Repitools dependency fail

[kunfundere]

# This file was generated by the {rix} R package v0.17.2 on 2026-02-13
# with following call:
# >rix(r_ver = "4.5.1",
#  > r_pkgs = c("Repitools",
#  > "gsmoothr@0.1.7"),
#  > system_pkgs = NULL,
#  > git_pkgs = NULL,
#  > ide = "none",
#  > project_path = "/path/test",
#  > overwrite = TRUE)
# It uses the `rstats-on-nix` fork of `nixpkgs` which provides improved
# compatibility with older R versions and R packages for Linux/WSL and
# Apple Silicon computers.
# Report any issues to https://github.com/ropensci/rix
let
 pkgs = import (fetchTarball "https://github.com/rstats-on-nix/nixpkgs/archive/2025-10-27.tar.gz") {};
 
  rpkgs = builtins.attrValues {
    inherit (pkgs.rPackages) 
      Repitools;
  };
  
    gsmoothr = (pkgs.rPackages.buildRPackage {
      name = "gsmoothr";
      src = pkgs.fetchzip {
       url = "https://cran.r-project.org/src/contrib/Archive/gsmoothr/gsmoothr_0.1.7.tar.gz";
       sha256 = "sha256-yV5Fpy4voKlR2Rn2qHbguOjA6WrNPwHqGZN5QMzP4t4=";
      };
      propagatedBuildInputs = builtins.attrValues {
        inherit (pkgs.rPackages) ;
      };
    });
     
  system_packages = builtins.attrValues {
    inherit (pkgs) 
      glibcLocales
      nix
      R;
  };
  
  shell = pkgs.mkShell {
    LOCALE_ARCHIVE = if pkgs.system == "x86_64-linux" then "${pkgs.glibcLocales}/lib/locale/locale-archive" else "";
    LANG = "en_US.UTF-8";
    LC_ALL = "en_US.UTF-8";
    LC_TIME = "en_US.UTF-8";
    LC_MONETARY = "en_US.UTF-8";
    LC_PAPER = "en_US.UTF-8";
    LC_MEASUREMENT = "en_US.UTF-8";
    
    buildInputs = [ gsmoothr rpkgs system_packages ];
    
  }; 
in
  {
    inherit pkgs shell;
  }

error: Cannot build '/nix/store/2dxn2al6y4qv1gx2qr0v04yqhli4fbyk-r-Repitools-1.54.0.drv'.
       Reason: builder failed with exit code 1.
       Output paths:
         /nix/store/waccsm8vkxw16jsiyzcmf9azai13lx12-r-Repitools-1.54.0
       Last 14 log lines:
       > Running phase: unpackPhase
       > unpacking source archive /nix/store/l09v3592bvcbxm3x6rj7mvap01gjixkm-Repitools_1.54.0.tar.gz
       > source root is Repitools
       > setting SOURCE_DATE_EPOCH to timestamp 1744761722 of file "Repitools/inst/doc/Repitools_vignette.pdf"
       > Running phase: patchPhase
       > Running phase: updateAutotoolsGnuConfigScriptsPhase
       > Running phase: configurePhase
       > Running phase: buildPhase
       > Running phase: checkPhase
       > Running phase: installPhase
       > ERROR: dependency 'gsmoothr' is not available for package 'Repitools'
       > Perhaps try a variation of:
       > install.packages('gsmoothr')
       > * removing '/nix/store/waccsm8vkxw16jsiyzcmf9azai13lx12-r-Repitools-1.54.0/library/Repitools'
       For full logs, run:
         nix log /nix/store/2dxn2al6y4qv1gx2qr0v04yqhli4fbyk-r-Repitools-1.54.0.drv
error: Cannot build '/nix/store/r2pbm5iwca25l2q1lfbhavank17wgm24-nix-shell.drv'.
       Reason: 1 dependency failed.
       Output paths:
         /nix/store/lwrm872h6iqjycdgr5sbh8761s39yqzp-nix-shell
error: Build failed due to failed dependency

This could be my inexperience with rix, but I cannot get Repitools to detect gsmoothr.

Not installing Repitools would let gmoothr work. (Can go into R and load library(gmoothr))

[b-rodrigues]

The issue is that gmsoothr was removed from CRAN on the 21 of May 2025: https://cran.r-project.org/web/packages/gsmoothr/index.html

Use a date just before it and it should work (the closest available date is May 19th)

[kunfundere]

Thank you for the reply.
I tried several dates before May 19 from available_dates(), but the issue persists.

# >rix(date = "2025-05-05",
#  > r_pkgs = c("Repitools",
#  > "gsmoothr@0.1.7"),
#  > system_pkgs = NULL,
#  > git_pkgs = NULL,
#  > ide = "none",
#  > project_path = "/path/test",
#  > overwrite = TRUE,
#  > r_ver = "4.5.0")

[b-rodrigues]

It is also possible to install Repitools and gsmoothr with a current date, but that would require manual adjustment of the expression, which reveals essentially what the maintainers of the R ecosystem for Nix do. But when a package gets removed from CRAN, that’s then on the end-users to fix.

It would look like this:

let
 pkgs = import (fetchTarball "https://github.com/rstats-on-nix/nixpkgs/archive/2025-10-27.tar.gz") {};

  rpkgs = builtins.attrValues {
    inherit (pkgs.rPackages) 
      rix; # put any current R packages here
  };

   repitools_deps = builtins.attrValues {
     inherit (pkgs.rPackages)
       BiocGenerics
       S4Vectors
       IRanges
       GenomeInfoDb
       GenomicRanges
       Biostrings
       Rsamtools
       GenomicAlignments
       rtracklayer
       BSgenome
       gplots
       MASS
       edgeR
       DNAcopy
       Rsolnp
       cluster
       ;
   };

    gsmoothr = (pkgs.rPackages.buildRPackage {
      name = "gsmoothr";
      src = pkgs.fetchzip {
       url = "https://cran.r-project.org/src/contrib/Archive/gsmoothr/gsmoothr_0.1.7.tar.gz";
       sha256 = "sha256-yV5Fpy4voKlR2Rn2qHbguOjA6WrNPwHqGZN5QMzP4t4=";
      };
      propagatedBuildInputs = builtins.attrValues {
        inherit (pkgs.rPackages) ;
      };
    });
 
    Repitools = (pkgs.rPackages.buildRPackage {
      name = "gsmoothr";
      src = pkgs.fetchzip {
       url = "https://bioconductor.org/packages/3.21/bioc/src/contrib/Repitools_1.54.0.tar.gz";
       sha256 = "sha256-e3F1PH3+K7Eft/kXb/qk5/bj+905hs+yLQ8v//HbrE8=";
      };
      propagatedBuildInputs = [ gsmoothr ] ++ repitools_deps;
    });
     
  system_packages = builtins.attrValues {
    inherit (pkgs) 
      glibcLocales
      nix
      R;
  };
  
  shell = pkgs.mkShell {
    LOCALE_ARCHIVE = if pkgs.system == "x86_64-linux" then "${pkgs.glibcLocales}/lib/locale/locale-archive" else "";
    LANG = "en_US.UTF-8";
    LC_ALL = "en_US.UTF-8";
    LC_TIME = "en_US.UTF-8";
    LC_MONETARY = "en_US.UTF-8";
    LC_PAPER = "en_US.UTF-8";
    LC_MEASUREMENT = "en_US.UTF-8";
    
    buildInputs = [ Repitools rpkgs system_packages ];
    
  }; 
in
  {
    inherit pkgs shell;
  }

EDIT: I just realized it’s probably best not to mix bioc releases, so instead of using a current date (which would correspond to Bioc 3.22, I put back a date with Bioc 3.21)

EDIT2: Actually, I tried again, and even with a recent date from this february, this still works.

[b-rodrigues]

Thank you for the reply. I tried several dates before May 19 from available_dates(), but the issue persists.

# >rix(date = "2025-05-05",
#  > r_pkgs = c("Repitools",
#  > "gsmoothr@0.1.7"),
#  > system_pkgs = NULL,
#  > git_pkgs = NULL,
#  > ide = "none",
#  > project_path = "/path/test",
#  > overwrite = TRUE,
#  > r_ver = "4.5.0")

remove gsmoothr, it is listed as a dependency of Repitools (at that point in time). I just tried it with that date, but without gsmoothr in there, and it works.

[kunfundere]

Thanks, it worked after I made a separate new directory and redid everything again.

I tried rix() without gsmoothr and it worked. Then I tried rix() with gsmoothr@0.1.7. And it still worked, even though before either method didn't. This was using 2025-05-05.

Tried r_ver = "4.4.0" with only Repitools, but another dependency broke.

cc1: some warnings being treated as errors
make: *** [/nix/store/4k0zxxr2kd7d2x94fa4x0mvhpmz37fsz-R-4.4.0/lib/R/etc/Makeconf:195: RDS_random_access.o] Error 1
make: *** Waiting for unfinished jobs....
ERROR: compilation failed for package 'XVector'
* removing '/nix/store/mpc939pqv5xjn89zr8h3z62niq8rxay2-r-XVector-0.42.0/library/XVector'

Other older dates had mixed results.

It is also possible to install Repitools and gsmoothr with a current date, but that would require manual adjustment of the expression, which reveals essentially what the maintainers of the R ecosystem for Nix do. But when a package gets removed from CRAN, that’s then on the end-users to fix.

Same thing with manually installing for after May 19. Before running this script didn't work at all, but after making a new directory and redo it, it worked (for 2025-10-27).

So I suspect something was broken maybe in my store directory and I had to clear it or not use it.