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quarto: allow overriding extra R and Python packages #211941

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merged 1 commit into from
Mar 29, 2023

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minijackson
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Description of changes

Tested by running a .qmd file needing ggplot2 and a .qmd file needing numpy and matplotlib.

Pinging @MrTarantoga

Things done
  • Built on platform(s)
    • x86_64-linux
    • aarch64-linux
    • x86_64-darwin
    • aarch64-darwin
  • For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
  • Tested, as applicable:
  • 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/)
  • 23.05 Release Notes (or backporting 22.11 Release notes)
    • (Package updates) Added a release notes entry if the change is major or breaking
    • (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
    • (Release notes changes) Ran nixos/doc/manual/md-to-db.sh to update generated release notes
  • Fits CONTRIBUTING.md.

@ofborg ofborg bot added 10.rebuild-darwin: 0 This PR does not cause any packages to rebuild 10.rebuild-linux: 0 This PR does not cause any packages to rebuild labels Jan 21, 2023
@MrTarantoga
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MrTarantoga commented Jan 22, 2023

Do you have an idea why the command nixpkgs-review pr 211941 seems to need 8 GB of memory?

[nix-shell:~/.cache/nixpkgs-review/pr-211941-2]$ quarto check all

[✓] Checking Quarto installation......OK
      Version: 1.2.313
      Path: /nix/store/kavcxwa1pbnsd3f1hi0nvljja825m1hm-quarto-1.2.313/bin

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
      Version: 3.10.9
      Path: /nix/store/56xf1f5vnw6mfc8b57hib23dwsifj6z0-python3-3.10.9-env/bin/python3.10
      Jupyter: 5.1.1
      Kernels: python3

(|) Checking Jupyter engine render....[IPKernelApp] WARNING | debugpy_stream undefined, debugging will not be enabled
[✓] Checking Jupyter engine render....OK

[✓] Checking R installation...........OK
      Version: 4.2.2
      Path: /nix/store/q1g6ywsgzllhmm65cqvdsidbmiaawg3z-R-4.2.2/lib/R
      LibPaths:
        - /home/goetz/R/x86_64-pc-linux-gnu-library/4.2
        - /nix/store/fn7p8nn7cvvqy386rfd4s5nad32i9jpb-r-boot-1.3-28.1/library
        - /nix/store/b8gfgrjxmm8847pqc5g7y8yff0afv31n-r-class-7.3-20/library
        - /nix/store/3p3r1z2pfabk4jdjp0zzzhhzyara4l52-r-MASS-7.3-58.1/library
        - /nix/store/b1xviywm3h12gq26jz8z6hg9rq5kccrf-r-cluster-2.1.4/library
        - /nix/store/anx23s3s489wafd1jhn96n1ywk0sl3fj-r-codetools-0.2-18/library
        - /nix/store/asq8jva5nff8phjxszqjy119fgkcfi50-r-foreign-0.8-84/library
        - /nix/store/8q9jgr9s1ypfkhblsxlf9g3fmqv9kg2h-r-KernSmooth-2.23-20/library
        - /nix/store/7n0zddl78qz5961vc55c0bv79qg90mfh-r-lattice-0.20-45/library
        - /nix/store/k8qbf1j5hj2c2s45nw6fxjvyi0vqypi5-r-Matrix-1.5-3/library
        - /nix/store/hl1sanysph60mma0j9ylx2qx22l2p4jd-r-mgcv-1.8-41/library
        - /nix/store/5fad64x2q4qfx5mxmn58qbwiasm16j4v-r-nlme-3.1-160/library
        - /nix/store/q7q90dvhpfsqcq4zjkvlyjarh5w7yma9-r-nnet-7.3-18/library
        - /nix/store/gasann6ma688s3p9g44988rv4y3b1xzq-r-rpart-4.1.19/library
        - /nix/store/bc4dfz665n03qfjw0gzjnhbqzgg6xbgl-r-spatial-7.3-15/library
        - /nix/store/l76m7dm5yq2g05lx35r4vx4x5ap89r5l-r-survival-3.4-0/library
        - /nix/store/7cry2pr8xa7dywxllmwyil6zz0m11igz-r-rmarkdown-2.18/library
        - /nix/store/mcis5lb03ziai0q7bs4zbzikm4l2kf2h-r-bslib-0.4.1/library
        - /nix/store/xq2xbxpi3rk6cpjh65krhys0s88z11hr-r-cachem-1.0.6/library
        - /nix/store/av87a4ma2gnp4c91yg19rsqr1vw8lp68-r-fastmap-1.1.0/library
        - /nix/store/p46n3is8fhbx31xki6fv08f9fhy4qavk-r-rlang-1.0.6/library
        - /nix/store/skmbarf6drnk5jf2cw1g2banx37kdyb5-r-htmltools-0.5.4/library
        - /nix/store/k3g8q3zkzhd5h8kj5ganygis74p3p01j-r-base64enc-0.1-3/library
        - /nix/store/kxgnflindrvraxq2db0v9vdiv656x0j0-r-digest-0.6.31/library
        - /nix/store/v81kghbnlwdr4rzcb4ja4y62wbafzplm-r-ellipsis-0.3.2/library
        - /nix/store/x1bcwbvprm2qgsfdavywq461q021gcih-r-jquerylib-0.1.4/library
        - /nix/store/rfiks020li4r59pqkajpzvifglzmchs1-r-jsonlite-1.8.4/library
        - /nix/store/bn12dsj955i9s07303yam095frrywjnq-r-memoise-2.0.1/library
        - /nix/store/hfqwq40s72dlfql7fyj7gs6msgcrp1xs-r-sass-0.4.4/library
        - /nix/store/6ajglc66adx574h1c3idwqwzimkdygal-r-fs-1.5.2/library
        - /nix/store/s5v785n59zy2nj347bya4an74rkk14a9-r-R6-2.5.1/library
        - /nix/store/zflfbp8jmjvx9rilydsdxma254qw5ks0-r-rappdirs-0.3.3/library
        - /nix/store/1656953gg3yi3d78xy3vfh5wzmqhhy21-r-evaluate-0.18/library
        - /nix/store/v6ivbf1j7ffs3r457h7bsggzvxjn9rnq-r-knitr-1.41/library
        - /nix/store/1x41kws8cqrpjr3nssbcr0sdxxsvm09n-r-highr-0.9/library
        - /nix/store/gsvhax7ckczn1gj08rdqxqh65gv2b0sq-r-xfun-0.35/library
        - /nix/store/663h6jbl98gl1rmk5rz8r8q90ibfmr8w-r-stringr-1.5.0/library
        - /nix/store/yfc8nj2i02swdrx07ql38aicv9b0641f-r-cli-3.4.1/library
        - /nix/store/m3mbljfpkiymjyws7vak7k42ws1d5rff-r-glue-1.6.2/library
        - /nix/store/65xgyklmlm9xccqyrj5a4hmmcasybr9l-r-lifecycle-1.0.3/library
        - /nix/store/lqvvr99rmcnp3kbfh6yiysxy6n8nn00g-r-magrittr-2.0.3/library
        - /nix/store/r9xa8p6n3wk9a7iqxz3fs50v2p30yafx-r-stringi-1.7.8/library
        - /nix/store/gh9cfqr4d46j04c0xc4agg3vbv6r523c-r-vctrs-0.5.1/library
        - /nix/store/h8d9cc97jy6g1pvzc4dw9prrd0x5pyrq-r-yaml-2.3.6/library
        - /nix/store/irfspz9spaifg8rnm8awqbss5lc7bgbk-r-tinytex-0.42/library
        - /nix/store/q1g6ywsgzllhmm65cqvdsidbmiaawg3z-R-4.2.2/lib/R/library
      rmarkdown: 2.18

[✓] Checking Knitr engine render......OK


@MrTarantoga
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Also quarto is not longer a part of PATH with your submission.

@minijackson
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That's very weird, if not overridden, it shouldn't change anything, as it's only concatenating an empty array.

Also quarto is not longer a part of PATH with your submission.

What do you mean by that?

@MrTarantoga
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I my case, I add the package to the local scope and quarto is able to have access to them. Why to you want to have an override option?

@MrTarantoga
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MrTarantoga commented Jan 22, 2023

That's very weird, if not overridden, it shouldn't change anything, as it's only concatenating an empty array.

Also quarto is not longer a part of PATH with your submission.

What do you mean by that?

As I said: I'm not able to run quarto inside nixpkgs-review pr 211941. It is not part of the path. Also your change need a huge amount of memory during the nixpkgs-review command. Also I do not see the needs for the change, because quarto is part of python and R, so it should be added like other packages in one scope.

@minijackson
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If I want to execute render the first R example from the documentation, I need to have the ggplot2 package available to R, which is not available by default.

If I install in my environment an R package with ggplot2 installed, quarto won't use that, since the QUARTO_R set in the wrapper takes priority. I think it is the same with Python

@MrTarantoga
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Thats how the command is processed:

➜  nixpkgs git:(master) ✗ nixpkgs-review pr 211941
$ git -c fetch.prune=false fetch --no-tags --force https://github.com/NixOS/nixpkgs master:refs/nixpkgs-review/0 pull/211941/head:refs/nixpkgs-review/1
remote: Enumerating objects: 776, done.
remote: Counting objects: 100% (632/632), done.
remote: Compressing objects: 100% (200/200), done.
remote: Total 776 (delta 507), reused 503 (delta 431), pack-reused 144
Empfange Objekte: 100% (776/776), 771.39 KiB | 5.76 MiB/s, fertig.
Löse Unterschiede auf: 100% (510/510), abgeschlossen mit 206 lokalen Objekten.
Von https://github.com/NixOS/nixpkgs
   25eeb4785c80..ad8d5cf731e7  master                -> refs/nixpkgs-review/0
   a3b7b770cec9..02641062d16b  refs/pull/211941/head -> refs/nixpkgs-review/1
$ git worktree add /home/goetz/.cache/nixpkgs-review/pr-211941/nixpkgs ad8d5cf731e7d0b2d0cca148fa01b805c4f5d3a3
Bereite Arbeitsverzeichnis vor (losgelöster HEAD ad8d5cf731e7)
Aktualisiere Dateien: 100% (33335/33335), fertig.
HEAD ist jetzt bei ad8d5cf731e7 nixos/manual: clarify mk{Enable,Package}Option MD usage
$ nix-env --option system x86_64-linux -f /home/goetz/.cache/nixpkgs-review/pr-211941/nixpkgs -qaP --xml --out-path --show-trace --no-allow-import-from-derivation
$ git merge --no-commit --no-ff 02641062d16b84b74c708fb99041b0421253759f
Automatischer Merge abgeschlossen; halte, wie gewünscht, vor dem Commit an
$ nix-env --option system x86_64-linux -f /home/goetz/.cache/nixpkgs-review/pr-211941/nixpkgs -qaP --xml --out-path --show-trace --no-allow-import-from-derivation --meta
derivation 'systemd-252.4' has invalid meta attribute 'badPlatforms'
derivation 'systemd-minimal-252.4' has invalid meta attribute 'badPlatforms'
derivation 'systemd-stage-1-252.4' has invalid meta attribute 'badPlatforms'
derivation 'systemd-stage-1-network-252.4' has invalid meta attribute 'badPlatforms'
Nothing to be built.

Link to currently reviewing PR:
https://github.com/NixOS/nixpkgs/pull/211941

$ /nix/store/pfaw5zpqfang1w1ms61lw8q60sg7fzxy-nix-2.12.0/bin/nix-shell /home/goetz/.cache/nixpkgs-review/pr-211941/shell.nix
these 37 paths will be fetched (66.61 MiB download, 306.07 MiB unpacked):
  /nix/store/04c0b1rmi9r6k9sl69a4gw3mhp3b5q2n-zlib-1.2.13
  /nix/store/117vi3xd5nm0ai52clm4w6ni9bdzixnm-glibc-2.35-224-bin
  /nix/store/178vvank67pg2ckr5ic5gmdkm3ri72f3-binutils-2.39
  /nix/store/2dpp3axxcm5w276xb4hmqgxf5whw8nrm-gnumake-4.4
  /nix/store/38db4p333ibll7r1v151yc5f6ms1fr00-bash-interactive-5.2-p15
  /nix/store/49zl26cmymymzzh1xqahd6cp1g10l141-glibc-2.35-224-dev
  /nix/store/4cjf65g6bacv9f279j5mv04iapzjx6m6-gnused-4.9
  /nix/store/7197cs5xf76z9r33nkm3xhkk800n0nr1-attr-2.5.1
  /nix/store/7nplxyjihfwhaw0cmrxwlfrq4xkbbz83-patch-2.7.6
  /nix/store/7xs3mva2z3z4hf48mh6d5alcin52qbm9-binutils-wrapper-2.39
  /nix/store/86gmg0dan51jsm3p2n2fnac1s8mq94i7-bzip2-1.0.8
  /nix/store/917bxk94dsm12bid472x3jpn4p512p7y-gmp-with-cxx-stage4-6.2.1
  /nix/store/96xa21yfzb43447lhmc76zg2628kvak4-readline-8.2p1
  /nix/store/b73ppzd6pcq3a8znjqjs5ivfdcxgz0rb-diffutils-3.8
  /nix/store/bw3mxk76xp3i5m53g9i67fagnwbhyc1k-xz-5.4.0
  /nix/store/chilfhdcsnmwjl7igrw26j1lrc0zar35-stdenv-linux
  /nix/store/g4qrlj5kr7iwcr81jsm1p55vk0z9rh0z-gnutar-1.34
  /nix/store/hcy4vanjxs86cynwn98hcagqyj3ihns4-gzip-1.12
  /nix/store/hm4l5k50h19k9285rp2p47a1z5ryyk9x-ed-1.18
  /nix/store/hr2vffa1w2ylqksrhg72p26ys8z930lh-expand-response-params
  /nix/store/iiq295j1z4q1sxmdbrl2j8ma3l5ns4wr-gcc-wrapper-11.3.0
  /nix/store/lx2yaqgvxhcwj65w65q539c2rgxh2bb7-pcre-8.45
  /nix/store/mhq6vmzb6w1q5kicv91x9ywqb57fb2x2-patchelf-0.15.0
  /nix/store/mlvjrnjdjj7p2dnsayy848yk7djgd5xk-findutils-4.9.0
  /nix/store/p3zp8ymx8rzc3q25jskg4hzz0kr5lyi1-xz-5.4.0-bin
  /nix/store/phwcwazlcabg1v6wwrdv6gr5mh2r3ld8-bzip2-1.0.8-bin
  /nix/store/pj1hnyxhcsw1krmhnbb9rjvqssbzliw8-bash-5.2-p15
  /nix/store/qn0xz86az3rcqfpfrcxhjiyp8s169792-file-5.43
  /nix/store/qrqwd1ji31vmas9gax819j11w5ickgz1-gnugrep-3.7
  /nix/store/r1lybmy0jzjsfcmbg24h26aknbgpfvad-coreutils-9.1
  /nix/store/sq78g74zs4sj7n1j5709g9c2pmffx1y8-gcc-11.3.0-lib
  /nix/store/v94mvmxwak89z8y1ijv1nhzp4j3h9jxm-ncurses-6.3-p20220507
  /nix/store/xm9x9kylgy1fq8xdw3z7irkrg57zh1h4-acl-2.3.1
  /nix/store/ycw1sij5z1kjcxdclz7gqlnf9hdxchlb-gawk-5.2.1
  /nix/store/yzjgl0h6a3qh1mby405428f16xww37h0-glibc-2.35-224
  /nix/store/z1yw9cw97bcdfmxz5wk7j1bycw42r1mw-gcc-11.3.0
  /nix/store/zzwqcifb2hgm1qii6ixh86cjryzlf5zh-linux-headers-6.1
copying path '/nix/store/yzjgl0h6a3qh1mby405428f16xww37h0-glibc-2.35-224' from 'https://cache.nixos.org'...
copying path '/nix/store/zzwqcifb2hgm1qii6ixh86cjryzlf5zh-linux-headers-6.1' from 'https://cache.nixos.org'...
copying path '/nix/store/7197cs5xf76z9r33nkm3xhkk800n0nr1-attr-2.5.1' from 'https://cache.nixos.org'...
copying path '/nix/store/pj1hnyxhcsw1krmhnbb9rjvqssbzliw8-bash-5.2-p15' from 'https://cache.nixos.org'...
copying path '/nix/store/86gmg0dan51jsm3p2n2fnac1s8mq94i7-bzip2-1.0.8' from 'https://cache.nixos.org'...
copying path '/nix/store/hm4l5k50h19k9285rp2p47a1z5ryyk9x-ed-1.18' from 'https://cache.nixos.org'...
copying path '/nix/store/hr2vffa1w2ylqksrhg72p26ys8z930lh-expand-response-params' from 'https://cache.nixos.org'...
copying path '/nix/store/ycw1sij5z1kjcxdclz7gqlnf9hdxchlb-gawk-5.2.1' from 'https://cache.nixos.org'...
copying path '/nix/store/sq78g74zs4sj7n1j5709g9c2pmffx1y8-gcc-11.3.0-lib' from 'https://cache.nixos.org'...
copying path '/nix/store/117vi3xd5nm0ai52clm4w6ni9bdzixnm-glibc-2.35-224-bin' from 'https://cache.nixos.org'...
copying path '/nix/store/2dpp3axxcm5w276xb4hmqgxf5whw8nrm-gnumake-4.4' from 'https://cache.nixos.org'...
copying path '/nix/store/xm9x9kylgy1fq8xdw3z7irkrg57zh1h4-acl-2.3.1' from 'https://cache.nixos.org'...
copying path '/nix/store/phwcwazlcabg1v6wwrdv6gr5mh2r3ld8-bzip2-1.0.8-bin' from 'https://cache.nixos.org'...
copying path '/nix/store/4cjf65g6bacv9f279j5mv04iapzjx6m6-gnused-4.9' from 'https://cache.nixos.org'...
copying path '/nix/store/hcy4vanjxs86cynwn98hcagqyj3ihns4-gzip-1.12' from 'https://cache.nixos.org'...
copying path '/nix/store/v94mvmxwak89z8y1ijv1nhzp4j3h9jxm-ncurses-6.3-p20220507' from 'https://cache.nixos.org'...
copying path '/nix/store/7nplxyjihfwhaw0cmrxwlfrq4xkbbz83-patch-2.7.6' from 'https://cache.nixos.org'...
copying path '/nix/store/g4qrlj5kr7iwcr81jsm1p55vk0z9rh0z-gnutar-1.34' from 'https://cache.nixos.org'...
copying path '/nix/store/lx2yaqgvxhcwj65w65q539c2rgxh2bb7-pcre-8.45' from 'https://cache.nixos.org'...
copying path '/nix/store/49zl26cmymymzzh1xqahd6cp1g10l141-glibc-2.35-224-dev' from 'https://cache.nixos.org'...
copying path '/nix/store/bw3mxk76xp3i5m53g9i67fagnwbhyc1k-xz-5.4.0' from 'https://cache.nixos.org'...
copying path '/nix/store/04c0b1rmi9r6k9sl69a4gw3mhp3b5q2n-zlib-1.2.13' from 'https://cache.nixos.org'...
copying path '/nix/store/qn0xz86az3rcqfpfrcxhjiyp8s169792-file-5.43' from 'https://cache.nixos.org'...
copying path '/nix/store/qrqwd1ji31vmas9gax819j11w5ickgz1-gnugrep-3.7' from 'https://cache.nixos.org'...
copying path '/nix/store/p3zp8ymx8rzc3q25jskg4hzz0kr5lyi1-xz-5.4.0-bin' from 'https://cache.nixos.org'...
copying path '/nix/store/178vvank67pg2ckr5ic5gmdkm3ri72f3-binutils-2.39' from 'https://cache.nixos.org'...
copying path '/nix/store/917bxk94dsm12bid472x3jpn4p512p7y-gmp-with-cxx-stage4-6.2.1' from 'https://cache.nixos.org'...
copying path '/nix/store/mhq6vmzb6w1q5kicv91x9ywqb57fb2x2-patchelf-0.15.0' from 'https://cache.nixos.org'...
copying path '/nix/store/96xa21yfzb43447lhmc76zg2628kvak4-readline-8.2p1' from 'https://cache.nixos.org'...
copying path '/nix/store/z1yw9cw97bcdfmxz5wk7j1bycw42r1mw-gcc-11.3.0' from 'https://cache.nixos.org'...
copying path '/nix/store/r1lybmy0jzjsfcmbg24h26aknbgpfvad-coreutils-9.1' from 'https://cache.nixos.org'...
copying path '/nix/store/38db4p333ibll7r1v151yc5f6ms1fr00-bash-interactive-5.2-p15' from 'https://cache.nixos.org'...
copying path '/nix/store/b73ppzd6pcq3a8znjqjs5ivfdcxgz0rb-diffutils-3.8' from 'https://cache.nixos.org'...
copying path '/nix/store/mlvjrnjdjj7p2dnsayy848yk7djgd5xk-findutils-4.9.0' from 'https://cache.nixos.org'...
copying path '/nix/store/7xs3mva2z3z4hf48mh6d5alcin52qbm9-binutils-wrapper-2.39' from 'https://cache.nixos.org'...
copying path '/nix/store/iiq295j1z4q1sxmdbrl2j8ma3l5ns4wr-gcc-wrapper-11.3.0' from 'https://cache.nixos.org'...
copying path '/nix/store/chilfhdcsnmwjl7igrw26j1lrc0zar35-stdenv-linux' from 'https://cache.nixos.org'...

[nix-shell:~/.cache/nixpkgs-review/pr-211941]$ quarto check all
The program 'quarto' is not in your PATH. You can make it available in an
ephemeral shell by typing:
  nix-shell -p quarto

[nix-shell:~/.cache/nixpkgs-review/pr-211941]$ exit
exit
$ git worktree prune
➜  nixpkgs git:(master) ✗ nixpkgs-review pr 211941
$ git -c fetch.prune=false fetch --no-tags --force https://github.com/NixOS/nixpkgs master:refs/nixpkgs-review/0 pull/211941/head:refs/nixpkgs-review/1
remote: Enumerating objects: 69, done.
remote: Counting objects: 100% (62/62), done.
remote: Compressing objects: 100% (29/29), done.
remote: Total 31 (delta 22), reused 6 (delta 2), pack-reused 0
Entpacke Objekte: 100% (31/31), 6.22 KiB | 132.00 KiB/s, fertig.
Von https://github.com/NixOS/nixpkgs
   ad8d5cf731e7..3f3524a4473d  master     -> refs/nixpkgs-review/0
$ git worktree add /home/goetz/.cache/nixpkgs-review/pr-211941-1/nixpkgs 3f3524a4473d9f0502a45d8bb10e59ef587e2230
Bereite Arbeitsverzeichnis vor (losgelöster HEAD 3f3524a4473d)
Aktualisiere Dateien: 100% (33336/33336), fertig.
HEAD ist jetzt bei 3f3524a4473d nixos/autosuspend: init at version 4.3.0
$ nix-env --option system x86_64-linux -f /home/goetz/.cache/nixpkgs-review/pr-211941-1/nixpkgs -qaP --xml --out-path --show-trace --no-allow-import-from-derivation
$ git merge --no-commit --no-ff 02641062d16b84b74c708fb99041b0421253759f
Automatischer Merge abgeschlossen; halte, wie gewünscht, vor dem Commit an
$ nix-env --option system x86_64-linux -f /home/goetz/.cache/nixpkgs-review/pr-211941-1/nixpkgs -qaP --xml --out-path --show-trace --no-allow-import-from-derivation --meta
derivation 'systemd-252.4' has invalid meta attribute 'badPlatforms'
derivation 'systemd-minimal-252.4' has invalid meta attribute 'badPlatforms'
derivation 'systemd-stage-1-252.4' has invalid meta attribute 'badPlatforms'
derivation 'systemd-stage-1-network-252.4' has invalid meta attribute 'badPlatforms'
Nothing to be built.

Link to currently reviewing PR:
https://github.com/NixOS/nixpkgs/pull/211941

$ /nix/store/pfaw5zpqfang1w1ms61lw8q60sg7fzxy-nix-2.12.0/bin/nix-shell /home/goetz/.cache/nixpkgs-review/pr-211941-1/shell.nix

[nix-shell:~/.cache/nixpkgs-review/pr-211941-1]$ quarto check all
The program 'quarto' is not in your PATH. You can make it available in an
ephemeral shell by typ

@minijackson
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nixpkgs-review reports:

Nothing to be built.

This is because this PR doesn't modify the quarto package if the package is not overridden, which is why nixpkgs-review doesn't try to build quarto: the hash is the same as on master. This is also why quarto is not part of your environment.

@MrTarantoga
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If I want to execute render the first R example from the documentation, I need to have the ggplot2 package available to R, which is not available by default.

If I install in my environment an R package with ggplot2 installed, quarto won't use that, since the QUARTO_R set in the wrapper takes priority. I think it is the same with Python

I see, that would it make less hacky to add additional packages. Well know I see the usage, thank you.

@MrTarantoga
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nixpkgs-review reports:

Nothing to be built.

This is because this PR doesn't modify the quarto package if the package is not overridden, which is why nixpkgs-review doesn't try to build quarto: the hash is the same as on master. This is also why quarto is not part of your environment.

So you mean, I have to install quarto first and then review the changes?

@MrTarantoga
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Yepp, that's it. Now it works, a bit strange behavior of the review function, but anyway i have it for the future.

Thank you, for the suggestion!

@SuperSandro2000 SuperSandro2000 added the 12.approvals: 1 This PR was reviewed and approved by one reputable person label Jan 23, 2023
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This pull request has been mentioned on NixOS Discourse. There might be relevant details there:

https://discourse.nixos.org/t/prs-already-reviewed/2617/884

@Kranzes Kranzes merged commit bede001 into NixOS:master Mar 29, 2023
@minijackson minijackson deleted the quarto-override-deps branch May 29, 2023 21:28
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10.rebuild-darwin: 0 This PR does not cause any packages to rebuild 10.rebuild-linux: 0 This PR does not cause any packages to rebuild 12.approvals: 1 This PR was reviewed and approved by one reputable person
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5 participants