Merge remote-tracking branch 'savannah/master' into core-updates

Conflicts:
	gnu/local.mk
	gnu/packages/autotools.scm
	gnu/packages/cmake.scm
	gnu/packages/gnuzilla.scm
	gnu/packages/haskell.scm
	gnu/packages/pdf.scm
	gnu/packages/python-xyz.scm
	gnu/packages/samba.scm
	gnu/packages/tex.scm
	gnu/packages/tls.scm
	gnu/packages/wxwidgets.scm

1 files changed, 110 insertions, 101 deletions

diff --git a/gnu/packages/mpi.scm b/gnu/packages/mpi.scm
index 70b14c30b3..baef62616f 100644
--- a/gnu/packages/mpi.scm
+++ b/gnu/packages/mpi.scm
@@ -25,6 +25,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages mpi)
+  #:use-module (guix gexp)
   #:use-module (guix packages)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix download)
@@ -53,8 +54,6 @@
   #:use-module (ice-9 match))
 
 (define-public hwloc-1
-  ;; Note: For now we keep 1.x as the default because many packages have yet
-  ;; to migrate to 2.0.
   (package
     (name "hwloc")
     (version "1.11.13")
@@ -140,7 +139,6 @@ bind processes, and much more.")
     (license license:bsd-3)))
 
 (define-public hwloc-2
-  ;; Note: 2.x isn't the default yet, see above.
   (package
     (inherit hwloc-1)
     (version "2.9.0")
@@ -167,10 +165,19 @@ bind processes, and much more.")
                (substitute* "tests/hwloc/linux-libnuma.c"
                  (("numa_available\\(\\)")
                   "-1"))))
-           (add-before 'check 'skip-test-that-requires-/sys
+           (add-before 'check 'skip-tests-that-require-/sys
              (lambda _
                ;; 'test-gather-topology.sh' requires /sys as of 2.9.0; skip it.
-               (setenv "HWLOC_TEST_GATHER_TOPOLOGY" "0")))
+               (setenv "HWLOC_TEST_GATHER_TOPOLOGY" "0")
+
+               ;; 'hwloc_backends' also requires /sys on non-x86 systems, for
+               ;; which hwloc lacks a topology backend not reliant on the
+               ;; operating system; skip it also on these machines.
+               (substitute* "tests/hwloc/hwloc_backends.c"
+                 ,@(if (not (target-x86?))
+                       '((("putenv\\(\\(char \\*\\) \"HWLOC_L" all)
+                          (string-append "exit (77);\n" all)))
+                       '()))))
            (add-before 'check 'skip-test-that-fails-on-qemu
              (lambda _
                ;; Skip test that fails on emulated hardware due to QEMU bug:
@@ -191,13 +198,13 @@ bind processes, and much more.")
     (version "4.1.4")
     (source
      (origin
-      (method url-fetch)
-      (uri (string-append "https://www.open-mpi.org/software/ompi/v"
-                          (version-major+minor version)
-                          "/downloads/openmpi-" version ".tar.bz2"))
-      (sha256
-       (base32 "03ckngrff1cl0l81vfvrfhp99rbgk7s0633kr1l468yibwbjx4cj"))
-      (patches (search-patches "openmpi-mtl-priorities.patch"))))
+       (method url-fetch)
+       (uri (string-append "https://www.open-mpi.org/software/ompi/v"
+                           (version-major+minor version)
+                           "/downloads/openmpi-" version ".tar.bz2"))
+       (sha256
+        (base32 "03ckngrff1cl0l81vfvrfhp99rbgk7s0633kr1l468yibwbjx4cj"))
+       (patches (search-patches "openmpi-mtl-priorities.patch"))))
 
     (properties
      ;; Tell the 'generic-html' updater to monitor this URL for updates.
@@ -228,68 +235,69 @@ bind processes, and much more.")
      (list pkg-config perl))
     (outputs '("out" "debug"))
     (arguments
-     `(#:configure-flags `("--enable-mpi-ext=affinity" ;cr doesn't work
-                           "--with-sge"
-
-                           ,@(if ,(package? (this-package-input "valgrind"))
-                               `("--enable-memchecker"
-                                 "--with-valgrind")
-                               `("--without-valgrind"))
-
-                           "--with-hwloc=external"
-                           "--with-libevent"
-
-                           ;; Help 'orterun' and 'mpirun' find their tools
-                           ;; under $prefix by default.
-                           "--enable-mpirun-prefix-by-default"
-
-                           ;; InfiniBand support
-                           "--enable-openib-control-hdr-padding"
-                           "--enable-openib-dynamic-sl"
-                           "--enable-openib-udcm"
-                           "--enable-openib-rdmacm"
-                           "--enable-openib-rdmacm-ibaddr"
-
-                           ;; Enable support for SLURM's Process Manager
-                           ;; Interface (PMI).
-                           ,(string-append "--with-pmi="
-                                           (assoc-ref %build-inputs "slurm")))
-       #:phases (modify-phases %standard-phases
-                  ;; opensm is needed for InfiniBand support.
-                  (add-after 'unpack 'find-opensm-headers
-                    (lambda* (#:key inputs #:allow-other-keys)
-                      (setenv "C_INCLUDE_PATH"
-                              (search-input-directory inputs
-                                                      "/include/infiniband"))
-                      (setenv "CPLUS_INCLUDE_PATH"
-                              (search-input-directory inputs
-                                                      "/include/infiniband"))))
-                  (add-before 'build 'remove-absolute
-                    (lambda _
-                      ;; Remove compiler absolute file names (OPAL_FC_ABSOLUTE
-                      ;; etc.) to reduce the closure size.  See
-                      ;; <https://lists.gnu.org/archive/html/guix-devel/2017-07/msg00388.html>
-                      ;; and
-                      ;; <https://www.mail-archive.com/[email protected]//msg31397.html>.
-                      (substitute* '("orte/tools/orte-info/param.c"
-                                     "oshmem/tools/oshmem_info/param.c"
-                                     "ompi/tools/ompi_info/param.c")
-                        (("_ABSOLUTE") ""))
-                      ;; Avoid valgrind (which pulls in gdb etc.).
-                      (substitute*
-                          '("./ompi/mca/io/romio321/src/io_romio321_component.c")
-                        (("MCA_io_romio321_COMPLETE_CONFIGURE_FLAGS")
-                         "\"[elided to reduce closure]\""))))
-                  (add-before 'build 'scrub-timestamps ;reproducibility
-                    (lambda _
-                      (substitute* '("ompi/tools/ompi_info/param.c"
-                                     "orte/tools/orte-info/param.c"
-                                     "oshmem/tools/oshmem_info/param.c")
-                        ((".*(Built|Configured) on.*") ""))))
-                  (add-after 'install 'remove-logs ;reproducibility
-                    (lambda* (#:key outputs #:allow-other-keys)
-                      (let ((out (assoc-ref outputs "out")))
-                        (for-each delete-file (find-files out "config.log"))))))))
+     (list
+      #:configure-flags #~`("--enable-mpi-ext=affinity" ;cr doesn't work
+                            "--with-sge"
+
+                            #$@(if (package? (this-package-input "valgrind"))
+                                   #~("--enable-memchecker"
+                                      "--with-valgrind")
+                                   #~("--without-valgrind"))
+
+                            "--with-hwloc=external"
+                            "--with-libevent"
+
+                            ;; Help 'orterun' and 'mpirun' find their tools
+                            ;; under $prefix by default.
+                            "--enable-mpirun-prefix-by-default"
+
+                            ;; InfiniBand support
+                            "--enable-openib-control-hdr-padding"
+                            "--enable-openib-dynamic-sl"
+                            "--enable-openib-udcm"
+                            "--enable-openib-rdmacm"
+                            "--enable-openib-rdmacm-ibaddr"
+
+                            ;; Enable support for SLURM's Process Manager
+                            ;; Interface (PMI).
+                            ,(string-append "--with-pmi="
+                                            #$(this-package-input "slurm")))
+      #:phases #~(modify-phases %standard-phases
+                   ;; opensm is needed for InfiniBand support.
+                   (add-after 'unpack 'find-opensm-headers
+                     (lambda* (#:key inputs #:allow-other-keys)
+                       (setenv "C_INCLUDE_PATH"
+                               (search-input-directory inputs
+                                                       "/include/infiniband"))
+                       (setenv "CPLUS_INCLUDE_PATH"
+                               (search-input-directory inputs
+                                                       "/include/infiniband"))))
+                   (add-before 'build 'remove-absolute
+                     (lambda _
+                       ;; Remove compiler absolute file names (OPAL_FC_ABSOLUTE
+                       ;; etc.) to reduce the closure size.  See
+                       ;; <https://lists.gnu.org/archive/html/guix-devel/2017-07/msg00388.html>
+                       ;; and
+                       ;; <https://www.mail-archive.com/[email protected]//msg31397.html>.
+                       (substitute* '("orte/tools/orte-info/param.c"
+                                      "oshmem/tools/oshmem_info/param.c"
+                                      "ompi/tools/ompi_info/param.c")
+                         (("_ABSOLUTE") ""))
+                       ;; Avoid valgrind (which pulls in gdb etc.).
+                       (substitute*
+                           '("./ompi/mca/io/romio321/src/io_romio321_component.c")
+                         (("MCA_io_romio321_COMPLETE_CONFIGURE_FLAGS")
+                          "\"[elided to reduce closure]\""))))
+                   (add-before 'build 'scrub-timestamps ;reproducibility
+                     (lambda _
+                       (substitute* '("ompi/tools/ompi_info/param.c"
+                                      "orte/tools/orte-info/param.c"
+                                      "oshmem/tools/oshmem_info/param.c")
+                         ((".*(Built|Configured) on.*") ""))))
+                   (add-after 'install 'remove-logs ;reproducibility
+                     (lambda* (#:key outputs #:allow-other-keys)
+                       (let ((out (assoc-ref outputs "out")))
+                         (for-each delete-file (find-files out "config.log"))))))))
     (home-page "https://www.open-mpi.org")
     (synopsis "MPI-3 implementation")
     (description
@@ -309,7 +317,7 @@ software vendors, application developers and computer science researchers.")
     (arguments
      (substitute-keyword-arguments (package-arguments openmpi)
        ((#:configure-flags flags)
-        `(cons "--enable-mpi-cxx" ,flags))))
+        #~(cons "--enable-mpi-cxx" #$flags))))
     (synopsis "C++ bindings for MPI")))
 
 ;; TODO: javadoc files contain timestamps.
@@ -325,34 +333,35 @@ software vendors, application developers and computer science researchers.")
        ,@(package-native-inputs openmpi)))
     (outputs '("out"))
     (arguments
-     `(#:modules ((guix build gnu-build-system)
+     (cons*
+      #:modules '((guix build gnu-build-system)
                   ((guix build ant-build-system) #:prefix ant:)
                   (guix build utils))
-       #:imported-modules ((guix build ant-build-system)
+      #:imported-modules `((guix build ant-build-system)
                            ,@%gnu-build-system-modules)
-       ,@(substitute-keyword-arguments (package-arguments openmpi)
-           ((#:configure-flags flags)
-            `(cons "--enable-mpi-java" ,flags))
-           ((#:make-flags flags ''())
-            `(append '("-C" "ompi/mpi/java")
-                     ,flags))
-           ((#:phases phases)
-            `(modify-phases ,phases
-               ;; We could provide the location of the JDK in the configure
-               ;; flags, but since the configure flags are embedded in the
-               ;; info binaries that would leave a reference to the JDK in
-               ;; the "out" output.  To avoid this we set JAVA_HOME.
-               (add-after 'unpack 'set-JAVA_HOME
-                 (lambda* (#:key inputs #:allow-other-keys)
-                   (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
-                   #t))
-               (add-after 'unpack 'link-with-existing-mpi-libraries
-                 (lambda* (#:key inputs #:allow-other-keys)
-                   (substitute* "ompi/mpi/java/c/Makefile.in"
-                     (("\\$\\(top_builddir\\)/ompi/lib@[email protected]")
-                      (search-input-file inputs "/lib/libmpi.la")))))
-               (add-after 'install 'strip-jar-timestamps
-                 (assoc-ref ant:%standard-phases 'strip-jar-timestamps)))))))
+      (substitute-keyword-arguments (package-arguments openmpi)
+        ((#:configure-flags flags)
+         #~(cons "--enable-mpi-java" #$flags))
+        ((#:make-flags flags ''())
+         #~(append '("-C" "ompi/mpi/java")
+                   #$flags))
+        ((#:phases phases)
+         #~(modify-phases #$phases
+             ;; We could provide the location of the JDK in the configure
+             ;; flags, but since the configure flags are embedded in the
+             ;; info binaries that would leave a reference to the JDK in
+             ;; the "out" output.  To avoid this we set JAVA_HOME.
+             (add-after 'unpack 'set-JAVA_HOME
+               (lambda* (#:key inputs #:allow-other-keys)
+                 (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
+                 #t))
+             (add-after 'unpack 'link-with-existing-mpi-libraries
+               (lambda* (#:key inputs #:allow-other-keys)
+                 (substitute* "ompi/mpi/java/c/Makefile.in"
+                   (("\\$\\(top_builddir\\)/ompi/lib@[email protected]")
+                    (search-input-file inputs "/lib/libmpi.la")))))
+             (add-after 'install 'strip-jar-timestamps
+               (assoc-ref ant:%standard-phases 'strip-jar-timestamps)))))))
     (synopsis "Java bindings for MPI")))
 
 (define-public openmpi-thread-multiple
@@ -361,7 +370,7 @@ software vendors, application developers and computer science researchers.")
     (arguments
      (substitute-keyword-arguments (package-arguments openmpi)
        ((#:configure-flags flags)
-        `(cons "--enable-mpi-thread-multiple" ,flags))))
+        #~(cons "--enable-mpi-thread-multiple" #$flags))))
     (description "This version of Open@tie{}MPI has an implementation of
 @code{MPI_Init_thread} that provides @code{MPI_THREAD_MULTIPLE}.  This won't
 work correctly with all transports (such as @code{openib}), and the