* guix/scripts/pull.scm (show-help, %options): Add '--profile'.
(build-and-install): Change 'config-dir' argument to 'profile'.
(guix-pull): Honor '--profile'.
* doc/guix.texi (Invoking guix pull): Document it.

* gnu/packages/cran.scm (r-ggformula): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

* gnu/packages/cran.scm (r-mosaiccore): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu/packages/cran.scm (r-ggstance): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

* gnu/packages/cran.scm (r-abctools): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

* gnu/packages/cran.scm (r-abcrf): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

* gnu/packages/cran.scm (r-abcp2): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

* gnu/packages/emacs.scm (emacs-ess): Update to 17.11
[url]: Use github for https
[snippet]: update julia-mode substitution, only build info doc, bypass failing test
[propagated-inputs]: Add emacs-julia-mode
[description]: Mention that ESS supports Julia and JAGS (which replaces OpenBUGS)
[arguments]: Remove 'set-home' phase.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

Fixes <https://bugs.gnu.org/32652>.

* gnu/system/vm.scm (operating-system-uuid)[service-name,
file-system-digest]: New procedures.
Map these over services and file systems and hash the result.
* tests/guix-system.sh: Add test.

* gnu/packages/dns.scm (knot): Update to 2.7.2.

* gnu/packages/networking.scm (wireshark): Update to 2.6.3.

* gnu/packages/curl.scm (curl)[replacement]: Update to 7.61.1.
(curl-7.61.0): Replace variable with ...
(curl-7.61.1): ... new variable.

* gnu/packages/music.scm (libgme): Update to 0.6.2.
[native-inputs]: Add gcc-4.9.

* doc/guix.texi (Web Services): Document 'channels' and
'package-list-expiration'.

Previously Git pulls over HTTPS would fail with:

  guix/git.scm:132:7: In procedure update-cached-checkout:
  Throw to key `git-error' with args `(#<<git-error> code: -17 message: "the SSL certificate is invalid" class: 16>)'.

* gnu/services/web.scm (hpcguix-web-shepherd-service): Pass
"SSL_CERT_DIR=/etc/ssl/certs".
* doc/guix.texi (Web Services): Mention certificates.

Reported by Paul Garlick <pgarlick@tourbillion-technology.com>.

Fixes a bug whereby "old" Guix instances (before mid-May 2018) would
fail to pull to current master.

Specifically, Paul reported being unable to upgrade from
6f84dc43 (a commit that predates that
addition of the 'bootstrap' phase on gnu-build-system on 'master' and
that also predates the new 'guix pull'.)

* build-aux/build-self.scm (guile-gcrypt)[arguments]: New field.

* gnu/packages/gcc.scm (gfortran-8, gcc-objc-8, gcc-objc++-8): New
variables.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

Reported by Alex Vong <alexvong1995@gmail.com>.

* config-daemon.ac: Do not add "-L$LIBGCRYPT_LIBDIR" to LIBGCRYPT_LIBS
when "$LIBGCRYPT_LIBDIR" is empty.

* gnu/packages/plotutils.scm (guile-present)[source](modules, snippet):
Remove.

* gnu/packages/plotutils.scm (guile-charting)[source](modules, snippet):
Remove.

* gnu/packages/web.scm (hpcguix-web): Update to 9ff40fc.
[arguments]: In 'wrap-program' phase, add guile-gcrypt, guile-git, and
guile-bytestructures to DEPS.

* gnu/packages/guile.scm (guile-commonmark)[source](snippet): Change the
"modir = " and "godir = " line separately, allowing .go files to be
installed to $(libdir).

This is a follow-up to commit 5dfe4912.
Sorry!

* gnu/packages/bioinformatics.scm, gnu/packages/graph.scm: Use (gnu packages
bioconductor).

* gnu/packages/ccache.scm (ccache): Update to 3.4.3.
[arguments]: Remove obsolete 'munge-failing-test' phase.

* gnu/packages/fonts.scm (font-fira-code): Update to 1.205.

* gnu/packages/mpd.scm (libmpdclient): Update to 2.15.

Fixes <https://bugs.gnu.org/32618>.
Reported by Eric Brown <brown@fastmail.com>.

* guix/git.scm (update-cached-checkout): Remove "origin/" from default
REF.  Define CANONICAL-REF and use it instead of REF.
(latest-repository-commit): Remove "origin/" from default REF.
* guix/channels.scm (%default-channels): Remove "origin/" from
'branch'.

This fixes a regression introduced in
ca719424 whereby external channels would
fail to build due to the lack of (gcrypt …) modules.

* guix/channels.scm (channel-instance-derivations): Add 'guile-gcrypt'.
Pass it along CORE to 'build-channel-instance'.

* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".

* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".

* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".

* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".

* gnu/packages/bioinformatics.scm (r-rcas)[native-inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc".

* gnu/packages/statistics.scm (r-modelmetrics): Update to 1.2.0.
[propagated-inputs]: Add r-data-table.

* gnu/packages/statistics.scm (r-robustbase): Update to 0.93-2.

* gnu/packages/statistics.scm (r-rann): Update to 2.6.

* gnu/packages/statistics.scm (r-ggthemes): Update to 4.0.1.
[propagated-inputs]: Remove r-assertthat and r-colorspace; add r-purrr,
r-stringr, and r-tibble.

* gnu/packages/statistics.scm (r-ztable): Update to 0.2.0.
[propagated-inputs]: Add r-flextable, r-magrittr, r-moonbook, r-officer,
r-rcolorbrewer, r-scales, and r-stringr.

* gnu/packages/statistics.scm (r-zoo): Update to 1.8-3.

* gnu/packages/statistics.scm (r-gtools): Update to 3.8.1.