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I have a large document which is compiling perfectly fine with my old app Latexian (which is now defunct, but still working great under the Rosetta 2 emulation on my Mac). When I try to compile the same document with TeXShop, using the pdflatexmk engine, I get a long compilation (the document is very large!) until it suddenly halts with a "no file " comment in TeXShop's console:

SyncTeX written on " Document principal.synctex.gz"
 Transcript written on " Document principal.log".
 Latexmk: Missing input file ' Document principal.aux' (or dependence on it) from following:
 No file " Document principal".aux.
 Latexmk: Missing input file ' Document principal.toc' (or dependence on it) from following:
 No file " Document principal".toc.
 Latexmk: Missing input file ' Document principal.lol' (or dependence on it) from following:
 No file " Document principal".lol.
 Latexmk: Missing input file ' Document principal.ind' (or dependence on it) from following:
 No file " Document principal".ind.
 Latexmk: Getting log file ' Document principal.log'
 Latexmk: Examining ' Document principal.fls'
 Latexmk: Examining ' Document principal.log'
 Latexmk: Index file ' Document principal.idx' was written
 Latexmk: Log file says output to ' Document principal.pdf'
 Latexmk: Summary of warnings from last run of *latex:
 Latex failed to resolve 4995 reference(s)
 =====Latex reported missing or unavailable character(s).
 =====See log file for details.
 Latex failed to resolve 21 citation(s)
 Latexmk: All targets () are up-to-date

This is happening on a new M2 Mac, with the latest MacTeX distribution. I don't understand what's going on. As I said, the same document is compiling fine with Latexian (under the Rosetta 2 emulation). No issue there at all with the cross reference numbers, when I do a 3 runs compilation.

So what are these missing files? There's no missing file! The issue appears to be related to the several compilation runs I need to get the cross reference numbers right, and the index numbering.

Cham
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    Presumably your filename doesn't actually start with a space? Can you show what the compilation instruction in TeXShop is set to? (I think it'll be under Preferences -> Engine) – Dai Bowen Apr 16 '23 at 17:31
  • @DaiBowen, the preferences->Engine is set to pdflatexmk. And yes I do have a space in front of the main file name, so it appears on top of my file list. Is that the source of the issue?? – Cham Apr 16 '23 at 17:35
  • Potentially relevant regarding spaces in file names: https://tex.stackexchange.com/q/406610/218142 – LaTeXereXeTaL Apr 16 '23 at 17:38
  • @DaiBowen Aaah! Removing the first space in the main file name solved the issue! I didn't had this issue with Latexian. Now I need to use files without any space in their name, and even ban underscore "_" in file names (which I use a lot)!? This is very restrictive! I must admit that I'm a bit deceived by TeXShop. – Cham Apr 16 '23 at 17:47
  • It's important to understand that different developers do different things. Latexian and Texifier (previously known as TeXPad) may do things that are not considered "standard" in LaTeX workflows, which is one reason I stopped using them. TeXShop preserves the more traditional workflows. Also, you don't even need an editor to create your documents of course. LaTeX and friends are designed to be used from a command line (despite Mac users' dislike of Terminal). – LaTeXereXeTaL Apr 16 '23 at 18:14

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