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Lots of times I get warnings or errors, but I can never figure out how to decipher them and I can't find any good documentation or guide going through how to understand these errors. For example:

I am using latexmk -pdf -pvc. For this, where does the section talking about the errors in Chapter 2. begin? Is it exactly where it says Chapter 2.? Also What is all the other stuff before that talking about? Like the usr/local/texlive/2018... What does it mean T1/cmr/m/n/12 (+20) in the error for Overfull hbox? In general how do I go about reading these?

Also, just as a side question, I can't figure out how to fix those hbox errors. I used to use sloppywhich fixed some errors but those errors aren't being solved using that. I have also tried using usepackage{microtype} which did not fix the problem either.

The comments have pointed you at existing answers describing the general issue but I'll try to describe the log output you show (it would have been a lot easier if you had posted that as text not an image) but I OCR'd the image here:

(/usr/local/texlive/2018/texmf-dist/tex/context/base/mkii/supp-pdf.mkii

[Loading MPS to PDF converter (version 2006.09.02).]

) (/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty

(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/grfext.sty)

(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))

ABD: EverySelectfont initializing macros ABD: EveryShipout initializing macros

(/usr/local/texlive/2018/texmf-dist/tex/latex/microtype/mt-cmr.cfg) [1{/usr/loc

al/texlive/2018/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]

(~/CS188Notes.tex

Chapter 2.

Overfull hbox (0.12741pt too wide) in paragraph at lines 27--29

T1/cmr/m/n/12 (+20) brains are good at making rational. But the main problem i

s that brains are not modular

[7] [8] Chapter 3.

The first thing to note is that TeX wraps the messages at a (user settable) width

and then whenever it input a file it logs ( followed by the file path, and when it finishes with that file and processing returns to the file that processed the input Tex logs ).

The graphics package internally does input{supp-pdf.mkii} which on your system gets logged as

(/usr/local/texlive/2018/texmf-dist/tex/context/base/mkii/supp-pdf.mkii

as that is the directory where the file was located. that file identifies itself with a message so then you see

[Loading MPS to PDF converter (version 2006.09.02).]

and a newline then that file is finished so you see ) At this point graphics inputs epstopdf-base.sty which in turn inputs grfext.sty and epstopdf-sys.cfg then you see )) as both levels of input have finished. Then some package outputs two identifying messages prefixed with ABD: then a microtype cfg file is input

(/usr/local/texlive/2018/texmf-dist/tex/latex/microtype/mt-cmr.cfg)

at this point TeX has finished typesetting page 1 and starts to output that page so you see [1 in the log, while generating the PDF for that page it needs to access some font data so you see (wrapped)

{/usr/local/texlive/2018/texmf-var/fonts/map/pdftex/updmap/pdftex.map}

where {...} is a pdftex logging of an internal input as oppsed to the classic (...0 logging of an explicit input.

then you see ] denoting page 1 being finally shipped out.

TeX now presumably sees an input of your CS188Notes file and logs

(~/CS188Notes.tex

The chapter` command in there logs:

Chapter 2.

so up to this point everything is good, the messages are just informational.

Now we see

Overfull hbox (0.12741pt too wide) in paragraph at lines 27--29

So something is .1pt (not very much:-) too wide on the page after page 1 and on line 27 of the source file ~/CS188Notes.tex Te actual text is logged as

T1/cmr/m/n/12 (+20) brains are good at making rational. But the main problem i

s that brains are not modular

so it is that sentence, set in T1 (Latin) encoded computer modern medium weight, normal shape 12pt font, adjusted (+20) by microtype.

then somewhat strangely TeX logs

 [7][8]

which means pages 7 and 8 got output (did you increment the page counter, what happened to pages 2 to 6 ?

Then another chapter command logs

chapter 3

So the only thing wrong is the text about brains where tex couldn't find an ideal line break, it's only .1pt so you could ignore it (if you set hfuzz to .2pt then TeX would not warn about this at all or you may want to adjust the typesetting (or wording) of that paragraph to help with line breaking.