guix: cmake: Add input and package libraries to the rpath, and adapt package
  definitions accordingly.

* guix/build/cmake-build-system.scm (configure): Add flags.
* gnu/packages/maths.scm (lapack): Drop special code.
* gnu/packages/ssh.scm (libssh): Drop special code.
* gnu/packages/slim.scm (slim): Drop special code and enable shared library.

Co-authored-by: Eric Bavier <bavier@member.fsf.org>

gnu: soprano: Add native input doxygen.

* gnu/packages/rdf.scm (soprano): Add native input doxygen.

gnu: doxygen: Add propagated input graphviz.

* gnu/packages/doxygen.scm (doxygen): Add propagated input graphviz.

gnu: libkate: Add native input doxygen and make input pkg-config native.

* gnu/packages/xiph.scm (libkate): Add native input doxygen.
    Make input pkg-config native.

gnu: libmpdclient: Add native input doxygen.

* gnu/packages/mpd.scm (libmpdclient): Add native input doxygen.

gnu: libdbusmenu-qt: Add native input doxygen for building the documentation,
  and make input qjson native.

* gnu/packages/kde.scm (libdbusmenu-qt): Add native input doxygen for
    building the documentation.
    Make input qjson native, as it is needed only for the tests.

gnu: Add doxygen.

* gnu/packages/doxygen.scm: New file.
* gnu/packages/patches/doxygen-test.patch,
  gnu/packages/patches/doxygen-tmake.patch: New files.
* gnu-system.am (GNU_SYSTEM_MODULES, dist_patch_DATA): Register the new files.

build: Add missing function checks for optional daemon features.

* config-daemon.ac: Check for lchown, posix_fallocate, vfork,
  sched_setaffinity, statvfs, nanosleep, and strsignal.  As a side
  effect, this enables daemon features depending on the corresponding
  feature test macros.

gnu: gp2c: Upgrade to 0.0.9pl1.

* gnu/packages/algebra.scm (gp2c): Upgrade to 0.0.9pl1.

vm: Clarify 'system-qemu-image/shared-store-script'.

* gnu/system/vm.scm (system-qemu-image/shared-store-script): Move
  'initrd' definition to the top-level.  Have a single definition of
  'initrd', 'image', and 'os-drv'.

system: Add 'operating-system-boot-script'.

* gnu/system.scm (operating-system-boot-script): New procedure.
  (operating-system-derivation): Use it.  Remove DMD-CONF from the
  file union.  Add BOOT-DRV to the inputs.

system: Factorize (gnu system).

* gnu/system.scm (operating-system-accounts,
  operating-system-etc-directory): New procedures.
  (operating-system-derivation): Use them.
* gnu/services/base.scm (%base-services): Add 'host-name-service'
  invocation.

gnu: cyrus-sasl: Add alternate source URL.

* gnu/packages/cyrus-sasl.scm (cyrus-sasl)[source]: Add alternate URL;
  the previous one is currently unreachable.

gnu: mplayer: Add mpg123 as an input.

* gnu/packages/video.scm (mplayer)[inputs]: Add mpg123.

gnu: Add mpg123.

* gnu/packages/mp3.scm (mpg123): New variable.

gnu: Add GCC 4.9.0.

* gnu/packages/gcc.scm (gcc-4.9): New variable.
* gnu/packages/base.scm (gcc-toolchain-4.9): New variable.

gnu: openssl: Fixes for CVE-2010-5298 and extension checking.

* gnu/packages/patches/openssl-CVE-2010-5298.patch: New file.
* gnu/packages/patches/openssl-extension-checking-fixes.patch: New file.
* gnu/packages/openssl.scm (openssl): Add them.
* gnu-system.am (dist_patch_DATA): Add them.

pk-crypto: Add pretty-printer to 'gcry-error' exceptions.

* guix/pk-crypto.scm (string->canonical-sexp, sign, generate-key): Pass
  the procedure name as the first argument to 'throw'.
  (gcrypt-error-printer): New procedure.
  <top level>: Add call to 'set-exception-printer!'.
* guix/nar.scm (restore-one-item): Add 'proc' parameter to 'catch'
  handler for 'gcry-error.
* guix/scripts/archive.scm (%options, generate-key-pair, authorize-key):
  Likewise.
* guix/scripts/substitute-binary.scm (narinfo-signature->canonical-sexp):
  Likewise.

authenticate: Allow signatures with binary data to be written to stdout.

Fixes <http://bugs.gnu.org/17312>.

* guix/scripts/authenticate.scm (guix-authenticate): Add calls to
  'set-port-encoding!' and 'set-port-conversion-strategy!'.  Wrap body
  in 'with-fluids' form that sets '%default-port-encoding' and
  '%default-port-conversion-strategy'.
* tests/guix-authenticate.sh: Add test.
* tests/pk-crypto.scm ("hash corrupt due to restrictive locale
  encoding"): Add reference to bug.

pk-crypto: Use ISO-8859-1 for strings passed to 'gcry_sexp_new'.

* guix/pk-crypto.scm (string->canonical-sexp): Pass "ISO-8859-1" as the
  2nd argument to 'string->pointer'.
* tests/pk-crypto.scm ("version"): New test.
  ("hash corrupt due to restrictive locale encoding"): New test.