If you wanted you could set propagatedBuildInputs to do this more conventionally.
But you already found that the WHICH is not set properly #58963 (comment). You could try adding definition like "WHICH=$(type -p which)" into configureFlagsArray. Worst case there is an ugly hack to directly substituteInPlace the @WHICH@ in src/library/base/R/unix/system.unix.R, but that should not be needed, I expect.

@peti, @veprbl, but stracing R showed that R is indeed trying to access to which under /nix/store.

Also, after configurePhase, the file config.status contained the line S["WHICH"]="/nix/store/ckd1dy6llxr1s17f9x27p9jwzdanl5yx-which-2.21/bin/which" and config.log contained the line ac_cv_path_WHICH=/nix/store/ckd1dy6llxr1s17f9x27p9jwzdanl5yx-which-2.21/bin/which.

@rhokue
In that trace the execve returns ENOENT which stands for

The file filename or a script or ELF interpreter does not exist, or a shared library needed for file or interpreter cannot be found.

So what happens? Does "which" get garbage collected? Or is it sandboxing?

@veprbl I don't know...

Yes, @veprbl, your description matches my experience and the investigations which @cleverca22 and I made while chatting on IRC, during which we used strings command to see if the path to the which binary is readable in any file. But it wasn't. Which is strange but it is how it is, I guess?

So, it would be nice if @peti could approve this PR as well. :)

@peti, @veprbl, but stracing R showed that R is indeed trying to access to which under /nix/store.

If that path were baked into the R executable (or any of its libraries), then Nix would recognize the run-time dependency. I don't know where that store path is coming from, but it's clearly not a part of the the R binary package, or else it could not possibly be missing at run-time.

Breaks my build.

builder for '/nix/store/ghsyv8c8677jyqc9c16vxphgdvh6hrrh-R-3.5.3.drv' failed with exit code 1; last 10 log lines:
  -texlive-combined-2018/share/texmf/fonts/type1/public/amsfonts/cm/cmti10.pfb></
  nix/store/2yfzvjnsgzvv1vr3f00idncsshyzzkxq-texlive-combined-2018/share/texmf/fo
  nts/type1/public/amsfonts/cm/cmtt10.pfb></nix/store/2yfzvjnsgzvv1vr3f00idncsshy
  zzkxq-texlive-combined-2018/share/texmf/fonts/type1/public/amsfonts/cm/cmtt9.pf
  b>
  Output written on R-lang.pdf (60 pages, 374816 bytes).
  Transcript written on R-lang.log.
  installing R manuals in PDF format ...
  make[1]: Leaving directory '/build/R-3.5.3/doc/manual'
  /nix/store/63karsgdg7fm3q0if4zfd7apbd8ac1ci-stdenv-linux/setup: line 99: /nix/store/l29hk8hpz3k8j4kha4p2mjvnhbax0d03-R-3.5.3/nix-support/undetected-runtime-dependencies: No such file or directory
cannot build derivation '/nix/store/hcz4in4mqix7kszjyp81d0cabnfmlsv7-R-3.5.3-wrapper.drv': 1 dependencies couldn't be built

Builds again after f7ddff5.