (base32
          "1i1nhdapyijvm58zx38q28zk01ndmi6smjivxk5xs2cx9b6v2av9"))))
     (build-system r-build-system)
-    (home-page "http://www.stat.umn.edu/geyer/mcmc/")
+    (home-page "https://www.stat.umn.edu/geyer/mcmc/")
     (synopsis "Markov chain Monte Carlo")
     (description
      "This package simulates continuous distributions of random vectors using
@@ -14319,7 +14319,7 @@ layer by layer.")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-randomforest" ,r-randomforest)))
-    (home-page "http://ligarto.org/rdiaz/Software/Software.html")
+    (home-page "https://www.ligarto.org/rdiaz/software/software")
     (synopsis "Variable selection using random forests")
     (description
      "This package provides tools for the variable selection from random
@@ -16892,7 +16892,7 @@ Components.  The Lasso solution paths can be computed by the same function.")
      `(("r-elasticnet" ,r-elasticnet)
        ("r-mass" ,r-mass)
        ("r-mda" ,r-mda)))
-    (home-page "http://www.imm.dtu.dk/~lhc")
+    (home-page "https://www.imm.dtu.dk/~lkhc/")
     (synopsis "Sparse discriminant analysis")
     (description
      "This package performs sparse linear discriminant analysis for Gaussians
@@ -18003,7 +18003,7 @@ actigraphy-measured activity counts data.")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-matrix" ,r-matrix)))
-    (home-page "http://www.functionaldata.org")
+    (home-page "https://www.functionaldata.org")
     (synopsis "Functional data analysis")
     (description
      "These functions were developed to support functional data analysis as
@@ -20727,3 +20727,26 @@ Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
 lines (isolines) and contour polygons (isobands) from regularly spaced grids
 containing elevation data.")
     (license license:expat)))
+
+(define-public r-ppcor
+  (package
+    (name "r-ppcor")
+    (version "1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ppcor" version))
+       (sha256
+        (base32
+         "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
+    (properties `((upstream-name . "ppcor")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)))
+    (home-page "https://cran.r-project.org/web/packages/ppcor/")
+    (synopsis "Partial and semi-partial correlation")
+    (description
+     "This package provides users not only with a function to readily
+calculate the higher-order partial and semi-partial correlations but also with
+statistics and p-values of the correlation coefficients.")
+    (license license:gpl2)))
diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm
index 82a57d4eaa..34cc479589 100644
--- a/gnu/packages/debug.scm
+++ b/gnu/packages/debug.scm
@@ -27,19 +27,25 @@
   #:use-module (guix git-download)
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system cmake)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
+  #:use-module (gnu packages code)
   #:use-module (gnu packages flex)
+  #:use-module (gnu packages gdb)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages golang)
-  #:use-module (gnu packages code)
   #:use-module (gnu packages llvm)
+  #:use-module (gnu packages ninja)
   #:use-module (gnu packages perl)
+  #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages pretty-print)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages readline)
+  #:use-module (gnu packages serialization)
   #:use-module (gnu packages virtualization)
   #:use-module (ice-9 match)
   #:use-module (srfi srfi-1))
@@ -406,3 +412,66 @@ the position of the variable and allows you to modify its value.")
     ;; The library is covered by LGPLv3 or later; the application is covered
     ;; by GPLv3 or later.
     (license (list lgpl3+ gpl3+))))
+
+(define-public rr
+  (package
+    (name "rr")
+    (version "5.3.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/mozilla/rr")
+                    (commit version)))
+              (sha256
+               (base32
+                "1x6l1xsdksnhz9v50p4r7hhmr077cq20kaywqy1jzdklvkjqzf64"))
+              (file-name (git-file-name name version))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags
+       ;; The 'rr_exec_stub' is a static binary, which leads CMake to fail
+       ;; with:
+       ;;
+       ;;   file RPATH_CHANGE could not write new RPATH:
+       ;;
+       ;; Clear CMAKE_INSTALL_RPATH to avoid that problem.
+       (list "-DCMAKE_INSTALL_RPATH="
+             ,@(if (and (not (%current-target-system))
+                        (member (%current-system)
+                                '("x86_64-linux" "aarch64-linux")))
+                   ;; The toolchain doesn't support '-m32'.
+                   '("-Ddisable32bit=ON")
+                   '()))
+
+       ;; XXX: Most tests fail with:
+       ;;
+       ;;  rr needs /proc/sys/kernel/perf_event_paranoid <= 1, but it is 2.
+       ;;
+       ;; This setting cannot be changed from the build environment, so skip
+       ;; the tests.
+       #:tests? #f
+
+       #:phases (modify-phases %standard-phases
+                  (add-before 'check 'set-home
+                    (lambda _
+                      ;; Some tests expect 'HOME' to be set.
+                      (setenv "HOME" (getcwd))
+                      #t)))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("ninja" ,ninja)
+       ("which" ,which)))
+    (inputs
+     `(("gdb" ,gdb)
+       ("cpanproto" ,capnproto)
+       ("python" ,python)
+       ("python-pexpect" ,python-pexpect)))
+    (home-page "https://rr-project.org/")
+    (synopsis "Record and reply debugging framework")
+    (description
+     "rr is a lightweight tool for recording, replaying and debugging
+execution of applications (trees of processes and threads).  Debugging extends
+GDB with very efficient reverse-execution, which in combination with standard
+GDB/x86 features like hardware data watchpoints, makes debugging much more
+fun.")
+    (license expat)))
diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 984613e54e..d45814379b 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -972,13 +972,13 @@ in certain cases.  It also enables recursion for anonymous functions.")
 (define-public emacs-xr
   (package
     (name "emacs-xr")
-    (version "1.17")
+    (version "1.18")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://elpa.gnu.org/packages/xr-" version ".tar"))
        (sha256
-        (base32 "0kicy15hww85kf7vii1j4yypa9z44d5vbpm65vwb6fzz0lv639zm"))))
+        (base32 "1nq9pj47sxgpkw97c2xrkhgcwh3zsfd2a22qiqbl4i9zf2l9yy91"))))
     (build-system emacs-build-system)
     (home-page "https://elpa.gnu.org/packages/xr.html")
     (synopsis "Convert string regexp to rx notation")
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 8e12f684e0..89a7ffe956 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -97,7 +97,7 @@
 (define-public bitcoin-core
   (package
     (name "bitcoin-core")
-    (version "0.19.0.1")
+    (version "0.19.1")
     (source (origin
              (method url-fetch)
              (uri
@@ -105,7 +105,7 @@
                              version "/bitcoin-" version ".tar.gz"))
              (sha256
               (base32
-               "1172dl4b8h2a80ilk9sfgbl8yi55k6hs4b1m07nic2ls4irgkjbs"))))
+               "1h3w7brc18145np920vy7j5ms5hym59hvr40swdjx34fbdaisngj"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
@@ -495,7 +495,7 @@ other machines/servers.  Electroncash does not download the Bitcoin Cash blockch
   ;; the system's dynamically linked library.
   (package
     (name "monero")
-    (version "0.15.0.1")
+    (version "0.15.0.5")
     (source
      (origin
        (method git-fetch)
@@ -516,7 +516,7 @@ other machines/servers.  Electroncash does not download the Bitcoin Cash blockch
            #t))
        (sha256
         (base32
-         "0sypa235lf2bbib4b71xpaw39h9304slgsvnsz8wmy9fq1zx009m"))))
+         "06zzwa0y8ic6x3y2fy501788r51p4klanyvmm76ywrwf087njlkv"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("doxygen" ,doxygen)
@@ -614,7 +614,7 @@ the Monero command line client and daemon.")
 (define-public monero-gui
   (package
     (name "monero-gui")
-    (version "0.15.0.3")
+    (version "0.15.0.4")
     (source
      (origin
        (method git-fetch)
@@ -624,7 +624,7 @@ the Monero command line client and daemon.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1v2mk6qp7dfdj4j4cilxp0s0phfwwnmjvpvjrz6jzzlpvbnavkr0"))))
+         "12m5fgnxkr11q2arx1m5ccpxqm5ljcvm6l547dwqn297zs5jim4z"))))
     (build-system qt-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm
index c302196104..5fb6bbbe18 100644
--- a/gnu/packages/fonts.scm
+++ b/gnu/packages/fonts.scm
@@ -1270,13 +1270,14 @@ emphasis while still being readable.")
     (source
      (origin
        (method url-fetch/zipbomb)
-       (uri (string-append "http://www.impallari.com/media/releases/dosis-"
+       (uri (string-append "https://web.archive.org/web/20180228233737/"
+                           "https://www.impallari.com/media/releases/dosis-"
                            "v" version ".zip"))
        (sha256
-        (base32
-         "1qhci68f68mf87jd69vjf9qjq3wydgw1q7ivn3amjb65ls1s0c4s"))))
+        (base32 "1qhci68f68mf87jd69vjf9qjq3wydgw1q7ivn3amjb65ls1s0c4s"))))
     (build-system font-build-system)
-    (home-page "http://www.impallari.com/dosis")
+    (home-page (string-append "https://web.archive.org/web/20180228233737/"
+                              "https://www.impallari.com/dosis"))
     (synopsis "Very simple, rounded, sans serif family")
     (description
      "Dosis is a very simple, rounded, sans serif family.
diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm
index 5e6482c53e..1e6485f6b4 100644
--- a/gnu/packages/freedesktop.scm
+++ b/gnu/packages/freedesktop.scm
@@ -179,6 +179,7 @@ freedesktop.org project.")
     (license license:expat)))
 
 (define-public libinput
+  ;; Updating this will rebuild over 700 packages through libinput-minimal.
   (package
     (name "libinput")
     (version "1.15.2")
diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 262633760b..7638a545ca 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -2078,7 +2078,7 @@ a.k.a. XenoCollide) as described in Game Programming Gems 7.")
      `(("glu" ,glu)
        ("libccd" ,libccd)
        ("mesa" ,mesa)))
-    (home-page "http://www.ode.org/")
+    (home-page "https://www.ode.org/")
     (synopsis "High performance library for simulating rigid body dynamics")
     (description "ODE is a high performance library for simulating
 rigid body dynamics.  It is fully featured, stable, mature and
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 322e309591..fa802c79fe 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -2054,7 +2054,7 @@ for common mesh file formats, and collision detection.")
          ("fribidi" ,fribidi)
          ("taglib" ,taglib)
          ("sfml" ,sfml)))
-      (home-page "http://marsshooter.org")
+      (home-page "http://mars-game.sourceforge.net/")
       (synopsis "2D space shooter")
       (description
        "M.A.R.S. is a 2D space shooter with pretty visual effects and
diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index fea50625b6..c69a4e7e03 100644
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@ -554,8 +554,8 @@ from forcing GEXP-PROMISE."
                       #:system system
                       #:guile-for-build guile)))
 
-(define %icecat-version "68.5.0-guix0-preview1")
-(define %icecat-build-id "20200211000000") ;must be of the form YYYYMMDDhhmmss
+(define %icecat-version "68.6.0-guix0-preview1")
+(define %icecat-build-id "20200309000000") ;must be of the form YYYYMMDDhhmmss
 
 ;; 'icecat-source' is a "computed" origin that generates an IceCat tarball
 ;; from the corresponding upstream Firefox ESR tarball, using the 'makeicecat'
@@ -577,11 +577,11 @@ from forcing GEXP-PROMISE."
                   "firefox-" upstream-firefox-version ".source.tar.xz"))
             (sha256
              (base32
-              "1ld6jinnln0si6p8qy93v5nzd21ckhl266vz425lwqipibwq9rsj"))))
+              "17qwfq9hwra8jarawy8k2sqfa6hdhwa9qk84ndr6gjvmxcy22a14"))))
 
-         (upstream-icecat-base-version "68.5.0") ; maybe older than base-version
+         (upstream-icecat-base-version "68.6.0") ; maybe older than base-version
          ;;(gnuzilla-commit (string-append "v" upstream-icecat-base-version))
-         (gnuzilla-commit "2dc3c0bed6f8a41a8426ae66db92729af5c27c70")
+         (gnuzilla-commit "9dcb24d885eae5973eb2245b532b158c685d707a")
          (gnuzilla-source
           (origin
             (method git-fetch)
@@ -593,7 +593,7 @@ from forcing GEXP-PROMISE."
                                       (string-take gnuzilla-commit 8)))
             (sha256
              (base32
-              "1xwr1xjs4j2i6skm8hknh37gzsd6r396n0lchbwlahig7w6z506y"))))
+              "1y3jmh055vmx44gsjgwxvwv3zcyvz8pc5mhgrwkzm0ybbwpp2pqi"))))
 
          (makeicecat-patch
           (local-file (search-patch "icecat-makeicecat.patch"))))
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 3116f3c30a..1d9d93d774 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -292,14 +292,18 @@ without requiring the source code to be rewritten.")
   (package
     (inherit guile-2.2)
     (name "guile-next")                           ;to be renamed to "guile"
-    (version "3.0.0")
+    (version "3.0.1")
     (source (origin
               (inherit (package-source guile-2.2))
               (uri (string-append "mirror://gnu/guile/guile-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "0x8ca6q1qdmk29lh12gj6ngvgn7kp79w42rxfgwrpxm9jmjqs4y9"))))
+                "1jakps3127h8g69ixgb4zwc8v2g29dmwql1vi3pwg30kzp8fm5nn"))
+              (patches
+               (append (search-patches "guile-3.0-crash.patch")
+                       (origin-patches (package-source guile-2.2))))))
+
     (arguments
      (substitute-keyword-arguments (package-arguments guile-2.2)
        ;; XXX: On ARMv7, work around <https://bugs.gnu.org/39208> by disabling
diff --git a/gnu/packages/haskell-apps.scm b/gnu/packages/haskell-apps.scm
index 521aaf5870..6005816260 100644
--- a/gnu/packages/haskell-apps.scm
+++ b/gnu/packages/haskell-apps.scm
@@ -269,14 +269,14 @@ unique algebra of patches called @url{http://darcs.net/Theory,Patchtheory}.
 (define-public git-annex
   (package
     (name "git-annex")
-    (version "8.20200226")
+    (version "8.20200309")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://hackage.haskell.org/package/"
                            "git-annex/git-annex-" version ".tar.gz"))
        (sha256
-        (base32 "09v80ni1w9z1im79lzrnpz7xlivwna44zqpwq4axwyd17cffqi9m"))))
+        (base32 "1yjb01jh5rccqg44nqh4iyxmbpkcpm6m82lnw7s0s2vizj8891p5"))))
     (build-system haskell-build-system)
     (arguments
      `(#:configure-flags
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 27f7820176..0573e70d07 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -1150,7 +1150,7 @@ MailCore 2.")
               (method url-fetch)
               (uri (string-append "https://ftp.heanet.ie/mirrors/"
                                   "ftp.xemacs.org/aux/"
-                                  name "-" version ".tar.gz"))
+                                  "compface-" version ".tar.gz"))
               (sha256
                (base32
                 "09b89wg63hg502hsz592cd2h87wdprb1dq1k1y07n89hym2q56d6"))))
@@ -1160,7 +1160,7 @@ MailCore 2.")
     (synopsis "Portrait image compressor")
     (description "This package takes your 48x48x1 portrait image and
 compresses it.")
-    (home-page "http://www.cs.indiana.edu/pub/faces/")
+    (home-page "https://legacy.cs.indiana.edu/ftp/faces/")
     (license (x11-style "file://README"))))
 
 (define-public claws-mail
diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index eddfffd662..1840f1c0f2 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -1516,7 +1516,7 @@ that block port 22.")
 supports tuning of various parameters related to timing, buffers and
 protocols (TCP, UDP, SCTP with IPv4 and IPv6).  For each test it reports
 the bandwidth, loss, and other parameters.")
-    (home-page "http://software.es.net/iperf/")
+    (home-page "https://software.es.net/iperf/")
     (license (list license:bsd-3             ; Main distribution.
                    license:ncsa              ; src/{units,iperf_locale,tcp_window_size}.c
                    license:expat             ; src/{cjson,net}.[ch]
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 23a0b2b4e8..b0457ba87a 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -110,8 +110,8 @@
   ;; Note: the 'update-guix-package.scm' script expects this definition to
   ;; start precisely like this.
   (let ((version "1.0.1")
-        (commit "c2f9ea2b502a617bb69227d5f858eee9d4288a6a")
-        (revision 14))
+        (commit "09844816c77caaa60f4149f99a34733966724627")
+        (revision 15))
     (package
       (name "guix")
 
@@ -127,7 +127,7 @@
                       (commit commit)))
                 (sha256
                  (base32
-                  "0hg6yrqlzqiv4gmk9liqar6m9qhhn66q75jsmh86awjwq4qmvyab"))
+                  "1fciffls6cw9zz13vig5x37r73qxc0irzyh0caimciddlksvabf7"))
                 (file-name (string-append "guix-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments
diff --git a/gnu/packages/patches/csvkit-fix-tests.patch b/gnu/packages/patches/csvkit-fix-tests.patch
deleted file mode 100644
index cb9ec39cb0..0000000000
--- a/gnu/packages/patches/csvkit-fix-tests.patch
+++ /dev/null
@@ -1,45 +0,0 @@
-diff --git a/tests/test_utilities/test_csvsql.py b/tests/test_utilities/test_csvsql.py
-index e6ec4af..4f47980 100644
---- a/tests/test_utilities/test_csvsql.py
-+++ b/tests/test_utilities/test_csvsql.py
-@@ -197,7 +197,7 @@ class TestCSVSQL(CSVKitTestCase, EmptyFileTests):
-         utility.run()
-         output = output_file.getvalue()
-         output_file.close()
--        self.assertEqual(output, 'a,b,c\n1,2,3\n0,5,6\n')
-+        self.assertEqual(output, 'a,b,c\n1,2.0,3.0\n0,5.0,6.0\n')
-
-     def test_no_prefix_unique_constraint(self):
-         self.get_output(['--db', 'sqlite:///' + self.db_file, '--insert', 'examples/dummy.csv', '--unique-constraint', 'a'])
-diff --git a/tests/test_utilities/test_sql2csv.py b/tests/test_utilities/test_sql2csv.py
-index a0c3d3e..babcfd6 100644
---- a/tests/test_utilities/test_sql2csv.py
-+++ b/tests/test_utilities/test_sql2csv.py
-@@ -121,23 +121,23 @@ class TestSQL2CSV(CSVKitTestCase, EmptyFileTests):
-         input_file.close()
-
-     def test_unicode(self):
--        expected = self.csvsql('examples/test_utf8.csv')
-+        self.csvsql('examples/test_utf8.csv')
-         csv = self.get_output(['--db', 'sqlite:///' + self.db_file, '--query', 'select * from foo'])
--        self.assertEqual(csv.strip(), expected)
-+        self.assertEqual(csv.strip(), 'foo,bar,baz\n1.0,2.0,3\n4.0,5.0,ʤ')
-
-     def test_no_header_row(self):
-         self.csvsql('examples/dummy.csv')
-         csv = self.get_output(['--db', 'sqlite:///' + self.db_file, '--no-header-row', '--query', 'select * from foo'])
-
-         self.assertTrue('a,b,c' not in csv)
--        self.assertTrue('1,2,3' in csv)
-+        self.assertTrue('1,2.0,3.0' in csv)
-
-     def test_linenumbers(self):
-         self.csvsql('examples/dummy.csv')
-         csv = self.get_output(['--db', 'sqlite:///' + self.db_file, '--linenumbers', '--query', 'select * from foo'])
-
-         self.assertTrue('line_number,a,b,c' in csv)
--        self.assertTrue('1,1,2,3' in csv)
-+        self.assertTrue('1,1,2.0,3.0' in csv)
-
-     def test_wildcard_on_sqlite(self):
-         self.csvsql('examples/iris.csv')
diff --git a/gnu/packages/patches/guile-3.0-crash.patch b/gnu/packages/patches/guile-3.0-crash.patch
new file mode 100644
index 0000000000..510834ab57
--- /dev/null
+++ b/gnu/packages/patches/guile-3.0-crash.patch
@@ -0,0 +1,17 @@
+Fix crash due to: <https://issues.guix.gnu.org/issue/39266>.
+
+diff --git a/libguile/struct.c b/libguile/struct.c
+index 3dbcc71d4..ddcbe46d2 100644
+--- a/libguile/struct.c
++++ b/libguile/struct.c
+@@ -139,7 +139,9 @@ set_vtable_access_fields (SCM vtable)
+   nfields = len / 2;
+ 
+   bitmask_size = (nfields + 31U) / 32U;
+-  unboxed_fields = scm_gc_malloc_pointerless (bitmask_size, "unboxed fields");
++  unboxed_fields =
++    scm_gc_malloc_pointerless (bitmask_size * sizeof (*unboxed_fields),
++                               "unboxed fields");
+   memset (unboxed_fields, 0, bitmask_size * sizeof(*unboxed_fields));
+ 
+   /* Update FLAGS according to LAYOUT.  */
diff --git a/gnu/packages/patches/icecat-makeicecat.patch b/gnu/packages/patches/icecat-makeicecat.patch
index beaddf9437..a90d7fdee8 100644
--- a/gnu/packages/patches/icecat-makeicecat.patch
+++ b/gnu/packages/patches/icecat-makeicecat.patch
@@ -25,7 +25,7 @@ index 8be2362..48716f2 100755
 -wget -N https://ftp.mozilla.org/pub/mozilla.org/firefox/releases/${FFVERSION}esr/source/firefox-${FFVERSION}esr.source.tar.xz.asc
 -gpg --recv-keys --keyserver keyserver.ubuntu.com 14F26682D0916CDD81E37B6D61B7B526D98F0353
 -gpg --verify firefox-${FFVERSION}esr.source.tar.xz.asc
--echo -n 52e784f98a37624e8b207f1b23289c2c88f66dd923798cae891a586a6d94a6d1 firefox-${FFVERSION}esr.source.tar.xz |sha256sum -c -
+-echo -n 2428213ceb75cb6772b3044d9c14870d1ae5b0161379aeb29248650e13761c9f firefox-${FFVERSION}esr.source.tar.xz |sha256sum -c -
 -
 -echo Extracting Firefox tarball
 -tar -xf firefox-${FFVERSION}esr.source.tar.xz
@@ -37,7 +37,7 @@ index 8be2362..48716f2 100755
 +# wget -N https://ftp.mozilla.org/pub/mozilla.org/firefox/releases/${FFVERSION}esr/source/firefox-${FFVERSION}esr.source.tar.xz.asc
 +# gpg --recv-keys --keyserver keyserver.ubuntu.com 14F26682D0916CDD81E37B6D61B7B526D98F0353
 +# gpg --verify firefox-${FFVERSION}esr.source.tar.xz.asc
-+# echo -n 52e784f98a37624e8b207f1b23289c2c88f66dd923798cae891a586a6d94a6d1 firefox-${FFVERSION}esr.source.tar.xz |sha256sum -c -
++# echo -n 2428213ceb75cb6772b3044d9c14870d1ae5b0161379aeb29248650e13761c9f firefox-${FFVERSION}esr.source.tar.xz |sha256sum -c -
 +# 
 +# echo Extracting Firefox tarball
 +# tar -xf firefox-${FFVERSION}esr.source.tar.xz
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 2428608a30..8576b1ecf9 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -2416,7 +2416,7 @@ e.g. filters, callbacks and errbacks can all be promises.")
        ;;   raise RuntimeError("setuptools >= 41 required to build")
        ("python-setuptools" ,python-setuptools)
        ("python-setuptools-scm" ,python-setuptools-scm)))
-    (inputs
+    (propagated-inputs
      `(("python-appdirs" ,python-appdirs)
        ("python-distlib" ,python-distlib)
        ("python-filelock" ,python-filelock)
diff --git a/gnu/packages/slang.scm b/gnu/packages/slang.scm
index 5a37480f67..404a4535ca 100644
--- a/gnu/packages/slang.scm
+++ b/gnu/packages/slang.scm
@@ -71,7 +71,7 @@
        ("libpng" ,libpng)
        ("pcre" ,pcre)
        ("ncurses" ,ncurses)))
-    (home-page "http://www.jedsoft.org/slang/")
+    (home-page "https://www.jedsoft.org/slang/")
     (synopsis "Library for interactive applications and extensibility")
     (description
      "S-Lang is a multi-platform programmer's library designed to allow a
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 13d64be498..547450c78b 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1414,7 +1414,7 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.")
        ("r-stringr" ,r-stringr)
        ("r-xfun" ,r-xfun)
        ("r-yaml" ,r-yaml)))
-    (home-page "http://yihui.name/knitr/")
+    (home-page "https://yihui.org/knitr/")
     (synopsis "General-purpose package for dynamic report generation in R")
     (description
      "This package provides a general-purpose tool for dynamic report
@@ -3151,7 +3151,7 @@ using the multicore functionality of the parallel package.")
        ("r-jsonlite" ,r-jsonlite)
        ("r-magrittr" ,r-magrittr)
        ("r-promises" ,r-promises)))
-    (home-page "http://rstudio.github.io/DT")
+    (home-page "https://rstudio.github.io/DT")
     (synopsis "R wrapper of the DataTables JavaScript library")
     (description
      "This package allows for data objects in R to be rendered as HTML tables
@@ -3922,7 +3922,7 @@ from within R.")
     (propagated-inputs
      `(("r-lattice" ,r-lattice)
        ("r-matrix" ,r-matrix)))
-    (home-page "http://spams-devel.gforge.inria.fr")
+    (home-page "https://spams-devel.gforge.inria.fr")
     (synopsis "Toolbox for solving sparse estimation problems")
     (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
 for solving various sparse estimation problems.  It includes tools for the
diff --git a/gnu/packages/telephony.scm b/gnu/packages/telephony.scm
index a645c58562..fe6c230693 100644
--- a/gnu/packages/telephony.scm
+++ b/gnu/packages/telephony.scm
@@ -15,6 +15,7 @@
 ;;; Copyright © 2019 Jan Wielkiewicz <tona_kosmicznego_smiecia@interia.pl>
 ;;; Copyright © 2019 Ivan Vilata i Balaguer <ivan@selidor.net>
 ;;; Copyright © 2020 Brett Gilio <brettg@gnu.org>
+;;; Copyright © 2020 Michael Rohleder <mike@rohleder.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -462,6 +463,12 @@ address of one of the participants.")
              (substitute* "src/mumble/TextToSpeech_unix.cpp"
                (("libspeechd.h") "speech-dispatcher/libspeechd.h"))
              #t))
+         ;; disable statistic gathering by default. see <https://bugs.gnu.org/25201>
+         (add-before 'configure 'fix-statistic-gathering-default
+           (lambda _
+             (substitute* "src/mumble/Settings.cpp"
+               (("bUsage = true;") "bUsage = false;"))
+             #t))
          (add-before 'install 'disable-murmur-ice
            (lambda _
              (substitute* "scripts/murmur.ini.system"
diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 74f26c03f9..c289e43d94 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -1310,7 +1310,7 @@ also walk each side of a merge and test those changes individually.")
     (propagated-inputs
      `(("git" ,git)
        ("openssh" ,openssh)))
-    (home-page "http://gitolite.com")
+    (home-page "https://gitolite.com")
     (synopsis "Git access control layer")
     (description
      "Gitolite is an access control layer on top of Git, providing fine access
@@ -1332,27 +1332,39 @@ control to Git repositories.")
     (arguments
      `(#:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'patch-tests
+           (lambda _
+             (substitute* '("tests/test-extdiff.t"
+                            "tests/test-logtoprocess.t"
+                            "tests/test-patchbomb.t"
+                            "tests/test-run-tests.t"
+                            "tests/test-transplant.t")
+               (("/bin/sh")
+                (which "sh")))
+             #t))
          (replace 'check
            (lambda* (#:key tests? #:allow-other-keys)
              (with-directory-excursion "tests"
                ;; The following tests are known to fail.
-               (for-each (lambda (file)
-                           (delete-file file))
-                         '("test-extdiff.t"
+               (for-each delete-file
+                         '(;; XXX: This test calls 'run-tests.py --with-hg=
+                           ;; `which hg`' and fails because there is no hg on
+                           ;; PATH from before (that's why we are building it!)?
                            "test-hghave.t"
+
+                           ;; FIXME: Why does this fail in the build container, but
+                           ;; not in 'guix environment -C' (even without /bin/sh)?
+                           "test-nointerrupt.t"
+
+                           ;; TODO: the fqaddr() call fails in the build
+                           ;; container, causing these server tests to fail.
                            "test-hgwebdir.t"
                            "test-http-branchmap.t"
-                           "test-logtoprocess.t"
-                           "test-merge-combination.t"
-                           "test-nointerrupt.t"
-                           "test-patchbomb.t"
                            "test-pull-bundle.t"
                            "test-push-http.t"
-                           "test-run-tests.t"
                            "test-serve.t"
                            "test-subrepo-deep-nested-change.t"
-                           "test-subrepo-recursion.t"
-                           "test-transplant.t"))
+                           "test-subrepo-recursion.t"))
                (when tests?
                  (invoke "./run-tests.py"
                          ;; ‘make check’ does not respect ‘-j’.
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index e2e314aac9..840083f021 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -1381,7 +1381,7 @@ unavailable.")
                             "CC=gcc"))
        ;; No 'check' target.
        #:tests? #f))
-    (home-page "http://www.pps.univ-paris-diderot.fr/~jch/software/polipo/")
+    (home-page "https://www.pps.univ-paris-diderot.fr/~jch/software/polipo/")
     (synopsis "Small caching web proxy")
     (description
      "Polipo is a small caching web proxy (web cache, HTTP proxy, and proxy
diff --git a/gnu/packages/wireservice.scm b/gnu/packages/wireservice.scm
index eab76970f4..0d772b54d1 100644
--- a/gnu/packages/wireservice.scm
+++ b/gnu/packages/wireservice.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2019 Pierre Langlois <pierre.langlois@gmx.com>
+;;; Copyright © 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -198,17 +199,16 @@ for xls and xlsx files support to all @code{agate.Table} instances.")))
 (define-public csvkit
   (package
     (name "csvkit")
-    (version "1.0.4")
+    (version "1.0.5")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "csvkit" version))
               (sha256
                (base32
-                "1830lb95rh1iyi3drlwxzb6y3pqkii0qiyzd40c1kvhvaf1s6lqk"))
-              (patches (search-patches "csvkit-fix-tests.patch"))))
+                "1ffmbzk4rxnl1yhqfl58v7kvl5m9cbvjm8v7xp4mvr00sgs91lvv"))))
     (build-system python-build-system)
     (native-inputs
-     `(("python-psycopg2" ,python-psycopg2) ;; Used to test PostgreSQL support.
+     `(("python-psycopg2" ,python-psycopg2) ; to test PostgreSQL support
        ("python-sphinx" ,python-sphinx)
        ("python-sphinx-rtd-theme" ,python-sphinx-rtd-theme)))
     (inputs
diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index 8193975555..f9b6ef9880 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -730,7 +730,7 @@ tiled on several screens.")
              (substitute* "test/Xmobar/Plugins/Monitors/AlsaSpec.hs"
                (("/bin/bash") (which "bash")))
              #t)))))
-    (home-page "http://xmobar.org")
+    (home-page "https://xmobar.org")
     (synopsis "Minimalistic text based status bar")
     (description
      "@code{xmobar} is a lightweight, text-based, status bar written in
diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm
index b86882e762..9882f4a723 100644
--- a/gnu/packages/xdisorg.scm
+++ b/gnu/packages/xdisorg.scm
@@ -410,7 +410,7 @@ X11 (yet).")
               ("libxinerama" ,libxinerama)
               ("libxtst" ,libxtst)
               ("libxkbcommon" ,libxkbcommon)))
-    (home-page "http://www.semicomplete.com/projects/xdotool")
+    (home-page "https://www.semicomplete.com/projects/xdotool/")
     (synopsis "Fake keyboard/mouse input, window management, and more")
     (description "Xdotool lets you simulate keyboard input and mouse activity,
 move and resize windows, etc.  It does this using X11's XTEST extension and