[OS X TeX] very slow pdflatexmk runs after upgrade TeXShop to 3.80

[Herbert Schulz]

> On Jul 14, 2017, at 9:45 AM, Murray Eisenberg <murrayeisenberg at gmail.com> wrote:
> 
> ===========Latexmk: Missing input file: 'front/frontmatter.aux' from line
>   'No file front/frontmatter.aux.'
> Latexmk: Missing input file: 'front/frontmatter.aux' from line
>   'No file front/frontmatter.aux.'
> ===========Latexmk: Missing input file: 'front/preface.aux' from line
>   'No file front/preface.aux.'
> Latexmk: Missing input file: 'front/preface.aux' from line
>   'No file front/preface.aux.'
> ===========Latexmk: Missing input file: 'notation.gls' from line
>   'No file notation.gls.'
> Latexmk: Missing input file: 'notation.gls' from line
>   'No file notation.gls.'
> ===========Latexmk: Missing input file: 'front/frontmatter.aux' from line
>   'No file front/frontmatter.aux.'
> Latexmk: Missing input file: 'front/frontmatter.aux' from line
>   'No file front/frontmatter.aux.'
> ===========Latexmk: Missing input file: 'front/preface.aux' from line
>   'No file front/preface.aux.'
> Latexmk: Missing input file: 'front/preface.aux' from line
>   'No file front/preface.aux.'
> Latexmk: Log file says output to 'topologybook.pdf'
> Latexmk: Couldn't find aux file 'front/frontmatter.aux'
> Latexmk: Couldn't find aux file 'front/preface.aux'
> === TeX engine is 'pdfTeX'
> Latexmk: Found bibliography file(s) [mytopologybook.bib mytopologyread.bib topologybook-blx.bib]
> Latexmk: Summary of warnings:
>   Latex failed to resolve 9 reference(s)
> Latexmk: All targets (topologybook.pdf) are up-to-date
> 

Howdy,

Was that really your pdflatexmkrc file? I've simply got
***************************
# DO NOT EDIT OR COPY THIS FILE. TEXSHOP WILL AUTOMATICALLY UPDATE IT 
# special latexmk settings for Herb Schulz
#$pdflatex = "pdflatex --shell-escape --synctex=1 --file-line-error %O %S";
$pdflatex = "pdflatex $TSUserCompileOptions --synctex=1 --file-line-error %O %S";

# if a bbl file is present but the generating bib file isn't available don't run bibtex. --- default in latexmk 4.13
#$bibtex_use = 1;

# Custom dependency and function(s) for epstopdf package

# FOR USERS OF epstopf v1.4 and before: should also work with v1.5 and later
# note: you may get extras runs if you use the .eps extension in the \includgraphics command
# deletes an outdated pdf-image, and triggers a pdflatex-run
#add_cus_dep('eps', 'pdf', 0, 'cus_dep_delete_dest');

# FOR USERS OF epstopdf v1.5 and later only:
# load it as \usepackage[update,prepend]{epstopdf}
# detects an outdated pdf-image, and triggers a pdflatex-run
#add_cus_dep('eps', 'pdf', 0, 'cus_dep_require_primary_run');

# Custom dependecy to convert tif to png
#add_cus_dep('tif', 'png', 0, 'maketif2png');
#		sub maketif2png {
#				system("convert '$_[0]'.tif '$_[0]'.png");
#		};
***************************

Also, what packages are you using; e.g. are you using the glossary package or the glossaries package?

Biber is having problems; see your log file. Also I see things like

===========Latexmk: Missing input file: 'front/frontmatter.aux' from line
  'No file front/frontmatter.aux.'
Latexmk: Missing input file: 'front/frontmatter.aux' from line
  'No file front/frontmatter.aux.'
===========Latexmk: Missing input file: 'front/preface.aux' from line
  'No file front/preface.aux.'
Latexmk: Missing input file: 'front/preface.aux' from line
  'No file front/preface.aux.'
===========Latexmk: Missing input file: 'notation.gls' from line
  'No file notation.gls.'
Latexmk: Missing input file: 'notation.gls' from line
  'No file notation.gls.'
===========Latexmk: Missing input file: 'front/frontmatter.aux' from line
  'No file front/frontmatter.aux.'
Latexmk: Missing input file: 'front/frontmatter.aux' from line
  'No file front/frontmatter.aux.'
===========Latexmk: Missing input file: 'front/preface.aux' from line
  'No file front/preface.aux.'
Latexmk: Missing input file: 'front/preface.aux' from line
  'No file front/preface.aux.'
Latexmk: Log file says output to 'topologybook.pdf'
Latexmk: Couldn't find aux file 'front/frontmatter.aux'
Latexmk: Couldn't find aux file 'front/preface.aux'
=== TeX engine is 'pdfTeX'
Latexmk: Found bibliography file(s) [mytopologybook.bib mytopologyread.bib topologybook-blx.bib]
Latexmk: Summary of warnings:
  Latex failed to resolve 9 reference(s)
Latexmk: All targets (topologybook.pdf) are up-to-date

at the console output.

Good Luck,

Herb Schulz
(herbs at wideopenwest dot com)