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

Fri Jul 14 10:45:57 EDT 2017

Under macOS Sierra 10.12.5, I upgraded toTeXShop 3.80 from the immediately preceding version, and with the same MacTeX 2017/TeXLive 2017 (except for any TeXLive package updates).

After updating TeXShop, when I run pdflatexmk on essentially the same complex document (about 300 pages with many source files that are included or inputted, multiple indexes, etc.), it takes many seconds more than it did under the previous version, with noticeable multi-second stops between each run during my single invocation of Typeset with pdflatexmk. 

With the previous version, pdflatexmk typesetting ran smoothly, with none of the hiccuping stops now occurring.

My pdflatexmkrc file and contents of the console are listed below. 

   ===========  BEGIN ~/Library/TewXShop/bin/tslatexmk/pdflatexmkrc  =============
# Don't edit this file IF it is named latexmkrcDONTedit directly since
#   TeXShop may replace it on update.
# If you wish to edit or add to this file, copy it to ~/Library/TeXShop/bin
# and rename it latexmkrcedit if that file doesn't already exist.

# Edit this File to add/change dependencies and rules
# The following is used by ALL the latexmk engine files

# change '--shell-escape' to an empty string, '', to remove the shell-escape default
#$TSUserCompileOptions = '--shell-escape';
$TSUserCompileOptions = '';

# turn recorder option off (no .fls file generated)
#$recorder=0;

# turn off duplicated missing references
$silence_logfile_warnings = 1;

# Custom dependency for glossaries package
# if you make custom glossaries you may have to add items to the @cus_dep_list and corresponding sub-routines
# NOTE: fileparse and $$Psource are undocumented latexmk as of version 4.40 --- Thanks to John Collins
# if you use the glossary package and DON'T use the glossaries package uncomment (remove the leading #)
# the single line with the system call and comment out (add leading #s) to the two following lines. No
# other changes are necessary. If you use both packages, place any project using the glossary package
# into a folder by itself and create a platexmkrc file containing the lines
#		sub makeglo2gls {
#				system("makeindex -s '$_[0]'.ist -t '$_[0]'.glg -o '$_[0]'.gls '$_[0]'.glo");
#		}
# (without the leading #s) in that folder.
add_cus_dep('glo', 'gls', 0, 'makeglo2gls');
		sub makeglo2gls {
#				system("makeindex -s '$_[0]'.ist -t '$_[0]'.glg -o '$_[0]'.gls '$_[0]'.glo");
				my ($name, $path) = fileparse($$Psource);
				return system("makeglossaries -d '$path' '$name'");
		}
# The glossaries package, with the [acronym] option, produces a .acn file when processed with (xe/pdf)latex and
# then makeindex/xindy to process the .acn into .acr and finally runs of (xe/pdf)latex to read in the .acr file.
add_cus_dep('acn', 'acr', 0, 'makeacn2acr');
		sub makeacn2acr {
#				system("makeindex -s '$_[0]'.ist -t '$_[0]'.alg -o '$_[0]'.acr '$_[0]'.acn");
				my ($name, $path) = fileparse($$Psource);
				return system("makeglossaries -d '$path' '$name'");
		}
# example of an added custom glossary type that is used in some of the glossaries example files:
# this is for the new glossary type command \newglossary[nlg]{notation}{not}{ntn}{Notation} from the glossaries package
add_cus_dep('ntn', 'not', 0, 'makeacn2acr');
# for other glossaries 4.xx examples
add_cus_dep('flo', 'flx', 0, 'makeacn2acr');
add_cus_dep('acn2', 'acr2', 0, 'makeacn2acr');

# the glossary package samples do acr->acn and not->ntn rather than the reverse for the glossaries package
add_cus_dep('acr', 'acn', 0, 'makeacr2acn');
		sub makeacr2acn {
				system("makeindex -s '$_[0]'.ist -t '$_[0]'.alg -o '$_[0]'.acn '$_[0]'.acr");
		}
add_cus_dep('not', 'ntn', 0, 'makenot2ntn');
		sub makenot2ntn {
				system("makeindex -s '$_[0]'.ist -t '$_[0]'.nlg -o '$_[0]'.ntn '$_[0]'.not");
		}

# dependencies for custom indexes using the index package
# examples for sample.tex for index package:
 add_cus_dep('adx', 'and', 0, 'makeadx2and');
 		sub makeadx2and {
 				system("makeindex -o '$_[0]'.and '$_[0]'.adx");
 		}
 add_cus_dep('ndx', 'nnd', 0, 'makendx2nnd');
 		sub makendx2nnd {
 				system("makeindex -o '$_[0]'.nnd '$_[0]'.ndx");
 		}
 add_cus_dep('ldx', 'lnd', 0, 'makeldx2lnd');
	 sub makeldx2lnd {
	 		 system("makeindex -o '$_[0]'.lnd '$_[0]'.ldx");
	 }

# dependency for biblatex example with a title index
 add_cus_dep('tdx', 'tnd', 0, 'maketdx2tnd');
 		sub maketdx2tnd {
 				system("makeindex -o '$_[0]'.tnd '$_[0]'.tdx");
 		}

# Custom dependency and function for nomencl package
add_cus_dep('nlo', 'nls', 0, 'makenlo2nls');
		sub makenlo2nls {
				system("makeindex -s nomencl.ist -o '$_[0]'.nls '$_[0]'.nlo");
		}

# Specify custom index style file:
#$makeindex = "makeindex  -s my.ist %O -o %D %S";# Don't edit this file IF it is named latexmkrcDONTedit directly since
#   TeXShop may replace it on update.
# If you wish to edit or add to this file, copy it to ~/Library/TeXShop/bin
# and rename it latexmkrcedit if that file doesn't already exist.

# Edit this File to add/change dependencies and rules
# The following is used by ALL the latexmk engine files

# change '--shell-escape' to an empty string, '', to remove the shell-escape default
#$TSUserCompileOptions = '--shell-escape';
$TSUserCompileOptions = '';

# turn recorder option off (no .fls file generated)
#$recorder=0;

# turn off duplicated missing references
$silence_logfile_warnings = 1;

# Custom dependency for glossaries package
# if you make custom glossaries you may have to add items to the @cus_dep_list and corresponding sub-routines
# NOTE: fileparse and $$Psource are undocumented latexmk as of version 4.40 --- Thanks to John Collins
# if you use the glossary package and DON'T use the glossaries package uncomment (remove the leading #)
# the single line with the system call and comment out (add leading #s) to the two following lines. No
# other changes are necessary. If you use both packages, place any project using the glossary package
# into a folder by itself and create a platexmkrc file containing the lines
#		sub makeglo2gls {
#				system("makeindex -s '$_[0]'.ist -t '$_[0]'.glg -o '$_[0]'.gls '$_[0]'.glo");
#		}
# (without the leading #s) in that folder.
add_cus_dep('glo', 'gls', 0, 'makeglo2gls');
		sub makeglo2gls {
#				system("makeindex -s '$_[0]'.ist -t '$_[0]'.glg -o '$_[0]'.gls '$_[0]'.glo");
				my ($name, $path) = fileparse($$Psource);
				return system("makeglossaries -d '$path' '$name'");
		}
# The glossaries package, with the [acronym] option, produces a .acn file when processed with (xe/pdf)latex and
# then makeindex/xindy to process the .acn into .acr and finally runs of (xe/pdf)latex to read in the .acr file.
add_cus_dep('acn', 'acr', 0, 'makeacn2acr');
		sub makeacn2acr {
#				system("makeindex -s '$_[0]'.ist -t '$_[0]'.alg -o '$_[0]'.acr '$_[0]'.acn");
				my ($name, $path) = fileparse($$Psource);
				return system("makeglossaries -d '$path' '$name'");
		}
# example of an added custom glossary type that is used in some of the glossaries example files:
# this is for the new glossary type command \newglossary[nlg]{notation}{not}{ntn}{Notation} from the glossaries package
add_cus_dep('ntn', 'not', 0, 'makeacn2acr');
# for other glossaries 4.xx examples
add_cus_dep('flo', 'flx', 0, 'makeacn2acr');
add_cus_dep('acn2', 'acr2', 0, 'makeacn2acr');

# the glossary package samples do acr->acn and not->ntn rather than the reverse for the glossaries package
add_cus_dep('acr', 'acn', 0, 'makeacr2acn');
		sub makeacr2acn {
				system("makeindex -s '$_[0]'.ist -t '$_[0]'.alg -o '$_[0]'.acn '$_[0]'.acr");
		}
add_cus_dep('not', 'ntn', 0, 'makenot2ntn');
		sub makenot2ntn {
				system("makeindex -s '$_[0]'.ist -t '$_[0]'.nlg -o '$_[0]'.ntn '$_[0]'.not");
		}

# dependencies for custom indexes using the index package
# examples for sample.tex for index package:
 add_cus_dep('adx', 'and', 0, 'makeadx2and');
 		sub makeadx2and {
 				system("makeindex -o '$_[0]'.and '$_[0]'.adx");
 		}
 add_cus_dep('ndx', 'nnd', 0, 'makendx2nnd');
 		sub makendx2nnd {
 				system("makeindex -o '$_[0]'.nnd '$_[0]'.ndx");
 		}
 add_cus_dep('ldx', 'lnd', 0, 'makeldx2lnd');
	 sub makeldx2lnd {
	 		 system("makeindex -o '$_[0]'.lnd '$_[0]'.ldx");
	 }

# dependency for biblatex example with a title index
 add_cus_dep('tdx', 'tnd', 0, 'maketdx2tnd');
 		sub maketdx2tnd {
 				system("makeindex -o '$_[0]'.tnd '$_[0]'.tdx");
 		}

# Custom dependency and function for nomencl package
add_cus_dep('nlo', 'nls', 0, 'makenlo2nls');
		sub makenlo2nls {
				system("makeindex -s nomencl.ist -o '$_[0]'.nls '$_[0]'.nlo");
		}

# Specify custom index style file:
#$makeindex = "makeindex  -s my.ist %O -o %D %S”;

   ===========  END ~/Library/TewXShop/bin/tslatexmk/pdflatexmkrc  =============

  ===========  BEGIN console file ===============

  Subroutine makeglo2gls redefined at (eval 9) line 2, <GEN2> chunk 1.
Latexmk: This is Latexmk, John Collins, 16 May 2017, version: 4.53a.
Rule 'pdflatex': Rules & subrules not known to be previously run:
   pdflatex
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  --synctex=1 --file-line-error  -recorder  "topologybook.tex"'
------------
Latexmk: applying rule 'pdflatex'...
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./topologybook.tex
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lh/m/n/10 (-20) by re-strict-ing its do-main to $\OMS/hlcy/m/n/10 f\T1/hlh/m/n/
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[]\T1/hlh/m/n/10 (-20) Now let $\OML/hlcm/m/it/10 n \OMS/hlcy/m/n/10 ^^U \T1/hl
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[]\T1/hlh/m/n/10 (-20) Since $\OML/hlcm/m/it/10 dÑx; yÖ \OMS/hlcy/m/n/10 É k\OM
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\OML/hlcm/m/it/10 d[]Ñy[]; y[]Ö \OMS/hlcy/m/n/10 É \OML/hlcm/m/it/10 d[][]fÑx[]
Ö; fÑx[]Ö[] \OMS/hlcy/m/n/10 É \OML/hlcm/m/it/10 dÑx[]; x[]Ö \OMS/hlcy/m/n/10 É
 \OML/hlcm/m/it/10 d[]f[]Ñy[]Ö; f[]Ñy[]Ö[]: []

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[]\T1/hlh/m/n/10 (-20) The met-ric space $\OML/hlcm/m/it/10 ÑÜ\T1/hlh/m/n/10 (-
20) 0\OML/hlcm/m/it/10 ; cá; dÖ$ \T1/hlh/m/n/10 (-20) is topo-log-i-cally equiv
-a-lent to $\OML/hlcm/m/it/10 ÑÜa; bá; d[]Ö$\T1/hlh/m/n/10 (-20) .
[154]
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\T1/hlh/m/n/10 (-20) ---the com-pos-ite of a trans-la-tion fol-lowed by a di-la
-tion or contraction---

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[155]

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[]\T1/hlh/m/n/10 (-20) Let $\OMS/hlcy/m/n/10 F$ \T1/hlh/m/n/10 (-20) be the col
-lec-tion of all nonempty $\OML/hlcm/m/it/10 d$\T1/hlh/m/n/10 (-20) -closed sub
-sets of a bounded
[156]

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[158]

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) (./main/MetricSpaces/contconv.tex

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[]\T1/hlh/m/it/10 (-20) For each $\OML/hlcm/m/it/10 d[]$\T1/hlh/m/it/10 (-20) -
neighborhood $\OML/hlcm/m/it/10 N$ \T1/hlh/m/it/10 (-20) of $\OML/hlcm/m/it/10 
fÑxÖ$ \T1/hlh/m/it/10 (-20) in $\OML/hlcm/m/it/10 Y$ \T1/hlh/m/it/10 (-20) ther
e ex-ists some $\OML/hlcm/m/it/10 d$\T1/hlh/m/it/10 (-20) -neighborhood

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[]\T1/hlh/m/n/10 (-20) Assume []. Let $\OML/hlcm/m/it/10 " > \T1/hlh/m/n/10 (-2
0) 0$. Since $\OML/hlcm/m/it/10 B[]ÑfÑxÖ\T1/hlh/m/n/10 (-20) ; \OML/hlcm/m/it/1
0 d[]Ö$ \T1/hlh/m/n/10 (-20) is a $\OML/hlcm/m/it/10 d[]$\T1/hlh/m/n/10 (-20) -
neighborhood

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[164]

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[]\T1/hlh/m/n/10 (-20) From [] we may now de-duce an es-pe-cially sim-ple cri-t
e-rion for continuity---

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[166]

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[]\T1/hlh/m/n/10 (-20) In fact, in view of [], the range $\OMS/hlcy/m/n/10 f []
 g$ \T1/hlh/m/n/10 (-20) will cer-tainly be bounded

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[173]

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[]\T1/hlh/m/n/10 (-20) Just sup-pose that $\OML/hlcm/m/it/10 x \LMR/hlcm/m/n/10
 î \OML/hlcm/m/it/10 y$\T1/hlh/m/n/10 (-20) . By [] there are dis-joint $\OML/h
lcm/m/it/10 d$\T1/hlh/m/n/10 (-20) -neighborhoods

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[177]

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81.

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\T1/hlh/m/n/10 (-20) of ad-di-tion and mul-ti-pli-ca-tion, re-spec-tively, are 
$\OML/hlcm/m/it/10 Ñd[]; dÖ$\T1/hlh/m/n/10 (-20) -continuous. 
[178]

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[179]

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\T1/hlh/m/n/10 (-20) For ex-am-ple, any isom-e-try from $\OML/hlcm/m/it/10 ÑX; 
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 \T1/hlh/m/n/10 (-20) De-fine $\OMS/hlcy/m/n/10 B$ \T1/hlh/m/n/10 (-20) to be t
he col-lec-tion of all such sub-sets $\OML/hlcm/m/it/10 B[]x[]; x[]; [] ; x[] \
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i-ble choices of $\OML/hlcm/m/it/10 k$\T1/hlh/m/n/10 (-20) , of $\OML/hlcm/m/it
/10 Ñ[]Ö$\T1/hlh/m/n/10 (-20) , and of $\OML/hlcm/m/it/10 Ñ[]Ö$\T1/hlh/m/n/10 (
-20) .

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(./main/ContinuityConvergence/continuityconvergence-init.tex)
(./main/ContinuityConvergence/continuous.tex [245]

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[]\T1/hlh/m/n/10 (-20) Example [] con-cern-ing the set $\OML/hlcm/m/it/10 X$ \T
1/hlh/m/n/10 (-20) of all con-tin-u-ous func-tions $\OML/hlcm/m/it/10 x [] [] Ü
\T1/hlh/m/n/10 (-20) 0\OML/hlcm/m/it/10 ; \T1/hlh/m/n/10 (-20) 1\OML/hlcm/m/it/
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\T1/hlh/m/n/10 (-20) map $\OML/hlcm/m/it/10 f [] [] ÑX; \OMS/hlcy/m/n/10 S\OML/
hlcm/m/it/10 Ö [] ÑY; \OMS/hlcy/m/n/10 U\OML/hlcm/m/it/10 Ö$ \T1/hlh/m/n/10 (-2
0) is also con-tin-u-ous as a map $\OML/hlcm/m/it/10 f [] [] ÑX; \OMS/hlcy/m/n/
10 T\OML/hlcm/m/it/10 Ö [] ÑY; \OMS/hlcy/m/n/10 U\OML/hlcm/m/it/10 Ö$\T1/hlh/m/
n/10 (-20) .

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) (./main/ContinuityConvergence/homeomorphism.tex [246])
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\T1/hlh/m/n/10 (-20) log-i-cal space $\OML/hlcm/m/it/10 X$ \T1/hlh/m/n/10 (-20)
 to a com-pact space $\OML/hlcm/m/it/10 Y$ \T1/hlh/m/n/10 (-20) whose graph $[]
$

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he col-lec-tion $\OMS/hlcy/m/n/10 f [] g$ \T1/hlh/m/n/10 (-20) where $\OML/hlcm
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) (./main/Compact/locallycompact.tex [278])) [279]
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[284]) (./main/Connected/pathconnected.tex) (./main/Connected/homotopy.tex)
(./main/Connected/simplyconnected.tex [285])) [286]
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[289] [290]) (./back/indexes.tex
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 )
(see the transcript file for additional information){/usr/local/texlive/2017/te
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=== TeX engine is 'pdfTeX'
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Database file #1: topologybook-blx.bib
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\T1/hlh/m/n/10 (-20) verse re-la-tion $[]$ is \T1/hlh/m/it/10 (-20) not \T1/hlh
/m/n/10 (-20) func-tional be-cause the set $\OMS/hlcy/m/n/10 f [] g$
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[]\T1/hlh/m/n/10 (-20) In examples ([][]*[][]) of the subsection ``Injections, 
surjections, and bijections''
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[]\T1/hlh/m/n/10 (-20) The union and in-ter-sec-tion of two sets in the sense o
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\T1/hlh/m/n/10 (-20) Moreover, the for-mu-las in-volv-ing union and in-ter-sec-
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[]\T1/hlh/m/n/10 (-20) Let $\OML/hlcm/m/it/10 n$ \T1/hlh/m/n/10 (-20) be a pos-
i-tive in-te-ger and let $\OML/hlcm/m/it/10 ÑX[]Ö[]$ \T1/hlh/m/n/10 (-20) be a 
fam-ily of \T1/hlh/m/it/10 (-20) nonempty
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\T1/hlh/m/n/10 (-20) Hence the map ob-tained from $\OML/hlcm/m/it/10 h[]$ \T1/h
lh/m/n/10 (-20) by re-strict-ing its do-main to $\OMS/hlcy/m/n/10 f\T1/hlh/m/n/
10 (-20) 1\OML/hlcm/m/it/10 ; \T1/hlh/m/n/10 (-20) 2\OML/hlcm/m/it/10 ; [] ; n;
 n \OMS/hlcy/m/n/10 Ç
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[]\T1/hlh/m/n/10 (-20) Now let $\OML/hlcm/m/it/10 n \OMS/hlcy/m/n/10 ^^U \T1/hl
h/m/n/10 (-20) 1$ and as-sume that each sub-set of $\OMS/hlcy/m/n/10 f\T1/hlh/m
/n/10 (-20) 1\OML/hlcm/m/it/10 ; \T1/hlh/m/n/10 (-20) 2\OML/hlcm/m/it/10 ; [] ;
 n\OMS/hlcy/m/n/10 g$
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[]\T1/hlh/m/n/10 (-20) The pre-ced-ing proof is a typ-i-cal pro-ce-dure for ap-
ply-ing Zorn's Lemma.To
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[]\T1/hls/b/n/10 1.9 Ex-am-ple. []\T1/hlh/m/n/10 (-20) Again let $\OML/hlcm/m/i
t/10 X$ \T1/hlh/m/n/10 (-20) be the set of all con-tin-u-ous func-tions $\OML/h
lcm/m/it/10 x [] [] Ü\T1/hlh/m/n/10 (-20) 0\OML/hlcm/m/it/10 ; \T1/hlh/m/n/10 (
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[]\T1/hlh/m/n/10 (-20) Are the taxi-cab and max met-rics on $\LMR/hlcm/m/n/10 R
[]$ \T1/hlh/m/n/10 (-20) also translation-invariant?
[115] [116] [117] [118]) (./main/MetricSpaces/openclosed.tex [119] [120]
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\OML/hlcm/m/it/10 d[]Ñy[]; y[]Ö \OMS/hlcy/m/n/10 É \OML/hlcm/m/it/10 d[][]fÑx[]
Ö; fÑx[]Ö[] \OMS/hlcy/m/n/10 É \OML/hlcm/m/it/10 dÑx[]; x[]Ö \OMS/hlcy/m/n/10 É
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[]\T1/hlh/m/n/10 (-20) The met-ric space $\OML/hlcm/m/it/10 ÑÜ\T1/hlh/m/n/10 (-
20) 0\OML/hlcm/m/it/10 ; cá; dÖ$ \T1/hlh/m/n/10 (-20) is topo-log-i-cally equiv
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[]\T1/hlh/m/n/10 (-20) Let $\OMS/hlcy/m/n/10 F$ \T1/hlh/m/n/10 (-20) be the col
-lec-tion of all nonempty $\OML/hlcm/m/it/10 d$\T1/hlh/m/n/10 (-20) -closed sub
-sets of a bounded
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[]\T1/hlh/m/it/10 (-20) For each $\OML/hlcm/m/it/10 d[]$\T1/hlh/m/it/10 (-20) -
neighborhood $\OML/hlcm/m/it/10 N$ \T1/hlh/m/it/10 (-20) of $\OML/hlcm/m/it/10 
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[]\T1/hlh/m/n/10 (-20) Assume ([][]3[][]). Let $\OML/hlcm/m/it/10 " > \T1/hlh/m
/n/10 (-20) 0$. Since $\OML/hlcm/m/it/10 B[]ÑfÑxÖ\T1/hlh/m/n/10 (-20) ; \OML/hl
cm/m/it/10 d[]Ö$ \T1/hlh/m/n/10 (-20) is a $\OML/hlcm/m/it/10 d[]$\T1/hlh/m/n/1
0 (-20) -neighborhood
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u-lar space, even a reg-u-lar $\OML/hlcm/m/it/10 T[]$\T1/hlh/m/n/10 (-20) -spac
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-20) .
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\T1/hlh/m/n/10 (-20) map $\OML/hlcm/m/it/10 f [] [] ÑX; \OMS/hlcy/m/n/10 S\OML/
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Database file #1: topologybook-blx.bib
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