gnu: Add r-pathview.

* gnu/packages/bioconductor.scm (r-pathview): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

gnu: Add r-kegggraph.

* gnu/packages/bioconductor.scm (r-kegggraph): New variable.

gnu: Add r-gagedata.

* gnu/packages/bioconductor.scm (r-gagedata): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

gnu: rust-lzma-sys-0.1: Update to 0.1.17.

* gnu/packages/crates-io.scm (rust-lzma-sys-0.1): Update to 0.1.17.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: rust-encoding-rs-0.8: Don't skip build.

* gnu/packages/crates-io.scm (rust-encoding-rs-0.8)[arguments]: Don't
skip build.

gnu: rust-encoding-rs-0.8: Update to 0.8.26.

* gnu/packages/crates-io.scm (rust-encoding-rs-0.8): Update to 0.8.26.
[arguments]: In cargo-inputs remove rust-packed-simd-0.3, add
rust-packed-simd-2-0.3, replace rust-cfg-if-0.1 with 1.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add rust-rkv-0.10.

* gnu/packages/crates-io.scm (rust-rkv-0.10): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: rust-sleef-sys-0.1: Adjust inputs.

* gnu/packages/crates-io.scm (rust-sleef-sys-0.1)[arguments]: Move all
crates from cargo-development-inputs to cargo-inputs.  Replace
rust-cbindgen-0.50 with 0.46.

gnu: Add rust-packed-simd-2-0.3.

* gnu/packages/crates-io.scm (rust-packed-simd-2-0.3): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add rust-rusqlite-0.23.

* gnu/packages/crates-io.scm (rust-rusqlite-0.23): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: rust-indexmap-1: Update to 1.6.1.

* gnu/packages/crates-io.scm (rust-indexmap-1): Update to 1.6.1.
[arguments]: Add rust-hashbrown-0.9 to cargo-inputs. In
cargo-development-inputs add rust-fxhash-0.2, replace rust-itertools-0.8
with 0.9, reust-serde-test-1 with rust-serde-derive-1.

gnu: rust-serde-json-1: Update to 1.0.60.

* gnu/packages/crates-io.scm (rust-serde-json-1): Update to 1.0.60.
[arguments]: Add rust-automod-1, rust-serde-stacker-0.1 to cargo-inputs.
Don't skip build.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add rust-serde-stacker-0.1.

* gnu/packages/crates-io.scm (rust-serde-stacker-0.1): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add rust-libsqlite3-sys-0.18.

* gnu/packages/crates-io.scm (rust-libsqlite3-sys-0.18): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add rust-lmdb-rkv-0.14.

* gnu/packages/crates-io.scm (rust-lmdb-rkv-0.14): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add rust-lmdb-rkv-sys-0.11.

* gnu/packages/crates-io.scm (rust-lmdb-rkv-sys-0.11): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: lmdb: Install pkg-config file.

* gnu/packages/databases.scm (lmdb)[arguments]: Add phase to create a
lmdb.pc file.

gnu: Add rust-nom-2.

* gnu/packages/crates-io.scm (rust-nom-2): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add rust-size-format-1.

* gnu/packages/crates-io.scm (rust-size-format-1): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add rust-tabwriter-1.

* gnu/packages/crates-io.scm (rust-tabwriter-1): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add nvc.

* gnu/packages/fpga.scm (nvc): New variable.

gnu: emacs-slime: Update to 2.26.1.

* gnu/packages/emacs-xyz.scm (emacs-slime): Update to 2.26.1.

gnu: emacs-project: Update to 0.5.3.

* gnu/packages/emacs-xyz.scm (emacs-project): Update to 0.5.3.

gnu: emacs-xref: Update to 1.0.4.

* gnu/packages/emacs-xyz.scm (emacs-xref): Update to 1.0.4.

doc: Emacs Packages: Fix typos.

* doc/contributing.texi (Emacs Packages): Fix typo. Also remove spurious white
space, and unnecessary quote.

gnu: Add emacs-elegant-agenda-mode.

* gnu/packages/emacs-xyz.scm (emacs-elegant-agenda-mode): New variable.

gnu: emacs-org-sidebar: Update to 0.3.2.

* gnu/packages/emacs-xyz.scm (emacs-org-sidebar): Update to 0.3.2.

gnu: emacs-org-ql: Update to 0.5.

* gnu/packages/emacs-xyz.scm (emacs-org-ql): Update to 0.5.
[propagated-inputs]: Add emacs-transient.
[native-inputs]: Add emacs-with-simulated-input.
[phases]{require-helm}: Remove.
{disable-failing-tests}: New phase.

gnu: Add emacs-with-simulated-input.

* gnu/packages/emacs-xyz.scm (emacs-with-simulated-input): New variable.

gnu: emacs-org-super-agenda: Update to 1.2 and enable tests.

* gnu/packages/emacs-xyz.scm (emacs-org-super-agenda): Update to 1.2.
[arguments]: Enable tests.
[phases]{prepare-for-tests}: New phase.
[native-inputs]: Add emacs-f and util-linux.

doc: Add Emacs packaging guidelines.

* doc/contributing.texi (Emacs Packages): New subsection.

gnu: linux-libre 5.4: Update to 5.4.84.

* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.84.
(deblob-scripts-5.4, linux-libre-5.4-pristine-source): Update hashes.

gnu: linux-libre: Update to 5.9.15.

* gnu/packages/linux.scm (linux-libre-5.9-version): Update to 5.9.15.
(deblob-scripts-5.9, linux-libre-5.9-pristine-source): Update hashes

gnu: bind: Update to 9.16.10.

* gnu/packages/dns.scm (isc-bind): Update to 9.16.10.

gnu: Add python-myhdl.

* gnu/packages/fpga.scm (python-myhdl): New variable.

gnu: icedove: Update to 78.6.0.

* gnu/packages/gnuzilla.scm (icedove): Update to 78.6.0.

gnu: Add emacs-project.

* gnu/packages/emacs-xyz.scm (emacs-project): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add emacs-xref.

* gnu/packages/emacs-xyz.scm (emacs-xref): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: emacs-org-caldav: Make description a full sentence.

* gnu/packages/emacs-xyz.scm (emacs-org-caldav)[description]: Make it a full
sentence.

gnu: emacs-org-caldav: Update to 0.0.0-2-8569941.

* gnu/packages/emacs-xyz.scm (emacs-org-caldav): Update to 0.0.0-2-8569941.

gnu: python-internetarchive: Fix typo.

* gnu/packages/web.scm (python-internetarchive): Fix typo.

gnu: obs: Update to 26.1.0.

* gnu/packages/video.scm (obs): Update to 26.1.0.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: webkitgtk: Update to 2.30.4.

* gnu/packages/webkit.scm (webkitgtk): Update to 2.30.4.

gnu: Add libcaption.

* gnu/packages/video.scm (libcaption): New variable.

gnu: Add bootterm.

* gnu/packages/terminals.scm (bootterm): New variable.

gnu: emacs-telega: Update homepage.

* gnu/packages/emacs-xyz.scm (emacs-doom-modeline)[home-page]: Use updated URL.

gnu: emacs-telega: Update to 0.7.1-1.

* gnu/packages/emacs-xyz.scm (emacs-telega): Update to 0.7.1-1.

import: cran: Use CRAN’s canonical URL as home-page.

* guix/import/cran.scm (%cran-canonical-url): New variable.
(description->package): Construct home-page using canonical URL.

Signed-off-by: Christopher Baines <mail@cbaines.net>

gnu: Add cfunge.

* gnu/packages/esolangs.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: foo2zjs: Fix installation.

* gnu/packages/cups.scm (foo2zjs)[inputs]: Add coreutils and sed.
[arguments]: Add new phases ''make-install-dirs', 'wrap-wrappers', and
'install-cups-filters-symlinks'.

Signed-off-by: Leo Famulari <leo@famulari.name>

services: 'references-file' depends on Guile-Gcrypt.

Regression introduced in 6a060ff27ff68384d7c90076baa36c349fff689d.

Reported by clone11 on #guix.

* gnu/services/base.scm (references-file): Wrap gexp in 'with-extensions'.

gnu: Add Okular.

* gnu/packages/kde.scm (okular): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: icecat: Update to 78.6.0-guix0-preview1 [security fixes].

Includes fixes for CVE-2020-16042, CVE-2020-26971, CVE-2020-26973,
CVE-2020-26974, CVE-2020-26978, CVE-2020-35111, CVE-2020-35112, and
CVE-2020-35113.

* gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update.
(icecat-source): Update gnuzilla commit, base version, and hashes.
* gnu/packages/patches/icecat-makeicecat.patch: Adapt to new version.

gnu: yelp-tools: Restore a comment.

* gnu/packages/gnome.scm (yelp-tools)[propagated-inputs]: Restore a
comment deleted in commit 416b1b9f56b514677660b56992cea1c78e00f519.

gnu: gobject-introspection: Restore a comment.

* gnu/packages/glib.scm (gobject-introspection)[propagated-inputs]: Restore a
comment deleted in commit c3264f9e100ad6aefe5216002b68f3bfdcf6be95.

gnu: youtube-dl: Avoid using pre-generated code.

* gnu/packages/video.scm (youtube-dl)[source]: Add 'snippet' to delete
pre-generated files.
[arguments]: Add 'build-generated-files' phase.
[native-inputs]: New field, to add 'zip'.

gnu: emacs-ivy-posframe: Update to 0.5.5.

* gnu/packages/emacs-xyz.scm (emacs-ivy-posframe): Update to 0.5.5.

deduplicate: Create the '.links' directory lazily.

This avoids repeated (mkdir-p "/gnu/store/.links") calls when
deduplicating lots of files.

* guix/store/deduplication.scm (deduplicate): Remove initial call to
'mkdir-p'.  Add ENOENT case in 'link' exception handler.  Reindent.
* tests/store-deduplication.scm ("deduplicate, ENOSPC"): Check
for (<= links 4) to account for the initial 'link' call.

database: Honor 'SOURCE_DATE_EPOCH'.

* guix/store/database.scm (timestamp): New procedure.
(sqlite-register): Use it as the default for #:time.
(register-items): Likewise for #:registeration-time.

database: Remove 'register-path'.

* guix/store/database.scm (register-path): Remove.
* tests/store-database.scm ("register-path"): Rename to...
("register-items"): ... this, and use 'register-items' instead of
'register-path'.
("register-path, directory"): Rename to...
("register-items, directory"): ... this, and use 'register-items'
instead of 'register-path'.
("register-path with unregistered references"): Rename to...
("sqlite-register with unregistered references"): ... this.

system: 'init' does not recompute the hash of each store item.

Fixes <https://bugs.gnu.org/44760>.

Previously, the 'register-path' call would re-traverse ITEM to compute
its nar hash, even though that hash is already known in the initial
store.  This patch also avoids repeated opening/closing of the
database.

* guix/store/database.scm (call-with-database): Export.
* guix/scripts/system.scm (copy-item): Add 'db' parameter.  Call
'sqlite-register' instead of 'register-path'.
(copy-closure): Remove redundant call to 'references*'.  Call
'call-with-database' and pass the database to 'copy-item'.

database: Remove #:deduplicate? and #:reset-timestamps? from 'register-path'.

* guix/store/database.scm (register-path): Remove #:deduplicate?
and #:reset-timestamps?.
* guix/scripts/system.scm (copy-item): Adjust accordingly.
* tests/store-database.scm ("register-path")
("register-path, directory"): Call 'reset-timestamps'.

guix system: 'init' copies, resets timestamps, and deduplicates at once.

Partly fixes <https://bugs.gnu.org/44760>.

* guix/build/store-copy.scm (copy-store-item): New procedure.
(populate-store): Use it instead of the inline 'copy-recursively' call.
* guix/scripts/system.scm (copy-item): Likewise.
Pass #:reset-timestamps? and #:deduplicate? to 'register-path'.

database: Remove #:deduplicate? from 'register-items'.

It is now up to the caller to deduplicate store contents.

* guix/store/database.scm (register-items): Remove #:deduplicate?
parameter and call to 'deduplicate'.
(register-path): Call 'deduplicate' when #:deduplicate? is true.
* gnu/build/image.scm (register-closure): Adjust call accordingly.
* gnu/build/vm.scm (register-closure): Likewise.
* guix/nar.scm (finalize-store-file): Likewise.
* guix/scripts/pack.scm (store-database): Likewise.

image: 'register-closure' leaves it up to the caller to deduplicate.

* gnu/build/image.scm (register-closure): Remove #:deduplicate?
parameter and pass #:deduplicate? #f to 'register-items'.
(initialize-root-partition): Adjust accordingly.
* gnu/build/vm.scm (register-closure, root-partition-initializer):
Likewise.

store-copy: 'populate-store' can optionally deduplicate files.

Until now deduplication was performed as an additional pass after
copying files, which involve re-traversing all the files that had just
been copied.

* guix/store/deduplication.scm (copy-file/deduplicate): New procedure.
* tests/store-deduplication.scm ("copy-file/deduplicate"): New test.
* guix/build/store-copy.scm (populate-store): Add #:deduplicate?
parameter and honor it.
* tests/gexp.scm ("gexp->derivation, store copy"): Pass #:deduplicate? #f
to 'populate-store'.
* gnu/build/image.scm (initialize-root-partition): Pass #:deduplicate?
to 'populate-store'.  Pass #:deduplicate? #f to 'register-closure'.
* gnu/build/vm.scm (root-partition-initializer): Likewise.
* gnu/build/install.scm (populate-single-profile-directory): Pass
 #:deduplicate? #f to 'populate-store'.
* gnu/build/linux-initrd.scm (build-initrd): Likewise.
* guix/scripts/pack.scm (self-contained-tarball)[import-module?]: New
procedure.
[build]: Pass it as an argument to 'source-module-closure'.
* guix/scripts/pack.scm (squashfs-image)[build]: Wrap in
'with-extensions'.
* gnu/system/linux-initrd.scm (expression->initrd)[import-module?]: New
procedure.
[builder]: Pass it to 'source-module-closure'.
* gnu/system/install.scm (cow-store-service-type)[import-module?]: New
procedure.  Pass it to 'source-module-closure'.

database: Remove #:reset-timestamps? from 'register-items'.

The assumption now is that the caller took care of resetting timestamps
and permissions.

* guix/store/database.scm (register-items): Remove #:reset-timestamps?
parameter and the call to 'reset-timestamps'.
(register-path): Adjust accordingly and add call to 'reset-timestamps'.
* gnu/build/image.scm (register-closure): Remove #:reset-timestamps?
parameter to 'register-items'.
* gnu/build/vm.scm (register-closure): Likewise.
* guix/nar.scm (finalize-store-file): Adjust accordingly.
* guix/scripts/pack.scm (store-database)[build]: Likewise.

image: 'register-closure' assumes already-reset timestamps.

* gnu/build/image.scm (register-closure): Remove #:reset-timestamps?
parameter.  Pass #:reset-timestamps? #f to 'register-items'.
(initialize-root-partition): Adjust accordingly.
* gnu/build/vm.scm (register-closure, root-partition-initializer):
Likewise.

store-copy: 'populate-store' resets timestamps.

Until now, 'populate-store' would reset permissions but not timestamps,
so callers would resort to going through an extra directory traversal to
reset timestamps.

* guix/build/store-copy.scm (reset-permissions): Remove.
(copy-recursively): New procedure.
(populate-store): Pass #:keep-permissions? to 'copy-recursively'.
Remove call to 'reset-permissions'.
* tests/gexp.scm ("gexp->derivation, store copy"): In BUILD-DRV, check
whether 'populate-store' canonicalizes permissions and timestamps.
* gnu/build/image.scm (initialize-root-partition): Pass #:reset-timestamps? #f
to 'register-closure'.
* gnu/build/vm.scm (root-partition-initializer): Likewise.

nar: Deduplicate files right as they are restored.

This avoids having to traverse and re-read the files that we have just
restored, thereby reducing I/O.

* guix/serialization.scm (dump-file): New procedure.
(restore-file): Add #:dump-file parameter and honor it.
* guix/store/deduplication.scm (tee, dump-file/deduplicate): New
procedures.
* guix/nar.scm (restore-one-item): Pass #:dump-file to 'restore-file'.
(finalize-store-file): Pass #:deduplicate? #f to 'register-items'.
* tests/nar.scm <top level>: Call 'setenv' to set "NIX_STORE".

serialization: 'restore-file' sets canonical timestamp and permissions.

* guix/serialization.scm (restore-file): Set the permissions and mtime
of FILE.
* guix/nar.scm (finalize-store-file): Pass #:reset-timestamps? #f to
'register-items'.
* tests/nar.scm (rm-rf): Add 'chmod' calls to ensure files are writable.
("write-file + restore-file with symlinks"): Ensure every file in OUTPUT
passes 'canonical-file?'.
* tests/guix-archive.sh: Run "chmod -R +w" before "rm -rf".

serialization: 'fold-archive' notifies about directory processing completion.

* guix/serialization.scm (fold-archive): Call PROC with a
'directory-complete tag when done with a directory.
(restore-file): Handle it.
* guix/scripts/archive.scm (list-contents): Likewise.
* guix/scripts/challenge.scm (archive-contents): Likewise.
* tests/nar.scm ("write-file-tree + fold-archive"): Adjust accordingly.

Revert "gnu: grub: Fix unicode font loading when booting over TFTP."

This reverts commit 03fb57ff77b57de510b59485845ed7cb4e0a77a7, which
breaks most system tests.  Specifically, grub.cfg.drv fails to build:

  ERROR: In procedure canonicalize-path:
  In procedure canonicalize-path: No such file or directory

gnu: Add ocaml-reactivedata.

* gnu/packages/ocaml.scm (ocaml-reactivedata): Add ocaml-reactivedata.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>

gnu: maven-wagon-http: Disable a failing test.

* gnu/packages/maven.scm (maven-wagon-http)[arguments]: Add
HugeFileDownloadTest to excluded tests.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>

offload: Print warning in context.

* guix/scripts/offload.scm (build-machine): Add `location` field.
(build-machine-system): Print location with warning.

gnu: iproute: Fix cross compiling.

* gnu/packages/linux.scm (iproute)[arguments]: Set CC and HOSTCC in
make-flags. Add custom phase to replace the value for PKG_CONFIG in
hand-written configure script.

gnu: Add rust-ndarray-0.12.

* gnu/packages/crates-io.scm (rust-ndarray-0.12): New variable.
* gnu/packages/patches/rust-ndarray-remove-blas-src-dep.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

gnu: rust-cblas-sys-0.1: Don't skip build.

* gnu/packages/crates-io.scm (rust-cblas-sys-0.1)[arguments]: Don't skip
build.

gnu: Add rust-handlegraph-0.3.

* gnu/packages/crates-io.scm (rust-handlegraph-0.3): New variable.

gnu: esbuild: Update to 0.8.23.

* gnu/packages/web.scm (esbuild): Update to 0.8.23.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: ffmpeg-2.8: Remove extraneous inputs.

These inputs are not used by FFmpeg 2.

* gnu/packages/video.scm (ffmpeg-2.8)[inputs]: Remove dav1d, libaom,
rav1e, and srt.

gnu: ffmpeg-4.2: Remove extraneous input rav1e.

* gnu/packages/video.scm (ffmpeg-4.2)[inputs]: Remove rav1e.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add python-sanic.

* gnu/packages/python-web.scm (python-sanic): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add python-pytest-sanic.

* gnu/packages/python-check.scm (python-pytest-sanic): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add python-pywatchman.

* gnu/packages/python-xyz.scm (python-pywatchman): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add python-dataclasses.

* gnu/packages/python-xyz.scm (python-dataclasses): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add python-nbsphinx.

* gnu/packages/sphinx.scm (python-nbsphinx): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add python-pyre-extensions.

* gnu/packages/python-xyz.scm (python-pyre-extensions): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add python-hstspreload.

* gnu/packages/python-web.scm (python-hstspreload): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add python-aiofiles.

* gnu/packages/python-xyz.scm (python-aiofiles): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add python-contextvars.

* gnu/packages/python-xyz.scm (python-contextvars): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add kanshi.

* gnu/packages/wm.scm (kanshi): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add r-lpme.

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

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add r-locpol.

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

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add r-decon.

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

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: emacs-transmission: Update to 0.12.2.

* gnu/packages/emacs-xyz.scm (emacs-transmission): Update to 0.12.2.

gnu: grub: Fix unicode font loading when booting over TFTP.

* gnu/bootloader/grub.scm (eye-candy)(font-file): Fix unicode font loading
when booting over TFTP.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

doc: Note different texlive-tiny & texline-union natures.

* doc/contributing.texi (Submitting Patches): Add ‘package’ and
‘procedure’.

Inspired-by: Jorge P. de Morais Neto

gnu: kitty: Re-order inputs and native-inputs alphabetically.

* gnu/packages/terminals.scm (kitty)[inputs, native-inputs]: Re-order
alphabetically.