gnu: Add cl-ana.makeres-table.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.makeres-table, cl-ana.makeres-table):
  New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.makeres-progress.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.makeres-progress,
  cl-ana.makeres-progress): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.makeres-block.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.makeres-block, cl-ana.makeres-block):
  New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.makeres-macro.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.makeres-macro, cl-ana.makeres-macro):
  New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.makeres.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.makeres, cl-ana.makeres): New
  variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.serialization.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.serialization, cl-ana.serialization):
  New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.table-viewing.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.table-viewing, cl-ana.table-viewing):
  New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.plotting.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.plotting, cl-ana.plotting): New
  variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.gnuplot-interface.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.gnuplot-interface,
  cl-ana.gnuplot-interface, ecl-cl-ana.gnuplot-interface): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.statistics.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.statistics, cl-ana.statistics): New
  variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.file-utils.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.file-utils, cl-ana.file-utils,
  ecl-cl-ana.file-utils): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.histogram.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.histogram, cl-ana.histogram): New
  variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.fitting.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.fitting, cl-ana.fitting): New
  variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.map.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.map, cl-ana.map, ecl-cl-ana.map): New
  variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.hash-table-utils.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.hash-table-utils,
  cl-ana.hash-table-utils, ecl-cl-ana.hash-table-utils): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.clos-utils.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.clos-utils, cl-ana.clos-utils,
  ecl-cl-ana.clos-utils): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.lorentz.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.lorentz, cl-ana.lorentz): New
  variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.linear-algebra.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.linear-algebra,
  cl-ana.linear-algebra): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.reusable-table.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.reusable-table,
  cl-ana.reusable-table, ecl-cl-ana.reusable-table): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.csv-table.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.csv-table, cl-ana.csv-table): New
  variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.ntuple-table.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.ntuple-table, cl-ana.ntuple-table):
  New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.gsl-cffi.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.gsl-cffi, cl-ana.gsl-cffi,
  ecl-cl-ana.gsl-cffi): New variables.

Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.hdf-table.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.hdf-table, cl-ana.hdf-table,
  ecl-cl-ana.hdf-table): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.typed-table.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.typed-table, cl-ana.typed-table,
  ecl-cl-ana.typed-table): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.hdf-utils.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.hdf-utils, cl-ana.hdf-utils,
  ecl-cl-ana.hdf-utils): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.hdf-typespec.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.hdf-typespec, cl-ana.hdf-typespec,
  ecl-cl-ana.hdf-typespec): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.typespec.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.typespec, cl-ana.typespec,
  ecl-cl-ana.typespec): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.memoization.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.memoization, cl-ana.memoization,
  ecl-cl-ana.memoization): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.int-char.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.int-char, cl-ana.int-char,
  ecl-cl-ana.int-char): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.hdf-cffi.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.hdf-cffi, cl-ana.hdf-cffi,
  ecl-cl-ana.hdf-cffi): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.table-utils.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.table-utils, cl-ana.table-utils,
  ecl-cl-ana.table-utils): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.table.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.table, cl-ana.table,
  ecl-cl-ana.table): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.quantity.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.quantity, cl-ana.quantity): New
  variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.error-propogation.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.error-propogation,
  cl-ana.error-propogation): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.tensor.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.tensor, cl-ana.tensor,
  ecl-cl-ana.tensor): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.binary-tree.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.binary-tree, cl-ana.binary-tree,
  ecl-cl-ana.binary-tree): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.macro-utils.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.macro-utils, cl-ana.macro-utils,
  ecl-cl-ana.macro-utils): New packages.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.symbol-utils.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.symbol-utils, cl-ana.symbol-utils,
  ecl-cl-ana.symbol-utils): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.calculus.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.calculus, cl-ana.calculus,
  ecl-cl-ana.calculus): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.math-functions.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.math-functions,
  cl-ana.math-functions): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.generic-math.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.generic-math, cl-ana.generic-math,
  ecl-cl-ana.generic-math): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.list-utils.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.list-utils, cl-ana.list-utils,
  ecl-cl-ana.list-utils): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.functional-utils.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.functional-utils,
  cl-ana.functional-utils, ecl-cl-ana.functional-utils): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.string-utils.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.string-utils, cl-ana.string-utils,
  ecl-cl-ana.string-utils): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.package-utils.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana.package-utils, cl-ana.package-utils,
  ecl-cl-ana.package-utils): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-ana.pathname-utils.

* gnu/packages/lisp-xyz.scm (sbcl-cl-ana-boot0, sbcl-cl-ana.pathname-utils,
  cl-ana.pathname-utils, ecl-cl-ana-pathname-utils): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add external-program.

* gnu/packages/lisp-xyz.scm (sbcl-external-program, cl-external-program,
  ecl-external-program): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-csv.

* gnu/packages/lisp-xyz.scm (sbcl-cl-csv, cl-csv, ecl-cl-csv): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add lisp-unit2.

* gnu/packages/lisp-xyz.scm (sbcl-lisp-unit2, cl-lisp-unit2, ecl-lisp-unit2):
  New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add symbol-munger.

* gnu/packages/lisp-xyz.scm (sbcl-symbol-munger, cl-symbol-munger,
  ecl-symbol-munger): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Preparations to add symbol-munger and lisp-unit2.

There is a cyclical dependency between symbol-munger and lisp-unit2. Here we
add '*-boot0' packages to cut this cycle.

* gnu/packages/lisp-xyz.scm (sbcl-symbol-munger-boot0, sbcl-lisp-unit2-boot0):
  New variables.

Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-interpol.

* gnu/packages/lisp-xyz.scm (sbcl-cl-interpol, cl-interpol, ecl-cl-interpol):
  New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add antik.

* gnu/packages/lisp-xyz.scm (sbcl-antik, cl-antik): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add gsll.

* gnu/packages/lisp-xyz.scm (sbcl-gsll, cl-gsll): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add science-data.

* gnu/packages/lisp-xyz.scm (sbcl-science-data, cl-science-data): New
  variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add physical-dimension.

* gnu/packages/lisp-xyz.scp (sbcl-physical-dimension, cl-physical-dimension):
  New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add foreign-array.

* gnu/packages/lisp-xyz.scm (sbcl-foreign-array, cl-foreign-array,
  ecl-foreign-array): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add antik-base.

* gnu/packages/lisp-xyz.scm (sbcl-antik-base, cl-antik-base, ecl-antik-base):
  New variables.

Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add fna.

* gnu/packages/game-development.scm (fna): New variable.

gnu: Add mojoshader-cs.

* gnu/packages/gl.scm (mojoshader-cs): New variable.

gnu: Add sdl2-cs.

* gnu/packages/sdl.scm (sdl2-cs): New variable.

gnu: Add plump.

* gnu/packages/lisp-xyz.scm (cl-plump, sbcl-plump): New variables.

gnu: Add array-utils.

* gnu/packages/lisp-xyz.scm (cl-array-utils, sbcl-array-utils): New variables.

gnu: Add parachute.

* gnu/packages/lisp-xyz.scm (cl-parachute, sbcl-parachute): New variables.

gnu: Add form-fiddle.

* gnu/packages/lisp-xyz.scm (cl-form-fiddle, sbcl-form-fiddle): New variables.

gnu: Add documentation-utils.

* gnu/packages/lisp-xyz.scm (cl-documentation-utils, sbcl-documentation-utils): New variables.

gnu: Add trivial-indent.

* gnu/packages/lisp-xyz.scm (cl-trivial-indent, sbcl-trivial-indent): New variables.

gnu: r-irkernel: Fix R kernel loading

* gnu/packages/cran.scm (r-irkernel): Absolute path to R binary
[propagated-inputs]: Generate proper search paths by adding r-minimal

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

import: cran: Fix file descriptor leak.

Fixes <https://bugs.gnu.org/38836>.
Reported by Ricardo Wurmus <rekado@elephly.net>.

* guix/import/cran.scm (bioconductor-packages-list): Close the port
returned by 'http-fetch/cached'.
(fetch-description): Likewise.

download: Do not leak file descriptors on TLS ports.

Fixes <https://bugs.gnu.org/20145>.

* guix/build/download.scm (%tls-ports, register-tls-record-port): Remove.
(tls-wrap): Remove call to 'register-tls-record-port'.  Return a custom
binary input/output port instead.  This is a backport of what Guile
2.2's (web client) module has been doing.
(close-connection): Define as an alias for 'close-port'.
* guix/http-client.scm (http-fetch): Remove #:keep-alive? parameter,
which was ignored and unused.
Pass #:keep-alive? #f to 'http-get'.
* guix/lint.scm (probe-uri): Use 'close-port' instead of 'close-connection'.
* guix/scripts/substitute.scm (http-multiple-get): Likewise.

gexp: 'gexp->script' marks its result as non-offloadable and non-substitutable.

* guix/gexp.scm (gexp->script): Pass #:local-build? and #:substitutable?
to 'gexp->derivation'.

bootloader: Mark "grub.cfg" and "extlinux.conf" as non-substitutable.

Suggested by <pkill9@runbox.com>.

* gnu/bootloader/grub.scm (grub-configuration-file): Pass #:options to
'computed-file'.
* gnu/bootloader/extlinux.scm (extlinux-configuration-file): Likewise.

gnu: sbcl: Update to 2.0.0.

* gnu/packages/lisp.scm (sbcl): Update to 2.0.0.

Revert "gnu: sbcl: Update to 1.5.9."

The boot0 package won't be needed anymore with 2.0.0.

This reverts commit edf8152563a898438708ec9b2b17284a9d55d271.

gnu: python-apsw: Update to 3.28.0-r1.

* gnu/packages/databases.scm (python-apsw): Update to 3.28.0-r1.

gnu: python-apsw: Use 'replace' for 'check phase.

* gnu/packages/databases.scm (python-apsw)[arguments]: Update build
phase order and replace stock 'check phase.

gnu: python-apsw: Don't use unstable tarball.

* gnu/packages/databases.scm (python-apsw)[source]: Download using
release zip archive.
[native-inputs]: Add unzip.

gnu: capstone: Don't use unstable tarball.

* gnu/packages/engineering.scm (capstone)[source]: Download using
git-fetch.

gnu: uglify-js: Move back next to sbcl-cl-uglify-js definition.

This fixes the bug which prevented uglify-js from being defined properly, and
cascaded back to all Common Lisp packages.

* gnu/packages/bioinformatics.scm: Replace javascript module with lisp-xyz.
* gnu/packages/cran.scm: Use lisp-xyz module.
* gnu/packages/javascript.scm (uglify-js): Move from here...
* gnu/packages/lisp-xyz.scm: ... To here.
* gnu/packages/web.scm: Replace javascript module with lisp-xyz.
* guix/build-system/minify.scm: Find uglify-js in the lisp-xyz module.

Revert "gnu: libetpan: Update to 1.9.4."

This version of libetpan does not ship with libetpan-config, which
prefents claws-mail from building.

This reverts commit e2f5de145562540a497bfc5b580011c9cf9000fd.

install: Add jfsutils to the installation image.

* gnu/system/install.scm (installation-os)[packages]: Add jfsutils.

tests: install: Test a JFS root file system.

* gnu/tests/install.scm (%jfs-root-os, %jfs-root-installation-script)
(%test-jfs-root-os): New variables.

linux-initrd: Add support for JFS.

* gnu/system/linux-initrd.scm (file-system-packages): Add jfs_fsck/static.
(file-system-type-modules): Add ‘jfs’ module.

gnu: Add jfs_fsck-static.

* gnu/packages/file-systems.scm (jfs_fsck-static): New public variable.

gnu: Add jfsutils-static.

gnu/packages/file-systems.scm (jfsutils/static): New public variable.

uuid: Add support for JFS.

* gnu/system/uuid.scm (string->jfs-uuid): New procedure.
(%uuid-parsers, %uuid-printers): Add ‘jfs’ file system type.

file-systems: Add support for JFS.

* gnu/build/file-systems.scm (%jfs-endianness): New syntax.
(jfs-superblock?, read-jfs-superblock, jfs-superblock-uuid)
(jfs-superblock-volume-name, check-jfs-file-system): New procedures.
(%partition-label-readers, %partition-uuid-readers, check-file-system):
Register them.

gnu: gloox: Update to 1.0.23.

* gnu/packages/messaging.scm (gloox): Update to 1.0.23.

gnu: hexchat: Update to 2.14.3.

* gnu/packages/messaging.scm (hexchat): Update to 2.14.3.
[source]: Remove patch.
* gnu/packages/patches/hexchat-crash-exit.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

gnu: tuxguitar: Update to 1.5.3.

* gnu/packages/music.scm (tuxguitar): Update to 1.5.3.

gnu: qtractor: Update to 0.9.12.

* gnu/packages/music.scm (qtractor): Update to 0.9.12.

gnu: padthv1: Update to 0.9.12.

* gnu/packages/music.scm (padthv1): Update to 0.9.12.

gnu: samplv1: Update to 0.9.12.

* gnu/packages/music.scm (samplv1): Update to 0.9.12.

gnu: drumkv1: Update to 0.9.12.

* gnu/packages/music.scm (drumkv1): Update to 0.9.12.

gnu: synthv1: Update to 0.9.12.

* gnu/packages/music.scm (synthv1): Update to 0.9.12.

gnu: eyed3: Update to 0.8.12.

* gnu/packages/mp3.scm (eyed3): Update to 0.8.12.

gnu: zam-plugins: Update to 3.12.

* gnu/packages/music.scm (zam-plugins): Update to 3.12.

gnu: x42-plugins: Update to 20191215.

* gnu/packages/music.scm (x42-plugins): Update to 20191215.

gnu: musl: Update to 1.1.24.

* gnu/packages/musl.scm (musl): Update to 1.1.24.

gnu: whois: Update to 5.5.4.

* gnu/packages/networking.scm (whois): Update to 5.5.4.