Fixes <http://bugs.gnu.org/18747>.

* guix/derivations.scm (substitutable-derivation?): Rewrite to check for
  "allowSubstitutes".
  (derivation): Add #:substitutable? parameter.
  [user+system-env-vars]: Honor it.
  (build-expression->derivation): Add #:substitutable? and honor it.
* guix/gexp.scm (gexp->derivation): Likewise.
* tests/derivations.scm ("derivation-prerequisites-to-build and substitutes,
  non-substitutable build"): Use #:substitutable? instead of #:local-build?.
  ("substitutable-derivation?", "derivation-prerequisites-to-build and
  substitutes, local build"): New tests.
* guix/download.scm (url-fetch): Adjust comment.
* guix/git-download.scm (git-fetch): Likewise.
* guix/build-system/gnu.scm (gnu-build, gnu-cross-build): Use #:substitutable?
  instead of #:local-build?.
* doc/guix.texi (Derivations, G-Expressions): Adjust accordingly.

This is a squashed commit of the following:

commit 0dccab9f417b406f5d4aedc81900fc7b2f16c9f6
Author: Eelco Dolstra <eelco.dolstra@logicblox.com>
Date:   Thu Jul 2 00:30:16 2015 +0200

    Typo

commit 2cd28517b13524c242c7758783b0b2d8250fdded
Author: Ludovic Courtès <ludo@gnu.org>
Date:   Wed Jul 1 14:56:34 2015 +0200

    Preserve supplementary groups of build users

    The following patch is an attempt to address this bug (see
    <http://bugs.gnu.org/18994>) by preserving the supplementary groups of
    build users in the build environment.

    In practice, I would expect that supplementary groups would contain only
    one or two groups: the build users group, and possibly the “kvm” group.

    [Changed &at(0) to data() and removed tabs - Eelco]

commit 6e38685ef65284093df79ebe7378bac33b0e7e5d
Author: Eelco Dolstra <eelco.dolstra@logicblox.com>
Date:   Tue Jun 30 21:41:26 2015 +0200

    GC: Handle ENOSPC creating/moving to the trash directory

    Issue #564.

commit 5e0a9ae2e25a1016389f4893a6ed6682aadcf51d
Author: Eelco Dolstra <eelco.dolstra@logicblox.com>
Date:   Mon Jun 22 15:54:55 2015 +0200

    Use posix_fallocate to create /nix/var/nix/db/reserved

commit 4e5ab98d6d14f8b0e3bd1d77b2f4f2354e7a49a8
Author: Eelco Dolstra <eelco.dolstra@logicblox.com>
Date:   Mon Jun 22 15:47:40 2015 +0200

    Make /nix/var/nix/db/reserved bigger

    Issue #564.

commit 60bda60fc06135aa97a93301b1a9e2270768f5b3
Author: Eelco Dolstra <eelco.dolstra@logicblox.com>
Date:   Wed Jun 10 16:17:06 2015 +0200

    Export outputPaths function

    This is useful for the new hydra-queue-runner.

commit 5dfea34048aa8541f20aeb2fbcd163561b609a49
Author: Eelco Dolstra <eelco.dolstra@logicblox.com>
Date:   Thu Jul 2 22:51:33 2015 +0200

    Use std::vector::data()

commit 2459458bc8257734ca78cb7a2db3df20bd730ec0
Author: Eelco Dolstra <eelco.dolstra@logicblox.com>
Date:   Thu Jun 4 16:04:41 2015 +0200

    Allow substitutes for builds that have preferLocalBuild set

    Not substituting builds with "preferLocalBuild = true" was a bad idea,
    because it didn't take the cost of dependencies into account. For
    instance, if we can't substitute a fetchgit call, then we have to
    download/build git and all its dependencies.

    Partially reverts 5558652709f27e8a887580b77b93c705659d7a4b and adds a
    new derivation attribute "allowSubstitutes" to specify whether a
    derivation may be substituted.

* guix/scripts/environment.scm (guix-environment): Return the exit
  status of the command.

* gnu/packages/gnupg.scm (gnupg)[native-inputs]: Add pkg-config.
  [inputs]: Add gnutls.
  (gnupg-2.0, gnupg-1)[native-inputs]: Override inherited value to be '().

* gnu/packages/gnupg.scm (gnupg): Update to 2.1.6.

* gnu/packages/bioinformatics.scm (python2-warpedlmm): New variable.

* gnu/packages/statistics.scm (r)[arguments]: Add phase "set-default-pager" to
  avoid "false" as a default pager.

* guix/scripts/environment.scm (create-environment): Define 'GUIX_ENVIRONMENT'.
* doc/guix.texi (Invoking guix environment): Document it.
* gnu/system/shadow.scm (default-skeletons): Adjust 'PS1' depending on whether
  'GUIX_ENVIRONMENT' is defined.

* doc/guix.texi (Invoking guix environment): Add footnote about .bashrc
  vs. .bash_profile.

This fixes two problems:

  1. Load errors would print an ugly backtrace.
  2. When FILE was an absolute name, 'load' was passed an incorrect file
     name.

* guix/scripts/environment.scm (options/resolve-packages): Use 'load*' instead
  of 'load'.

* guix/scripts/environment.scm (package+propagated-inputs): Add 'output'
  parameter.  Use it in return value.
  (options/resolve-packages): Use 'append-map' instead of 'map'.  For 'load'
  and 'expression', return all the outputs of the resulting package.  For
  'package', use 'specification->package+output' instead of
  'specification->package'.
  (guix-environment): Adjust uses of PACKAGES accordingly.
* doc/guix.texi (Invoking guix environment): Document it.
* tests/guix-environment.sh: Add test for --ad-hoc guile-bootstrap:out.

* guix/scripts/environment.scm (show-help, %options): Add -s/--system.
  (%default-options): Add 'system' pair.
  (guix-environment): Pass 'system' value from OPTS to 'lower-inputs'.
* doc/guix.texi (Invoking guix environment): Document it.

Before that, 'guix environment guile' (for instance) would define environment
variables that would refer to the "include" output of Bash, the "debug" output
of libgc, etc., even though these are not listed as inputs in the recipe of
'guile'.

* guix/gexp.scm (lower-inputs): Export.
* guix/scripts/environment.scm (evaluate-input-search-paths): Remove
  'derivations' parameter; add 'search-paths'.  Expect 'inputs' to be
  a list of tuples.  Adjust callers.
  (create-environment): Remove 'derivations' parameter; add 'search-paths'.
  (show-search-paths): Likewise.
  (package+propagated-inputs): New procedure.
  (packages->transitive-inputs, packages+propagated-inputs): Remove.
  (build-inputs): Expect INPUTS to be a list of derivation tuples.
  (guix-environment): Compute INPUTS using 'package+propagated-inputs',
  'package->bag', and 'bag-transitive-inputs'.  Move 'run-with-store' higher.
* tests/guix-environment.sh: Add test with FINDUTILS-BOOT0.

* tests/guix-environment.sh: New file.
* Makefile.am (SH_TESTS): Add it.

* gnu/packages/music.scm (powertabeditor)[inputs]: Replace "gcc" with
  "libiberty".

* gnu/packages/music.scm (hydrogen): New variable.

* gnu/packages/linux.scm (linux-libre): Update to 4.1.1.

* gnu/packages/version-control.scm (package-transitive-propagated-labels*)
  (package-propagated-input-refs): New procedures.
  (git)[inputs]: Add perl-authen-sasl, perl-net-smtp-ssl, and perl-io-socket-ssl.
  [outputs]: Add send-email output.
  [arguments]: Add #:modules argument with srfi-1.  In 'split phase, wrap
  git-send-email.

* gnu/packages/web.scm (perl-authen-sasl): New variable.

* gnu/packages/web.scm (perl-gssapi): New variable.

* gnu/packages/web.scm (perl-net-smtp-ssl): New variable.

* gnu/packages/curl.scm (arguments): Disable test 1510.

* gnu/packages/curl.scm (curl): Update to 7.43.0.

* gnu/packages/maths.scm (dealii, dealii-openmpi): New variables.
* gnu/packages/patches/dealii-p4est-interface.patch: New patch.
* gnu-system.am (dist_patch_DATA): Add it.

* gnu/packages/maths.scm (slepc, slepc-complex, slepc-openmpi)
  (slepc-complex-openmpi): New variables.

* gnu/packages/maths.scm (arpack-ng-openmpi): New variable.

* gnu/packages/maths.scm (petsc): Upgrade to 3.6.0.
* gnu/packages/patches/petsc-fix-threadcomm.patch: Delete patch.
* gnu-system.am (dist_patch_DATA): Remove it.

* gnu/packages/maths.scm (mumps, mumps-metis, mumps-openmpi)
  (mumps-metis-openmpi): New variables.
* gnu/packages/patches/mumps-build-parallelism.patch: New patch.
* gnu-system.am (dist_patch_DATA): Add it.

* gnu/packages/maths.scm (metis): New variable.

* gnu/packages/maths.scm (p4est, p4est-openmpi): New variables.

* gnu/packages/maths.scm (scalapack): New variable.

* gnu/packages/maths.scm (scotch)[arguments]: Add 'build-esmumps
  phase.  Install esmumps libraries and headers in 'install phase.
  (pt-scotch)[arguments]: Build ptesmumps in 'build phase.  Add
  make parallelism.

* gnu/packages/maths.scm (scotch, pt-scotch)[arguments]: Use modify-phases.

* gnu/packages/maths.scm (scotch): Update to 6.0.4.
  [arguments]: Add -fPIC to CFLAGS.
* gnu/packages/patches/scotch-test-threading.patch: Adjust patch for a
  new set of test fixes.
* gnu/packages/patches/pt-scotch-build-parallelism.patch: New patch.
* gnu-system.am (dist_patch_DATA): Add it.

* gnu/packages/mpi.scm (openmpi): Upgrade to 1.8.5.
  [native-inputs]: Add perl.
  [arguments]: Add configure flags for thread support.

* gnu/packages/mpi.scm (hwloc)[propagated-inputs]: Move numactl from here...
  [inputs]: ...to here.
  [arguments]: New 'refine-libnuma' phase.

* gnu/packages/patches/hwloc-gather-topology-lstopo.patch: New patch.
* gnu/packages/mpi.scm (hwloc): Upgrade to 1.10.1.
  [source]: Use patch.
  [propagated-inputs]: Remove libpci.
  [inputs]: Add libpciaccess.
* gnu-system.am (dist_patch_DATA): Add patch.

* gnu/packages/python.scm (python-mccabe)[license]: 'expat' ->
  'license:expat'.

* gnu/packages/python.scm (python-flake8, python2-flake8): New variables.

* gnu/packages/python.scm (python-mccabe, python2-mccabe): New variables.