rstudio: 2025.05.0+496 -> 2025.05.1+513, unlock jdk version, do minor cleanup, move to pkgs/by-name

[TomaSajt]

Since the version bump was very trivial, I also included some other changes I've wanted to make to the package.

Things done

• Built on platform(s)
  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin
• For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)
  • sandbox = relaxed
  • sandbox = true
• Tested, as applicable:
  • NixOS test(s) (look inside nixos/tests)
  • and/or package tests
  • or, for functions and "core" functionality, tests in lib/tests or pkgs/test
  • made sure NixOS tests are linked to the relevant packages
• Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
• Tested basic functionality of all binary files (usually in ./result/bin/)
• Nixpkgs 25.11 Release Notes (or backporting 24.11 and 25.05 Nixpkgs Release notes)
  • (Package updates) Added a release notes entry if the change is major or breaking
• NixOS 25.11 Release Notes (or backporting 24.11 and 25.05 NixOS Release notes)
  • (Module updates) Added a release notes entry if the change is significant
  • (Module addition) Added a release notes entry if adding a new NixOS module
• Fits CONTRIBUTING.md.

---

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[b-rodrigues]

Failing on aarch64-darwin, because there seems to be something wrong with libfaketime on this platform:

nix-shell -I nixpkgs=. -p R rstudio

error: builder for '/nix/store/jnh1d6g68bw3sd186z45p07d81691wjl-libfaketime-0.9.11.drv' failed with exit code 2;
       last 25 log lines:
       > out=16384 (skipping test, install gdate) - ok
       > out=32768 (skipping test, install gdate) - ok
       > out=65536 (skipping test, install gdate) - ok
       > out=131072 (skipping test, install gdate) - ok
       > out=262144 (skipping test, install gdate) - ok
       > out=524288 (skipping test, install gdate) - ok
       > out=1048576 (skipping test, install gdate) - ok
       > out=2097152 (skipping test, install gdate) - ok
       > out=4194304 (skipping test, install gdate) - ok
       > out=8388608 (skipping test, install gdate) - ok
       > out=16777216 (skipping test, install gdate) - ok
       > out=33554432 (skipping test, install gdate) - ok
       > out=67108864 (skipping test, install gdate) - ok
       > out=134217728 (skipping test, install gdate) - ok
       > out=268435456 (skipping test, install gdate) - ok
       > out=536870912 (skipping test, install gdate) - ok
       > out=1073741824 (skipping test, install gdate) - ok
       > # functests/test_walkone.sh summary: 31 succeeded, 0 failed
       > # End functests/test_walkone.sh - OK
       >
       > # Test Suites summary: 3 succeeded, 1 failed
       > # End Test Suites - BAD
       > make[1]: *** [Makefile.OSX:22: functest] Error 1
       > make[1] : on quitte le répertoire « /private/tmp/nix-build-libfaketime-0.9.11.drv-0/source/test »
       > make: *** [Makefile:12: test] Error 2
       For full logs, run:
         nix log /nix/store/jnh1d6g68bw3sd186z45p07d81691wjl-libfaketime-0.9.11.drv
error: 1 dependencies of derivation '/nix/store/apw2yagnnfvj2p3k692bd4mdkn0wa1ds-texlive-2024-env.drv' failed to build
error: 1 dependencies of derivation '/nix/store/9j0zad0swgkjs3h989j16vnyc3yjhw9r-R-4.5.0.drv' failed to build
error (ignored): error: cannot unlink "/private/tmp/nix-build-rstudio-2025.05.1+513-npm-deps.drv-1/source/src/cpp/session/modules": Directory not empty
error: build of '/nix/store/9j0zad0swgkjs3h989j16vnyc3yjhw9r-R-4.5.0.drv', '/nix/store/yqapzgl1hm7r61asi40njr33ab749fh6-RStudio-2025.05.1+513.drv' failed

[b-rodrigues]

maybe rebase on master, seems to be fixed there with fe9d231

[b-rodrigues]

builds and runs on both aarch64-darwin and x86-linux!