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branch staging updated (0d65f7daae -> d9bcd1a8d6)

From: guix-commits
Subject: branch staging updated (0d65f7daae -> d9bcd1a8d6)
Date: Mon, 9 Jan 2023 18:27:25 -0500 (EST)

mbakke pushed a change to branch staging
in repository guix.

    from 0d65f7daae gnu: vulkan-loader: Don't build (and install) googletest.
     add 6ca59eec9a gnu: git-annex: Patch 'git-annex webapp' to use hardcoded 
     add 812ecf7ee6 gnu: tectonic: Update to 0.12.0.
     add 064c5b7e45 gnu: Remove linux-libre 4.9.
     add 56b56db13e news: Add entry about the removal of linux-libre 4.9.
     new a4d9ce5488 gnu: Move Java XML packages to new module.
     new aac0605de3 gnu: Move Java bootstrap packages to separate module.
     new f206682903 gnu: java-jgit-4.2: Do not build with icedtea-7.
     new d977bb8d6b gnu: java-jgit-4.2: Remove trailing #T from build phase.
     new 84543eae06 gnu: java-cisd-args4j: Remove trailing #T from build phase.
     new f1babf56da gnu: java-cisd-args4j: Use later version of ECJ.
     new 2703b6feef gnu: java-cisd-args4j: Do not build with icedtea-7.
     new 649ea550e7 gnu: Remove java-ecj-3.5.
     new 3b62c2804c gnu: java-ecj: Do not inherit from java-ecj-3.
     new a4eb83fee7 gnu: java-cisd-jhdf5: Remove trailing #T.
     new 882baf4b7d gnu: java-cisd-jhdf5: Do not override default JDK.
     new f05d228472 gnu: ant-apache-bcel: Fix inheritance by using gexp.
     new 9e14a7b4d2 gnu: ant-junit: Fix inheritance by using gexp.
     new 2463e9f1fe gnu: Remove java-ecj-3.
     new 1efe7de096 gnu: python-afdko: Fix failing tests.
     new 37aeb85f45 gnu: ikiwiki: Add missing inputs.
     new d0044216c9 gnu: ikiwiki: Remove input labels.
     new 2acce55a00 home: environment-variables: Return support for file-likes 
and gexps.
     new 35ecbb418c home: environment-variables: Fix escaping.
     new de48bcee07 gnu: Add r-gg3d.
     new 8b314efd50 services: base: Add environment support to 
     new 47c1de22df doc: cookbook: Add "Installing Guix on a Cluster" chapter.
     new 007e697560 substitute: Parse '_NIX_OPTIONS' once.
     new 5d24e57a61 derivations: 'read-derivation' correctly handles case with 
empty hash.
     new 407175a1d0 daemon: Improve error message for wrong hash sizes.
     new 6c343d0d0f read-print: Do not use extended notation when printing 
'1+', '1-', etc.
     new e8b90b1d5d gnu: Add minetest-wielded-light.
     new 735e915bbd gnu: Add minetest-mobs-monster.
     new 84f117f495 gnu: LLVM, Clang, libomp, lld: Update to 15.0.6.
     new f62ac25ca3 news: Add 'de' translation.
     new b688e283dc gnu: Add r-httr2.
     new b147c4a7f3 gnu: r-collections: Update to 0.3.7.
     new 15b612a328 gnu: r-htmlwidgets: Update to 1.6.1.
     new 47184a91f1 gnu: r-rstpm2: Update to 1.5.9.
     new 8c83db6a38 gnu: r-lava: Update to 1.7.1.
     new ba4117bf61 gnu: r-timedate: Update to 4022.108.
     new 77895d9d6b gnu: r-mitml: Update to 0.4-4.
     new f05c1a46ff gnu: r-seriation: Update to 1.4.1.
     new a161409264 gnu: r-zlog: Update to 1.0.2.
     new 407f58a9ad gnu: r-expm: Update to 0.999-7.
     new e758675070 gnu: r-heatmaply: Update to 1.4.2.
     new 0943ee5c9c gnu: r-rastervis: Update to 0.51.5.
     new 3090a07f90 gnu: r-reticulate: Update to 1.27.
     new 18ea1e2085 gnu: r-billboarder: Update to 0.4.0.
     new c7d61d2077 gnu: r-officer: Update to 0.5.1.
     new fa9f02dc9f gnu: r-writexl: Update to 1.4.2.
     new 8d696f2728 gnu: r-precrec: Update to 0.14.1.
     new 8b322c5967 gnu: r-netrep: Update to 1.2.6.
     new fd82a783eb gnu: r-drtmle: Update to 1.1.2.
     new c63bbd4348 gnu: r-raster: Update to 3.6-13.
     new 1ce7003fb1 gnu: r-afex: Update to 1.2-1.
     new 4f9b35d55c gnu: r-ncdf4: Update to 1.21.
     new 4e69d047c8 gnu: r-rgl: Update to 0.111.6.
     new b24219443d gnu: r-fmsb: Update to 0.7.5.
     new 8b7de31e7a gnu: r-rncl: Update to 0.8.7.
     new a2c77eec88 gnu: r-lavaan: Update to 0.6-13.
     new dcf8c29277 gnu: r-gkmsvm: Update to 0.82.0.
     new 20e6139df3 gnu: r-qqconf: Update to 1.3.1.
     new 63921834e9 gnu: r-forecast: Update to 8.20.
     new 848c318aa0 gnu: r-tidytext: Update to 0.4.1.
     new 302f55fd9d gnu: r-qtl: Update to 1.58.
     new fa0dc85d40 gnu: r-mlr3learners: Update to 0.5.6.
     new 5aacc2bd98 gnu: r-rtweet: Update to 1.1.0.
     new 8c33135953 gnu: r-bien: Update to 1.2.6.
     new 1e3990d313 gnu: r-sendmailr: Update to 1.3-2.
     new bd0da7c791 gnu: r-statmod: Update to 1.5.0.
     new 387c486591 gnu: r-fpc: Update to 2.2-10.
     new 6e75790fc0 import/cran: Fix Bioconductor updater.
     new 51e79fe737 gnu: Update copyright header.
     new 8e864f2a3b gnu: Add r-clustergeneration.
     new 349d110ae0 gnu: Add r-remacor.
     new 3072990b03 gnu: r-biocparallel: Update to 1.32.5.
     new b37a9bfba6 gnu: r-bsgenome: Update to 1.66.2.
     new f5629558b1 gnu: r-genomeinfodb: Update to 1.34.6.
     new aca59da931 gnu: r-msnbase: Update to 2.24.2.
     new 3ac0f4e62c gnu: r-batchelor: Update to 1.14.1.
     new 850638df5a gnu: r-flowworkspace: Update to 4.10.1.
     new d41e85678a gnu: r-variancepartition: Update to 1.28.1.
     new 8ee7f8df76 gnu: r-biocviews: Update to 1.66.2.
     new 8423ca9da8 gnu: r-biocset: Update to 1.12.1.
     new df33c8de73 gnu: Add automatic-component-toolkit.
     new 5e101ab56f gnu: lib3mf: Remove bundled ACT.
     new 5e36d4381f gnu: lib3mf: Remove input labels.
     new f29a17c84b gnu: lib3mf: Remove bundled software.
     new 73d5abd003 gnu: lib3mf: Update to 2.2.0.
     new 79a9bb25bc gnu: perftest: Update to 4.5-0.20.
     new d9bcd1a8d6 Merge branch 'master' into staging

The 87 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "add" were already present in the repository and have only
been added to this reference.

Summary of changes:                                        |    2 -
 doc/guix-cookbook.texi                             |  433 +-
 doc/guix.texi                                      |    4 +
 etc/news.scm                                       |   14 +-
 gnu/home/services.scm                              |    8 +-
 gnu/                                       |    3 +
 gnu/packages/aux-files/linux-libre/4.9-i686.conf   | 9062 --------------------
 gnu/packages/aux-files/linux-libre/4.9-x86_64.conf | 8910 -------------------
 gnu/packages/axoloti.scm                           |    4 +-
 gnu/packages/batik.scm                             |    4 +-
 gnu/packages/bioconductor.scm                      |   50 +-
 gnu/packages/bioinformatics.scm                    |   33 +
 gnu/packages/code.scm                              |   41 +-
 gnu/packages/cran.scm                              |  233 +-
 gnu/packages/crates-io.scm                         |  109 +-
 gnu/packages/engineering.scm                       |   47 +-
 gnu/packages/fontutils.scm                         |    1 +
 gnu/packages/groovy.scm                            |    1 +
 gnu/packages/haskell-apps.scm                      |   12 +-
 gnu/packages/java-bootstrap.scm                    |  724 ++
 gnu/packages/java-xml.scm                          |  688 ++
 gnu/packages/java.scm                              | 1086 +--
 gnu/packages/linux.scm                             |   69 +-
 gnu/packages/llvm.scm                              |    8 +-
 gnu/packages/maven.scm                             |    2 +-
 gnu/packages/minetest.scm                          |   47 +
 .../python-afdko-suppress-copyright-test.patch     |   20 +
 gnu/packages/rust-apps.scm                         |   15 +-
 gnu/packages/statistics.scm                        |   12 +-
 gnu/packages/web.scm                               |   50 +-
 gnu/packages/xml.scm                               |  642 --
 gnu/services/base.scm                              |   10 +-
 gnu/tests/base.scm                                 |    4 -
 guix/derivations.scm                               |   10 +-
 guix/import/cran.scm                               |    6 +-
 guix/read-print.scm                                |   22 +-
 guix/scripts/substitute.scm                        |   10 +-
 nix/libutil/                                |    7 +-
 tests/derivations.scm                              |   52 +-
 tests/                                 |   12 +-
 tests/read-print.scm                               |    7 +-
 41 files changed, 2702 insertions(+), 19772 deletions(-)
 delete mode 100644 gnu/packages/aux-files/linux-libre/4.9-i686.conf
 delete mode 100644 gnu/packages/aux-files/linux-libre/4.9-x86_64.conf
 create mode 100644 gnu/packages/java-bootstrap.scm
 create mode 100644 gnu/packages/java-xml.scm
 create mode 100644 

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