Error from nix-build

[simonreif]

I want to set up different nix environments to see how outputs change over time. For one time periode it worked well, now I tried if for another time and I get the following error message from nix-build:

@nix { "action": "setPhase", "phase": "unpackPhase" }
Running phase: unpackPhase
unpacking source archive /nix/store/hz2c03addb61x2gzxnzwc7wdaf6z6fwr-bitops_1.0-7.tar.gz
source root is bitops
setting SOURCE_DATE_EPOCH to timestamp 1619264408 of file bitops/MD5
@nix { "action": "setPhase", "phase": "patchPhase" }
Running phase: patchPhase
@nix { "action": "setPhase", "phase": "updateAutotoolsGnuConfigScriptsPhase" }
Running phase: updateAutotoolsGnuConfigScriptsPhase
@nix { "action": "setPhase", "phase": "configurePhase" }
Running phase: configurePhase
@nix { "action": "setPhase", "phase": "buildPhase" }
Running phase: buildPhase
@nix { "action": "setPhase", "phase": "checkPhase" }
Running phase: checkPhase
@nix { "action": "setPhase", "phase": "installPhase" }
Running phase: installPhase
dyld[84462]: Library not loaded: /nix/store/gslza0pkc7hwjljhw34n3dl21awva7jc-gfortran-13.3.0-lib/lib/libgfortran.5.dylib
  Referenced from: <D95ED927-7832-3C3D-97A2-5DC6BAA63E8D> /nix/store/xw9736275vnvnjv7d8wnmg0cjs5gmznv-R-4.4.1/lib/R/lib/libR.dylib
  Reason: tried: '/nix/store/gslza0pkc7hwjljhw34n3dl21awva7jc-gfortran-13.3.0-lib/lib/libgfortran.5.dylib' (duplicate LC_RPATH '/nix/store/gslza0pkc7hwjljhw34n3dl21awva7jc-gfortran-13.3.0-lib/lib'), '/System/Volumes/Preboot/Cryptexes/OS/nix/store/gslza0pkc7hwjljhw34n3dl21awva7jc-gfortran-13.3.0-lib/lib/libgfortran.5.dylib' (no such file), '/nix/store/gslza0pkc7hwjljhw34n3dl21awva7jc-gfortran-13.3.0-lib/lib/libgfortran.5.dylib' (duplicate LC_RPATH '/nix/store/gslza0pkc7hwjljhw34n3dl21awva7jc-gfortran-13.3.0-lib/lib'), '/nix/store/xw9736275vnvnjv7d8wnmg0cjs5gmznv-R-4.4.1/lib/R/lib/libgfortran.5.dylib' (no such file), '/nix/store/rbbf1i5q3ip0hm7m9mwna53wn4byg8gv-zulu-ca-jdk-21.0.2/zulu-21.jdk/Contents/Home/lib/server/libgfortran.5.dylib' (no such file), '/nix/store/xw9736275vnvnjv7d8wnmg0cjs5gmznv-R-4.4.1/lib/R/lib/libgfortran.5.dylib' (no such file), '/nix/store/rbbf1i5q3ip0hm7m9mwna53wn4byg8gv-zulu-ca-jdk-21.0.2/zulu-21.jdk/Contents/Home/lib/server/libgfortran.5.dylib' (no such file)   /nix/store/xw9736275vnvnjv7d8wnmg0cjs5gmznv-R-4.4.1/lib/R/bin/INSTALL: line 34: 84460 Done                    echo 'tools:::.install_packages()'
     84462 Abort trap: 6           | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}  

Below is my rix setup file. I am lost with respect to

• how to solve this
• what additional information you need to know what went wrong
• whether this is a problem from the specific version I try to get or from repeatedly trying different versions.

Any help is appreciated :)

library(rix)
path_default_nix <- getwd()
rix(
  date = "2024-06-14",
  r_pkgs = c(
    "tidyverse",
    "broom",
    "ggpubr",
    "modelsummary",
    "gtsummary",
    "gt",
    "estimatr",
    "sf",
    "quarto",
    "showtext",
    "here",
  "igraph",
  "plyr",
  "data.table",
  "tidyr",
  "cld2",
  "lubridate",
  "fixest",
  "Synth",
  "lmtest",
  "readxl",
  "jsonlite"
  ),
  system_pkgs = c("quarto", "git", "gnumake"),
  tex_pkgs = c(
    "setspace",
    "lipsum",
    "txfonts",
    "csquotes",
    "geometry",
    "float",
    "multirow",
    "colortbl",
    "booktabs",
    "threeparttable",
    "caption",
    "xcolor",
    "fontspec",
    "amsfonts",
    "titling",
    "biblatex",
    "collection-bibtexextra",
    "hyperref",
    "placeins",
    "pdflscape",
    "framed"
  ),
  git_pkgs = NULL,
  project_path = path_default_nix,
  overwrite = TRUE,
  print = FALSE
)

[b-rodrigues]

Are you on apple silicon?

[simonreif]

Are you on apple silicon?

Yes

[b-rodrigues]

I did some digging yesterday evening, and this is most likely a macOS-specific toolchain issue rather than a problem with rix itself. R is trying to load a specific gfortran runtime library that no longer matches your current macOS/Xcode environment. Older nixpkgs snapshots often continue to work on Linux but can break on macOS after system updates because Darwin depends on Apple’s SDK and dynamic loader behavior. I would recommend either trying a newer snapshot date or running historical environments on Linux for maximum reproducibility.

I’ll update this section of the documentation to set expectations more clearly:
https://docs.ropensci.org/rix/articles/setting-up-macos.html#more-macos-specificities

Unfortunately, this is outside the control of the Nix package maintainers. Linux builds tend to remain reproducible long term because nixpkgs controls the entire toolchain and libc stack. The environment you’re trying to build for example, builds and runs successfully on a current Linux installation. On macOS, nixpkgs must rely on Apple’s SDK, system libraries, and dynamic loader, all of which change across OS and Xcode updates. As a result, older nixpkgs snapshots may keep working on Linux but fail on newer macOS systems due to toolchain drift and stricter dynamic linking behavior.

I have to admit, I didn’t expect that two years would already be enough to see environments break on macOS.

For historical nixpkgs snapshots in particular, I recommend running them inside Docker (on a Linux base image) rather than directly on macOS. Linux environments are significantly more stable over time for the reasons mentioned above, and Docker isolates the setup from host system changes. This provides much more reliable long-term reproducibility when comparing results across time. If you use Positron or VS Code, you can connect to the dev container seamlessly from your native installation, so the workflow remains smooth.

[b-rodrigues]

I rewrote the intro of the vignette to make this issue appear more clearly

4588eda

[simonreif]

Thanks for your effort!! I had hoped to postpone digging deeper into Linux for a while ;) But your answer is very helpful! I will see whether another date in the range I am looking at works (it does for at least one later and one earlier date - but June 2024 is bad...so it's is somewhat wores than the short time, it seems to be rather ideosyncratic).

Regarding the local cache solution: Wouldn't that also break if I update my system?

[b-rodrigues]

I don’t think so. The way the binary cache works is that Nix stores and substitutes derivations based on their hash. Anything macOS-specific outside the Nix store doesn’t affect that hash I believe, so from Nix’s perspective, the binary is the same and will simply be reused from the cache. The caveat is that the binary must have been built on that specific macOS version; if the system changes drastically, rebuilding may still be necessary, but the cached binaries themselves remain valid.