Merge branch 'master' into staging-next

7 files changed, 49 insertions, 42 deletions

diff --git a/doc/languages-frameworks/coq.section.md b/doc/languages-frameworks/coq.section.md
index 7fa71ddc6f8d..5e16a4c546a3 100644
--- a/doc/languages-frameworks/coq.section.md
+++ b/doc/languages-frameworks/coq.section.md
@@ -3,37 +3,39 @@
 ## Coq derivation: `coq`
 
 The Coq derivation is overridable through the `coq.override overrides`, where overrides is an attribute set which contains the arguments to override. We recommend overriding either of the following
-+ `version` (optional, defaults to the latest version of Coq selected for nixpkgs, see `pkgs/top-level/coq-packages` to witness this choice), which follows the conventions explained in the `coqPackages` section below,
-+ `customOCamlPackage` (optional, defaults to `null`, which lets Coq choose a version automatically), which can be set to any of the ocaml packages attribute of `ocaml-ng` (such as `ocaml-ng.ocamlPackages_4_10` which is the default for Coq 8.11 for example).
-+ `coq-version` (optional, defaults to the short version e.g. "8.10"), is a version number of the form "x.y" that indicates which Coq's version build behavior to mimic when using a source which is not a release. E.g. `coq.override { version = "d370a9d1328a4e1cdb9d02ee032f605a9d94ec7a"; coq-version = "8.10"; }`.
+
+* `version` (optional, defaults to the latest version of Coq selected for nixpkgs, see `pkgs/top-level/coq-packages` to witness this choice), which follows the conventions explained in the `coqPackages` section below,
+* `customOCamlPackage` (optional, defaults to `null`, which lets Coq choose a version automatically), which can be set to any of the ocaml packages attribute of `ocaml-ng` (such as `ocaml-ng.ocamlPackages_4_10` which is the default for Coq 8.11 for example).
+* `coq-version` (optional, defaults to the short version e.g. "8.10"), is a version number of the form "x.y" that indicates which Coq's version build behavior to mimic when using a source which is not a release. E.g. `coq.override { version = "d370a9d1328a4e1cdb9d02ee032f605a9d94ec7a"; coq-version = "8.10"; }`.
 
 ## Coq packages attribute sets: `coqPackages`
 
 The recommended way of defining a derivation for a Coq library, is to use the `coqPackages.mkCoqDerivation` function, which is essentially a specialization of `mkDerivation` taking into account most of the specifics of Coq libraries. The following attributes are supported:
-- `pname` (required) is the name of the package,
-- `version` (optional, defaults to `null`), is the version to fetch and build,
+
+* `pname` (required) is the name of the package,
+* `version` (optional, defaults to `null`), is the version to fetch and build,
   this attribute is interpreted in several ways depending on its type and pattern:
-  + if it is a known released version string, i.e. from the `release` attribute below, the according release is picked, and the `version` attribute of the resulting derivation is set to this release string,
-  + if it is a majorMinor `"x.y"` prefix of a known released version (as defined above), then the latest `"x.y.z"` known released version is selected (for the ordering given by `versionAtLeast`),
-  + if it is a path or a string representing an absolute path (i.e. starting with `"/"`), the provided path is selected as a source, and the `version` attribute of the resulting derivation is set to `"dev"`,
-  + if it is a string of the form `owner:branch` then it tries to download the `branch` of owner `owner` for a project of the same name using the same vcs, and the `version` attribute of the resulting derivation is set to `"dev"`, additionally if the owner is not provided (i.e. if the `owner:` prefix is missing), it defaults to the original owner of the package (see below),
-  + if it is a string of the form `"#N"`, and the domain is github, then it tries to download the current head of the pull request `#N` from github,
-- `defaultVersion` (optional). Coq libraries may be compatible with some specific versions of Coq only. The `defaultVersion` attribute is used when no `version` is provided (or if `version = null`) to select the version of the library to use by default, depending on the context. This selection will mainly depend on a `coq` version number but also possibly on other packages versions (e.g. `mathcomp`). If its value ends up to be `null`, the package is marked for removal in end-user `coqPackages` attribute set.
-- `release` (optional, defaults to `{}`), lists all the known releases of the library and for each of them provides an attribute set with at least a `sha256` attribute (you may use the shell command `nix-prefetch-url --unpack <archive-url>` to find it, where `<archive-url>` is for example `https://github.com/owner/repo/archive/version.tar.gz`), each attribute set of the list of releases also takes optional overloading arguments for the fetcher as below (i.e.`domain`, `owner`, `repo`, `rev` assuming the default fetcher is used) and optional overrides for the result of the fetcher (i.e. `version` and `src`).
-- `fetcher` (optional, default to a generic fetching mechanism supporting github or gitlab based infrastructures), is a function that takes at least an `owner`, a `repo`, a `rev`, and a `sha256` and returns an attribute set with a `version` and `src`.
-- `repo` (optional, defaults to the value of `pname`),
-- `owner` (optional, defaults to `"coq-community"`).
-- `domain` (optional, defaults to `"github.com"`), domains including the strings `"github"` or `"gitlab"` in their names are automatically supported, otherwise, one must change the `fetcher` argument to support them (cf `pkgs/development/coq-modules/heq/default.nix` for an example),
-- `releaseRev` (optional, defaults to `(v: v)`), provides a default mapping from release names to revision hashes/branch names/tags,
-- `displayVersion` (optional), provides a way to alter the computation of `name` from `pname`, by explaining how to display version numbers,
-- `namePrefix` (optional), provides a way to alter the computation of `name` from `pname`, by explaining which dependencies must occur in `name`,
-- `extraBuildInputs` (optional), by default `buildInputs` just contains `coq`, this allows to add more build inputs,
-- `mlPlugin` (optional, defaults to `false`). Some extensions (plugins) might require OCaml and sometimes other OCaml packages. Standard dependencies can be added by setting the current option to `true`. For a finer grain control, the `coq.ocamlPackages` attribute can be used in `extraBuildInputs` to depend on the same package set Coq was built against.
-- `enableParallelBuilding` (optional, defaults to `true`), since it is activated by default, we provide a way to disable it.
-- `extraInstallFlags` (optional), allows to extend `installFlags` which initializes the variable `COQMF_COQLIB` so as to install in the proper subdirectory. Indeed Coq libraries should be installed in `$(out)/lib/coq/${coq.coq-version}/user-contrib/`. Such directories are automatically added to the `$COQPATH` environment variable by the hook defined in the Coq derivation.
-- `setCOQBIN` (optional, defaults to `true`), by default, the environment variable `$COQBIN` is set to the current Coq's binary, but one can disable this behavior by setting it to `false`,
-- `useMelquiondRemake` (optional, default to `null`) is an attribute set, which, if given, overloads the `preConfigurePhases`, `configureFlags`, `buildPhase`, and `installPhase` attributes of the derivation for a specific use in libraries using `remake` as set up by Guillaume Melquiond for `flocq`, `gappalib`, `interval`, and `coquelicot` (see the corresponding derivation for concrete examples of use of this option). For backward compatibility, the attribute `useMelquiondRemake.logpath` must be set to the logical root of the library (otherwise, one can pass `useMelquiondRemake = {}` to activate this without backward compatibility).
-- `dropAttrs`, `keepAttrs`, `dropDerivationAttrs` are all optional and allow to tune which attribute is added or removed from the final call to `mkDerivation`.
+  * if it is a known released version string, i.e. from the `release` attribute below, the according release is picked, and the `version` attribute of the resulting derivation is set to this release string,
+  * if it is a majorMinor `"x.y"` prefix of a known released version (as defined above), then the latest `"x.y.z"` known released version is selected (for the ordering given by `versionAtLeast`),
+  * if it is a path or a string representing an absolute path (i.e. starting with `"/"`), the provided path is selected as a source, and the `version` attribute of the resulting derivation is set to `"dev"`,
+  * if it is a string of the form `owner:branch` then it tries to download the `branch` of owner `owner` for a project of the same name using the same vcs, and the `version` attribute of the resulting derivation is set to `"dev"`, additionally if the owner is not provided (i.e. if the `owner:` prefix is missing), it defaults to the original owner of the package (see below),
+  * if it is a string of the form `"#N"`, and the domain is github, then it tries to download the current head of the pull request `#N` from github,
+* `defaultVersion` (optional). Coq libraries may be compatible with some specific versions of Coq only. The `defaultVersion` attribute is used when no `version` is provided (or if `version = null`) to select the version of the library to use by default, depending on the context. This selection will mainly depend on a `coq` version number but also possibly on other packages versions (e.g. `mathcomp`). If its value ends up to be `null`, the package is marked for removal in end-user `coqPackages` attribute set.
+* `release` (optional, defaults to `{}`), lists all the known releases of the library and for each of them provides an attribute set with at least a `sha256` attribute (you may use the shell command `nix-prefetch-url --unpack <archive-url>` to find it, where `<archive-url>` is for example `https://github.com/owner/repo/archive/version.tar.gz`), each attribute set of the list of releases also takes optional overloading arguments for the fetcher as below (i.e.`domain`, `owner`, `repo`, `rev` assuming the default fetcher is used) and optional overrides for the result of the fetcher (i.e. `version` and `src`).
+* `fetcher` (optional, default to a generic fetching mechanism supporting github or gitlab based infrastructures), is a function that takes at least an `owner`, a `repo`, a `rev`, and a `sha256` and returns an attribute set with a `version` and `src`.
+* `repo` (optional, defaults to the value of `pname`),
+* `owner` (optional, defaults to `"coq-community"`).
+* `domain` (optional, defaults to `"github.com"`), domains including the strings `"github"` or `"gitlab"` in their names are automatically supported, otherwise, one must change the `fetcher` argument to support them (cf `pkgs/development/coq-modules/heq/default.nix` for an example),
+* `releaseRev` (optional, defaults to `(v: v)`), provides a default mapping from release names to revision hashes/branch names/tags,
+* `displayVersion` (optional), provides a way to alter the computation of `name` from `pname`, by explaining how to display version numbers,
+* `namePrefix` (optional), provides a way to alter the computation of `name` from `pname`, by explaining which dependencies must occur in `name`,
+* `extraBuildInputs` (optional), by default `buildInputs` just contains `coq`, this allows to add more build inputs,
+* `mlPlugin` (optional, defaults to `false`). Some extensions (plugins) might require OCaml and sometimes other OCaml packages. Standard dependencies can be added by setting the current option to `true`. For a finer grain control, the `coq.ocamlPackages` attribute can be used in `extraBuildInputs` to depend on the same package set Coq was built against.
+* `enableParallelBuilding` (optional, defaults to `true`), since it is activated by default, we provide a way to disable it.
+* `extraInstallFlags` (optional), allows to extend `installFlags` which initializes the variable `COQMF_COQLIB` so as to install in the proper subdirectory. Indeed Coq libraries should be installed in `$(out)/lib/coq/${coq.coq-version}/user-contrib/`. Such directories are automatically added to the `$COQPATH` environment variable by the hook defined in the Coq derivation.
+* `setCOQBIN` (optional, defaults to `true`), by default, the environment variable `$COQBIN` is set to the current Coq's binary, but one can disable this behavior by setting it to `false`,
+* `useMelquiondRemake` (optional, default to `null`) is an attribute set, which, if given, overloads the `preConfigurePhases`, `configureFlags`, `buildPhase`, and `installPhase` attributes of the derivation for a specific use in libraries using `remake` as set up by Guillaume Melquiond for `flocq`, `gappalib`, `interval`, and `coquelicot` (see the corresponding derivation for concrete examples of use of this option). For backward compatibility, the attribute `useMelquiondRemake.logpath` must be set to the logical root of the library (otherwise, one can pass `useMelquiondRemake = {}` to activate this without backward compatibility).
+* `dropAttrs`, `keepAttrs`, `dropDerivationAttrs` are all optional and allow to tune which attribute is added or removed from the final call to `mkDerivation`.
 
 It also takes other standard `mkDerivation` attributes, they are added as such, except for `meta` which extends an automatically computed `meta` (where the `platform` is the same as `coq` and the homepage is automatically computed).
 
diff --git a/doc/languages-frameworks/lua.section.md b/doc/languages-frameworks/lua.section.md
index 248e5971818b..d81949c75f69 100644
--- a/doc/languages-frameworks/lua.section.md
+++ b/doc/languages-frameworks/lua.section.md
@@ -181,7 +181,7 @@ luaposix = buildLuarocksPackage {
   disabled = (luaOlder "5.1") || (luaAtLeast "5.4");
   propagatedBuildInputs = [ bit32 lua std_normalize ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "https://github.com/luaposix/luaposix/";
     description = "Lua bindings for POSIX";
     maintainers = with maintainers; [ vyp lblasc ];
@@ -243,4 +243,3 @@ Following rules should be respected:
 
 * Make sure libraries build for all Lua interpreters.
 * Commit names of Lua libraries should reflect that they are Lua libraries, so write for example `luaPackages.luafilesystem: 1.11 -> 1.12`.
-
diff --git a/doc/languages-frameworks/maven.section.md b/doc/languages-frameworks/maven.section.md
index 5f3979d69fdd..7a863c500bc3 100644
--- a/doc/languages-frameworks/maven.section.md
+++ b/doc/languages-frameworks/maven.section.md
@@ -116,7 +116,7 @@ The first step will be to build the Maven project as a fixed-output derivation i
 > Traditionally the Maven repository is at `~/.m2/repository`. We will override this to be the `$out` directory.
 
 ```nix
-{ stdenv, maven }:
+{ stdenv, lib, maven }:
 stdenv.mkDerivation {
   name = "maven-repository";
   buildInputs = [ maven ];
@@ -139,7 +139,7 @@ stdenv.mkDerivation {
   outputHashAlgo = "sha256";
   outputHashMode = "recursive";
   # replace this with the correct SHA256
-  outputHash = stdenv.lib.fakeSha256;
+  outputHash = lib.fakeSha256;
 }
 ```
 
diff --git a/doc/languages-frameworks/ocaml.section.md b/doc/languages-frameworks/ocaml.section.md
index 1c5a5473a05e..fa85a27e84f0 100644
--- a/doc/languages-frameworks/ocaml.section.md
+++ b/doc/languages-frameworks/ocaml.section.md
@@ -7,7 +7,7 @@ Given that most of the OCaml ecosystem is now built with dune, nixpkgs includes
 Here is a simple package example. It defines an (optional) attribute `minimumOCamlVersion` that will be used to throw a descriptive evaluation error if building with an older OCaml is attempted. It uses the `fetchFromGitHub` fetcher to get its source. It sets the `doCheck` (optional) attribute to `true` which means that tests will be run with `dune runtest -p angstrom` after the build (`dune build -p angstrom`) is complete. It uses `alcotest` as a build input (because it is needed to run the tests) and `bigstringaf` and `result` as propagated build inputs (thus they will also be available to libraries depending on this library). The library will be installed using the `angstrom.install` file that dune generates.
 
 ```nix
-{ stdenv
+{ lib
 , fetchFromGitHub
 , buildDunePackage
 , alcotest
@@ -35,8 +35,8 @@ buildDunePackage rec {
   meta = {
     homepage = "https://github.com/inhabitedtype/angstrom";
     description = "OCaml parser combinators built for speed and memory efficiency";
-    license = stdenv.lib.licenses.bsd3;
-    maintainers = with stdenv.lib.maintainers; [ sternenseemann ];
+    license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [ sternenseemann ];
   };
 }
 ```
@@ -44,7 +44,7 @@ buildDunePackage rec {
 Here is a second example, this time using a source archive generated with `dune-release`. It is a good idea to use this archive when it is available as it will usually contain substituted variables such as a `%%VERSION%%` field. This library does not depend on any other OCaml library and no tests are run after building it.
 
 ```nix
-{ stdenv
+{ lib
 , fetchurl
 , buildDunePackage
 }:
@@ -60,7 +60,7 @@ buildDunePackage rec {
     sha256 = "1msg3vycd3k8qqj61sc23qks541cxpb97vrnrvrhjnqxsqnh6ygq";
   };
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "https://github.com/flowtype/ocaml-wtf8";
     description = "WTF-8 is a superset of UTF-8 that allows unpaired surrogates.";
     license = licenses.mit;
diff --git a/doc/languages-frameworks/perl.section.md b/doc/languages-frameworks/perl.section.md
index 2b31da84553e..309d8ebcc2b3 100644
--- a/doc/languages-frameworks/perl.section.md
+++ b/doc/languages-frameworks/perl.section.md
@@ -110,7 +110,7 @@ ClassC3Componentised = buildPerlPackage rec {
 On Darwin, if a script has too many `-Idir` flags in its first line (its “shebang line”), it will not run. This can be worked around by calling the `shortenPerlShebang` function from the `postInstall` phase:
 
 ```nix
-{ stdenv, buildPerlPackage, fetchurl, shortenPerlShebang }:
+{ stdenv, lib, buildPerlPackage, fetchurl, shortenPerlShebang }:
 
 ImageExifTool = buildPerlPackage {
   pname = "Image-ExifTool";
@@ -121,8 +121,8 @@ ImageExifTool = buildPerlPackage {
     sha256 = "0d8v48y94z8maxkmw1rv7v9m0jg2dc8xbp581njb6yhr7abwqdv3";
   };
 
-  buildInputs = stdenv.lib.optional stdenv.isDarwin shortenPerlShebang;
-  postInstall = stdenv.lib.optional stdenv.isDarwin ''
+  buildInputs = lib.optional stdenv.isDarwin shortenPerlShebang;
+  postInstall = lib.optional stdenv.isDarwin ''
     shortenPerlShebang $out/bin/exiftool
   '';
 };
@@ -151,7 +151,7 @@ $ nix-generate-from-cpan XML::Simple
     propagatedBuildInputs = [ XMLNamespaceSupport XMLSAX XMLSAXExpat ];
     meta = {
       description = "An API for simple XML files";
-      license = with stdenv.lib.licenses; [ artistic1 gpl1Plus ];
+      license = with lib.licenses; [ artistic1 gpl1Plus ];
     };
   };
 ```
diff --git a/doc/languages-frameworks/r.section.md b/doc/languages-frameworks/r.section.md
index d7154adc55bc..32a39ade2796 100644
--- a/doc/languages-frameworks/r.section.md
+++ b/doc/languages-frameworks/r.section.md
@@ -105,6 +105,12 @@ mv cran-packages.nix.new cran-packages.nix
 
 Rscript generate-r-packages.R bioc  > bioc-packages.nix.new
 mv bioc-packages.nix.new bioc-packages.nix
+
+Rscript generate-r-packages.R bioc-annotation > bioc-annotation-packages.nix.new
+mv bioc-annotation-packages.nix.new bioc-annotation-packages.nix
+
+Rscript generate-r-packages.R bioc-experiment > bioc-experiment-packages.nix.new
+mv bioc-experiment-packages.nix.new bioc-experiment-packages.nix
 ```
 
 `generate-r-packages.R <repo>` reads  `<repo>-packages.nix`, therefor the renaming.
diff --git a/doc/languages-frameworks/rust.section.md b/doc/languages-frameworks/rust.section.md
index 231cbe900e7d..092e84461b81 100644
--- a/doc/languages-frameworks/rust.section.md
+++ b/doc/languages-frameworks/rust.section.md
@@ -32,7 +32,7 @@ rustPlatform.buildRustPackage rec {
 
   cargoSha256 = "03wf9r2csi6jpa7v5sw5lpxkrk4wfzwmzx7k3991q3bdjzcwnnwp";
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     description = "A fast line-oriented regex search tool, similar to ag and ack";
     homepage = "https://github.com/BurntSushi/ripgrep";
     license = licenses.unlicense;
@@ -58,13 +58,13 @@ then be taken from the failed build. A fake hash can be used for
 `cargoSha256` as follows:
 
 ```
-  cargoSha256 = stdenv.lib.fakeSha256;
+  cargoSha256 = lib.fakeSha256;
 ```
 
 For `cargoHash` you can use:
 
 ```
-  cargoHash = stdenv.lib.fakeHash;
+  cargoHash = lib.fakeHash;
 ```
 
 Per the instructions in the [Cargo Book](https://doc.rust-lang.org/cargo/guide/cargo-toml-vs-cargo-lock.html)