LaTeX-Workshop: makeindex.exe: file not writable for security reasons

Preliminary questions [Required]

I’m having trouble building a project with the latexmk recipe in Windows regarding makeindex and apparent security problems when running it from the extension. I have little to no experience in Windows, so there is a chance I’m missing something silly here, but I’ve tried to search for similar problems and debug for a couple of days with no success now.

Disable all the other extensions except for LaTeX Workshop, and check that you still see this issue. [Required]

You still see this issue?: Yes

Fresh VS Code install, only installed the LaTeX-Workshop extension

Make sure to visit the wiki FAQ before filling an issue.

You visited the wiki?: Yes

If your issue is with compiling a document (not having to do with finding the root file of a project), check first that you can compile manually.

You can compile a TeX document manually?: Yes

If I run the command equivalent to the standard recipe latexmk -pdf -synctex=1 etc in PowerShell the build completes without any errors.

Describe the bug [Required]

latexmk recipe fails to build, log says: “makeindex.exe: file not writable for security reasons”. I’m running Windows 10 and MikTex. Tried from a fresh Windows installation and got the exact same results. latexmk works as expected when running from command line (PowerShell).

Expected behavior

Using the latexmk recipe should successfully complete like when running from PowerShell

Logs [Required]

Please paste the whole log messages here, not parts of ones. The log should start with Initializing LaTeX Workshop. It is very important to identify problems.

[21:04:18] Initializing LaTeX Workshop.
[21:04:18] Extension root: c:\Users\victo\.vscode\extensions\james-yu.latex-workshop-8.14.0
[21:04:18] Creating PDF file watcher.
[21:04:18] pdflatex is provided by MiKTeX
[21:04:18] Creating LaTeX Workshop http and websocket server.
[21:04:18] LaTeX Workshop initialized.
[21:04:18] Current workspace folders: ["file:///c:/Users/victo/Documents/phd-thesis-master"]
[21:04:18] Current workspaceRootDir: c:\Users\victo\Documents\phd-thesis-master
[21:04:18] Server created on 127.0.0.1:50340
[21:04:18] Snippet data loaded.
[21:04:18] LaTeX Workshop version: 8.14.0
[21:04:18] Restoring the PDF viewer at the column 2 from the state: {"type":"state","state":{"path":"c:\\Users\\victo\\Documents\\phd-thesis-master\\tese\\trabalho.pdf","scale":"auto","scrollMode":0,"spreadMode":0,"scrollTop":18800,"scrollLeft":0,"trim":0}}
[21:04:18] Found files that might be root, choose the first one: c:\Users\victo\Documents\phd-thesis-master\vb-mrf\vb2.tex,c:\Users\victo\Documents\phd-thesis-master\vb-mrf\vb-mrf.tex,c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:18] Root file changed: from undefined to c:\Users\victo\Documents\phd-thesis-master\vb-mrf\vb2.tex
[21:04:18] Start to find all dependencies.
[21:04:18] Root file languageId: latex
[21:04:18] Instantiating a new file watcher for c:\Users\victo\Documents\phd-thesis-master\vb-mrf\vb2.tex
[21:04:18] Creating Bib file watcher.
[21:04:18] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\vb-mrf\vb2.tex
[21:04:18] Found .bib file: c:\Users\victo\Documents\phd-thesis-master\tese\biblio.bib
[21:04:18] Added to bib file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\biblio.bib
[21:04:18] Parsing .bib entries from c:\Users\victo\Documents\phd-thesis-master\tese\biblio.bib
[21:04:18] Parse fls file.
[21:04:18] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\vb-mrf\vb2.fls
[21:04:18] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\vb-mrf\vb2.tex
[21:04:18] Parsed 33 bib entries from c:\Users\victo\Documents\phd-thesis-master\tese\biblio.bib.
[21:04:20] Preview PDF file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.pdf
[21:04:21] Handle data type: open
[21:04:21] Handle data type: request_params
[21:04:21] Sending the settings of the PDF viewer for initialization: {"type":"params","scale":"auto","trim":0,"scrollMode":0,"spreadMode":0,"hand":false,"invertMode":{"enabled":false,"brightness":1,"grayscale":0.6,"hueRotate":180,"invert":0,"sepia":0},"bgColor":"#ffffff","keybindings":{"synctex":"ctrl-click"}}
[21:04:21] Handle data type: loaded
[21:04:21] Current workspace folders: ["file:///c:/Users/victo/Documents/phd-thesis-master"]
[21:04:21] Current workspaceRootDir: c:\Users\victo\Documents\phd-thesis-master
[21:04:21] Current workspace folders: ["file:///c:/Users/victo/Documents/phd-thesis-master"]
[21:04:21] Current workspaceRootDir: c:\Users\victo\Documents\phd-thesis-master
[21:04:21] Found root file from active editor: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:21] Found root file from active editor: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:21] Root file changed: from c:\Users\victo\Documents\phd-thesis-master\vb-mrf\vb2.tex to c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:21] Start to find all dependencies.
[21:04:21] Root file languageId: latex
[21:04:21] Root file changed -> cleaning up old file watcher.
[21:04:21] Instantiating a new file watcher for c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\pacotes.tex
[21:04:21] Parse fls file.
[21:04:21] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\tese\pacotes.fls
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\dados.tex
[21:04:21] Parse fls file.
[21:04:21] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\tese\dados.fls
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\configglobal.tex
[21:04:21] Parse fls file.
[21:04:21] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\tese\configglobal.fls
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\resumos.tex
[21:04:21] Parse fls file.
[21:04:21] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\tese\resumos.fls
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\introducao.tex
[21:04:21] Parse fls file.
[21:04:21] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\tese\introducao.fls
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\1-mrf.tex
[21:04:21] Parse fls file.
[21:04:21] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\tese\1-mrf.fls
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\2-bayesian-mrf.tex
[21:04:21] Parse fls file.
[21:04:21] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\tese\2-bayesian-mrf.fls
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\3-bayes-mixed-models.tex
[21:04:21] Parse fls file.
[21:04:21] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\tese\3-bayes-mixed-models.fls
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\considfinais.tex
[21:04:21] Parse fls file.
[21:04:21] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\tese\considfinais.fls
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\apendices.tex
[21:04:21] Parse fls file.
[21:04:21] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\tese\apendices.fls
[21:04:21] Found .bib file: c:\Users\victo\Documents\phd-thesis-master\tese\biblio.bib
[21:04:21] Parse fls file.
[21:04:21] Fls file found: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.fls
[21:04:21] Parse aux file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.aux
[21:04:21] Found .bib file: c:\Users\victo\Documents\phd-thesis-master\tese\biblio.bib
[21:04:21] Parse aux file: c:\Users\victo\Documents\phd-thesis-master\tese\resumos.aux
[21:04:21] Parse aux file: c:\Users\victo\Documents\phd-thesis-master\tese\introducao.aux
[21:04:21] Parse aux file: c:\Users\victo\Documents\phd-thesis-master\tese\1-mrf.aux
[21:04:21] Parse aux file: c:\Users\victo\Documents\phd-thesis-master\tese\2-bayesian-mrf.aux
[21:04:21] Parse aux file: c:\Users\victo\Documents\phd-thesis-master\tese\3-bayes-mixed-models.aux
[21:04:21] Parse aux file: c:\Users\victo\Documents\phd-thesis-master\tese\considfinais.aux
[21:04:21] Parse aux file: c:\Users\victo\Documents\phd-thesis-master\tese\apendices.aux
[21:04:21] Keep using the same root file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\pacotes.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\dados.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\configglobal.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\resumos.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\introducao.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\1-mrf.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\2-bayesian-mrf.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\3-bayes-mixed-models.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\considfinais.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\apendices.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\imecc-unicamp.cls
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\example_cliques.eps
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\example_cliques-eps-converted-to.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\interactions.eps
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\interactions-eps-converted-to.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\pseudolikelihood-example.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\example_ising_vars.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\ising_exd_1.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\ising_exf_1.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\ising_exd_2.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\ising_exf_2.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\ising_exd_3.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\ising_exf_3.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\example_mcl_field.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\triple_plot_pl.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\triple_plot_mcl.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\triple_plot_wl.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\triple_plot_mclmixC.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.ind
[21:04:39] RECIPES command invoked.
[21:04:39] BUILD command invoked.
[21:04:39] The document of the active editor: file:///c%3A/Users/victo/Documents/phd-thesis-master/tese/trabalho.tex
[21:04:39] The languageId of the document: latex
[21:04:39] Current workspace folders: ["file:///c:/Users/victo/Documents/phd-thesis-master"]
[21:04:39] Current workspaceRootDir: c:\Users\victo\Documents\phd-thesis-master
[21:04:39] Found root file from active editor: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:39] Keep using the same root file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:39] Building root file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:39] Build root file c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:39] Recipe step 1: latexmk, --max-print-line=10000,-synctex=1,-interaction=nonstopmode,-file-line-error,-pdf,-outdir=c:/Users/victo/Documents/phd-thesis-master/tese,c:/Users/victo/Documents/phd-thesis-master/tese/trabalho
[21:04:39] cwd: c:\Users\victo\Documents\phd-thesis-master\tese
[21:04:39] LaTeX build process spawned. PID: 3576.
[21:04:45] LaTeX log parsed with 7 messages.
[21:04:45] Recipe returns with error: 12/null. PID: 3576. message: Rc files read:
  NONE
Latexmk: This is Latexmk, John Collins, 29 September 2020, version: 4.70b.
Latexmk: In reading rule 'pdflatex' in 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.fdb_latexmk',
  destination has different name than configured...
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  --max-print-line=10000 -synctex=1 -interaction=nonstopmode -file-line-error -recorder -output-directory="c:/Users/victo/Documents/phd-thesis-master/tese"  "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.tex"'
------------
Latexmk: Index file 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx' was written
Latexmk: Found input bbl file 'trabalho.bbl'
Latexmk: Log file says output to 'trabalho.pdf'
Latexmk: Found bibliography file(s) [biblio.bib]
Rule 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx'
------------
Run number 1 of rule 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx'
------------
------------
Running 'makeindex  -o "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind" "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx"'
------------

makeindex.exe: file not writable for security reasons: c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind
Can't create output index file c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind.
Usage: makeindex [-ilqrcgLT] [-s sty] [-o ind] [-t log] [-p num] [idx0 idx1 ...]
Collected error summary (may duplicate other messages):
  makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx: Command for 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx' gave return code 1
      Refer to 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ilg' for details
Latexmk: Use the -f option to force complete processing,
 unless error was exceeding maximum runs, or warnings treated as errors.
.
[21:04:45] The environment variable $PATH: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Windows\System32\OpenSSH\;C:\rtools40\usr\bin;C:\Program Files\MiKTeX\miktex\bin\x64\;C:\Users\victo\AppData\Local\Programs\Python\Python39\Scripts\;C:\Users\victo\AppData\Local\Programs\Python\Python39\;C:\Users\victo\AppData\Local\Microsoft\WindowsApps;;C:\Users\victo\AppData\Local\Programs\Microsoft VS Code\bin
[21:04:45] The environment variable $SHELL: undefined
[21:04:45] Cleaning auxiliary files and retrying build after toolchain error.
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\1-mrf.aux
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\3-bayes-mixed-models.aux
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\apendices.aux
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\2-bayesian-mrf.aux
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\considfinais.aux
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\introducao.aux
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\resumos.aux
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.aux
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.bbl
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.blg
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.ind
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.idx
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.lof
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.lot
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.toc
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.fls
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.log
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.fdb_latexmk
[21:04:45] Recipe step 1: latexmk, --max-print-line=10000,-synctex=1,-interaction=nonstopmode,-file-line-error,-pdf,-outdir=c:/Users/victo/Documents/phd-thesis-master/tese,c:/Users/victo/Documents/phd-thesis-master/tese/trabalho
[21:04:45] cwd: c:\Users\victo\Documents\phd-thesis-master\tese
[21:04:45] LaTeX build process spawned. PID: 10552.
[21:04:46] File watcher - file deleted: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.ind
[21:04:51] LaTeX log parsed with 79 messages.
[21:04:51] Recipe returns with error: 12/null. PID: 10552. message: Rc files read:
  NONE
Latexmk: This is Latexmk, John Collins, 29 September 2020, version: 4.70b.
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  --max-print-line=10000 -synctex=1 -interaction=nonstopmode -file-line-error -recorder -output-directory="c:/Users/victo/Documents/phd-thesis-master/tese"  "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.tex"'
------------
Latexmk: Index file 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx' was written
Latexmk: Non-existent bbl file 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.bbl in line'
 No file trabalho.bbl.
Latexmk: Missing input file: 'trabalho.ind' from line
  'No file trabalho.ind.'
Latexmk: References changed.
Latexmk: References changed.
Latexmk: Log file says output to 'trabalho.pdf'
Latexmk: List of undefined refs and citations:
  Citation `arnold1991pseudolikelihood' on page 20 undefined on input line 161
  Citation `atchade2013bayesian' on page 29 undefined on input line 21
  Citation `besag1974spatial' on page 16 undefined on input line 52
  Citation `besag1975statistical' on page 20 undefined on input line 145
  Citation `besag1982point' on page 17 undefined on input line 68
  Citation `bouranis2017efficient' on page 29 undefined on input line 31
  Citation `cliff1981spatial' on page 16 undefined on input line 52
  Citation `cross1983markov' on page 16 undefined on input line 52
  Citation `freguglia2020hidden' on page 17 undefined on input line 76
  Citation `friedli2017statistical' on page 15 undefined on input line 39
  Citation `geman1984stochastic' on page 16 undefined on input line 52
  Citation `georgii2011gibbs' on page 15 undefined on input line 39
  Citation `geyer1992constrained' on page 24 undefined on input line 329
  Citation `gimel1996texture' on page 16 undefined on input line 52
  Citation `gimel1996texture' on page 17 undefined on input line 76
  Citation `green1995reversible' on page 31 undefined on input line 73
  Citation `hammersley1971markov' on page 14 undefined on input line 33
  Citation `hastings1970monte' on page 29 undefined on input line 15
  Citation `jensen1993asymptotic' on page 20 undefined on input line 159
  Citation `mccoy2014two' on page 16 undefined on input line 52
  Citation `moller2003statistical' on page 17 undefined on input line 68
  Citation `pauli2011bayesian' on page 29 undefined on input line 25
  Citation `propp1996exact' on page 22 undefined on input line 287
  Citation `robbins1951stochastic' on page 22 undefined on input line 297
  Citation `robins2007introduction' on page 17 undefined on input line 68
  Citation `snijders2006new' on page 17 undefined on input line 68
  Citation `strauss1975model' on page 17 undefined on input line 68
  Citation `varin2008composite' on page 20 undefined on input line 145
  Citation `varin2011overview' on page 20 undefined on input line 145
  Citation `wang1990cluster' on page 22 undefined on input line 287
  Citation `wu1982potts' on page 16 undefined on input line 52
  Reference `eq:exponential_family_mrf' on page 16 undefined on input line 52
  Reference `eq:exponential_family_mrf' on page 17 undefined on input line 64
  Reference `eq:exponential_family_mrf' on page 17 undefined on input line 70
  Reference `eq:exponential_family_mrf' on page 17 undefined on input line 74
  Reference `eq:exponential_family_mrf' on page 18 undefined on input line 109
  Reference `eq:exponential_family_mrf' on page 22 undefined on input line 299
  Reference `eq:exponential_family_mrf' on page 24 undefined on input line 307
  Reference `eq:exponential_family_mrf' on page 24 undefined on input line 332
  Reference `eq:exponential_family_mrf' on page 25 undefined on input line 356
  Reference `eq:identifiability' on page 19 undefined on input line 122
  Reference `eq:ising_original' on page 19 undefined on input line 122
  Reference `eq:ising_original' on page 19 undefined on input line 131
  Reference `eq:lhat_gradient' on page 25 undefined on input line 384
  Reference `eq:lhat_gradient' on page 25 undefined on input line 395
  Reference `eq:markov_property' on page 14 undefined on input line 20
  Reference `eq:markov_property' on page 14 undefined on input line 33
  Reference `eq:mrf_factorized' on page 15 undefined on input line 39
  Reference `eq:mrf_factorized' on page 16 undefined on input line 41
  Reference `eq:mrf_factorized' on page 16 undefined on input line 43
  Reference `eq:mrf_factorized' on page 17 undefined on input line 63
  Reference `eq:mrf_pairs' on page 18 undefined on input line 98
  Reference `eq:pl_definition' on page 20 undefined on input line 151
  Reference `ex:pl_gaussian' on page 20 undefined on input line 161
  Reference `ex:pl_gaussian' on page 21 undefined on input line 232
  Reference `ex:pl_ising' on page 20 undefined on input line 161
  Reference `ex:pl_ising' on page 22 undefined on input line 278
  Reference `example:ising_original' on page 19 undefined on input line 120
  Reference `example_mcl' on page 25 undefined on input line 410
  Reference `fig:interactions' on page 18 undefined on input line 89
  Reference `fig:ising_example' on page 22 undefined on input line 282
  Reference `fig:pl_example' on page 21 undefined on input line 227
  Reference `prop:expected_gt' on page 25 undefined on input line 364
  Reference `prop:mcl_convergence' on page 25 undefined on input line 387
  Reference `tab:ising_parameters' on page 19 undefined on input line 122
Latexmk: Found bibliography file(s) [biblio.bib]
Rule 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx'
------------
Run number 1 of rule 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx'
------------
------------
Running 'makeindex  -o "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind" "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx"'
------------

makeindex.exe: file not writable for security reasons: c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind
Can't create output index file c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind.
Usage: makeindex [-ilqrcgLT] [-s sty] [-o ind] [-t log] [-p num] [idx0 idx1 ...]
Latexmk: Summary of warnings from last run of *latex:
  Latex failed to resolve 38 reference(s)
  Latex failed to resolve 31 citation(s)
Collected error summary (may duplicate other messages):
  makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx: Command for 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx' gave return code 1
      Refer to 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ilg' for details
Latexmk: Use the -f option to force complete processing,
 unless error was exceeding maximum runs, or warnings treated as errors.
.
[21:04:51] The environment variable $PATH: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Windows\System32\OpenSSH\;C:\rtools40\usr\bin;C:\Program Files\MiKTeX\miktex\bin\x64\;C:\Users\victo\AppData\Local\Programs\Python\Python39\Scripts\;C:\Users\victo\AppData\Local\Programs\Python\Python39\;C:\Users\victo\AppData\Local\Microsoft\WindowsApps;;C:\Users\victo\AppData\Local\Programs\Microsoft VS Code\bin
[21:04:51] The environment variable $SHELL: undefined
[21:04:53] Current workspace folders: ["file:///c:/Users/victo/Documents/phd-thesis-master"]
[21:04:53] Current workspaceRootDir: c:\Users\victo\Documents\phd-thesis-master
[21:04:53] Found root file from active editor: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:53] Keep using the same root file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:14:51] LOG command invoked.
[21:14:51] Current workspace folders: ["file:///c:/Users/victo/Documents/phd-thesis-master"]
[21:14:51] Current workspaceRootDir: c:\Users\victo\Documents\phd-thesis-master
[21:14:51] Found root file from active editor: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:14:51] Keep using the same root file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex

LaTeX Workshop Output [Required]

[21:04:18] Initializing LaTeX Workshop.
[21:04:18] Extension root: c:\Users\victo\.vscode\extensions\james-yu.latex-workshop-8.14.0
[21:04:18] Creating PDF file watcher.
[21:04:18] pdflatex is provided by MiKTeX
[21:04:18] Creating LaTeX Workshop http and websocket server.
[21:04:18] LaTeX Workshop initialized.
[21:04:18] Current workspace folders: ["file:///c:/Users/victo/Documents/phd-thesis-master"]
[21:04:18] Current workspaceRootDir: c:\Users\victo\Documents\phd-thesis-master
[21:04:18] Server created on 127.0.0.1:50340
[21:04:18] Snippet data loaded.
[21:04:18] LaTeX Workshop version: 8.14.0
[21:04:18] Restoring the PDF viewer at the column 2 from the state: {"type":"state","state":{"path":"c:\\Users\\victo\\Documents\\phd-thesis-master\\tese\\trabalho.pdf","scale":"auto","scrollMode":0,"spreadMode":0,"scrollTop":18800,"scrollLeft":0,"trim":0}}
[21:04:18] Found files that might be root, choose the first one: c:\Users\victo\Documents\phd-thesis-master\vb-mrf\vb2.tex,c:\Users\victo\Documents\phd-thesis-master\vb-mrf\vb-mrf.tex,c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:18] Root file changed: from undefined to c:\Users\victo\Documents\phd-thesis-master\vb-mrf\vb2.tex
[21:04:18] Start to find all dependencies.
[21:04:18] Root file languageId: latex
[21:04:18] Instantiating a new file watcher for c:\Users\victo\Documents\phd-thesis-master\vb-mrf\vb2.tex
[21:04:18] Creating Bib file watcher.
[21:04:18] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\vb-mrf\vb2.tex
[21:04:18] Found .bib file: c:\Users\victo\Documents\phd-thesis-master\tese\biblio.bib
[21:04:18] Added to bib file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\biblio.bib
[21:04:18] Parsing .bib entries from c:\Users\victo\Documents\phd-thesis-master\tese\biblio.bib
[21:04:18] Parse fls file.
[21:04:18] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\vb-mrf\vb2.fls
[21:04:18] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\vb-mrf\vb2.tex
[21:04:18] Parsed 33 bib entries from c:\Users\victo\Documents\phd-thesis-master\tese\biblio.bib.
[21:04:20] Preview PDF file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.pdf
[21:04:21] Handle data type: open
[21:04:21] Handle data type: request_params
[21:04:21] Sending the settings of the PDF viewer for initialization: {"type":"params","scale":"auto","trim":0,"scrollMode":0,"spreadMode":0,"hand":false,"invertMode":{"enabled":false,"brightness":1,"grayscale":0.6,"hueRotate":180,"invert":0,"sepia":0},"bgColor":"#ffffff","keybindings":{"synctex":"ctrl-click"}}
[21:04:21] Handle data type: loaded
[21:04:21] Current workspace folders: ["file:///c:/Users/victo/Documents/phd-thesis-master"]
[21:04:21] Current workspaceRootDir: c:\Users\victo\Documents\phd-thesis-master
[21:04:21] Current workspace folders: ["file:///c:/Users/victo/Documents/phd-thesis-master"]
[21:04:21] Current workspaceRootDir: c:\Users\victo\Documents\phd-thesis-master
[21:04:21] Found root file from active editor: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:21] Found root file from active editor: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:21] Root file changed: from c:\Users\victo\Documents\phd-thesis-master\vb-mrf\vb2.tex to c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:21] Start to find all dependencies.
[21:04:21] Root file languageId: latex
[21:04:21] Root file changed -> cleaning up old file watcher.
[21:04:21] Instantiating a new file watcher for c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\pacotes.tex
[21:04:21] Parse fls file.
[21:04:21] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\tese\pacotes.fls
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\dados.tex
[21:04:21] Parse fls file.
[21:04:21] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\tese\dados.fls
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\configglobal.tex
[21:04:21] Parse fls file.
[21:04:21] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\tese\configglobal.fls
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\resumos.tex
[21:04:21] Parse fls file.
[21:04:21] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\tese\resumos.fls
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\introducao.tex
[21:04:21] Parse fls file.
[21:04:21] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\tese\introducao.fls
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\1-mrf.tex
[21:04:21] Parse fls file.
[21:04:21] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\tese\1-mrf.fls
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\2-bayesian-mrf.tex
[21:04:21] Parse fls file.
[21:04:21] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\tese\2-bayesian-mrf.fls
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\3-bayes-mixed-models.tex
[21:04:21] Parse fls file.
[21:04:21] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\tese\3-bayes-mixed-models.fls
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\considfinais.tex
[21:04:21] Parse fls file.
[21:04:21] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\tese\considfinais.fls
[21:04:21] Parsing a file and its subfiles: c:\Users\victo\Documents\phd-thesis-master\tese\apendices.tex
[21:04:21] Parse fls file.
[21:04:21] Cannot find fls file: c:\Users\victo\Documents\phd-thesis-master\tese\apendices.fls
[21:04:21] Found .bib file: c:\Users\victo\Documents\phd-thesis-master\tese\biblio.bib
[21:04:21] Parse fls file.
[21:04:21] Fls file found: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.fls
[21:04:21] Parse aux file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.aux
[21:04:21] Found .bib file: c:\Users\victo\Documents\phd-thesis-master\tese\biblio.bib
[21:04:21] Parse aux file: c:\Users\victo\Documents\phd-thesis-master\tese\resumos.aux
[21:04:21] Parse aux file: c:\Users\victo\Documents\phd-thesis-master\tese\introducao.aux
[21:04:21] Parse aux file: c:\Users\victo\Documents\phd-thesis-master\tese\1-mrf.aux
[21:04:21] Parse aux file: c:\Users\victo\Documents\phd-thesis-master\tese\2-bayesian-mrf.aux
[21:04:21] Parse aux file: c:\Users\victo\Documents\phd-thesis-master\tese\3-bayes-mixed-models.aux
[21:04:21] Parse aux file: c:\Users\victo\Documents\phd-thesis-master\tese\considfinais.aux
[21:04:21] Parse aux file: c:\Users\victo\Documents\phd-thesis-master\tese\apendices.aux
[21:04:21] Keep using the same root file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\pacotes.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\dados.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\configglobal.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\resumos.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\introducao.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\1-mrf.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\2-bayesian-mrf.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\3-bayes-mixed-models.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\considfinais.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\apendices.tex
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\imecc-unicamp.cls
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\example_cliques.eps
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\example_cliques-eps-converted-to.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\interactions.eps
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\interactions-eps-converted-to.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\pseudolikelihood-example.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\example_ising_vars.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\ising_exd_1.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\ising_exf_1.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\ising_exd_2.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\ising_exf_2.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\ising_exd_3.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\ising_exf_3.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\example_mcl_field.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\triple_plot_pl.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\triple_plot_mcl.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\triple_plot_wl.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\img\triple_plot_mclmixC.pdf
[21:04:21] Added to file watcher: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.ind
[21:04:39] RECIPES command invoked.
[21:04:39] BUILD command invoked.
[21:04:39] The document of the active editor: file:///c%3A/Users/victo/Documents/phd-thesis-master/tese/trabalho.tex
[21:04:39] The languageId of the document: latex
[21:04:39] Current workspace folders: ["file:///c:/Users/victo/Documents/phd-thesis-master"]
[21:04:39] Current workspaceRootDir: c:\Users\victo\Documents\phd-thesis-master
[21:04:39] Found root file from active editor: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:39] Keep using the same root file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:39] Building root file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:39] Build root file c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:39] Recipe step 1: latexmk, --max-print-line=10000,-synctex=1,-interaction=nonstopmode,-file-line-error,-pdf,-outdir=c:/Users/victo/Documents/phd-thesis-master/tese,c:/Users/victo/Documents/phd-thesis-master/tese/trabalho
[21:04:39] cwd: c:\Users\victo\Documents\phd-thesis-master\tese
[21:04:39] LaTeX build process spawned. PID: 3576.
[21:04:45] LaTeX log parsed with 7 messages.
[21:04:45] Recipe returns with error: 12/null. PID: 3576. message: Rc files read:
  NONE
Latexmk: This is Latexmk, John Collins, 29 September 2020, version: 4.70b.
Latexmk: In reading rule 'pdflatex' in 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.fdb_latexmk',
  destination has different name than configured...
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  --max-print-line=10000 -synctex=1 -interaction=nonstopmode -file-line-error -recorder -output-directory="c:/Users/victo/Documents/phd-thesis-master/tese"  "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.tex"'
------------
Latexmk: Index file 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx' was written
Latexmk: Found input bbl file 'trabalho.bbl'
Latexmk: Log file says output to 'trabalho.pdf'
Latexmk: Found bibliography file(s) [biblio.bib]
Rule 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx'
------------
Run number 1 of rule 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx'
------------
------------
Running 'makeindex  -o "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind" "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx"'
------------

makeindex.exe: file not writable for security reasons: c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind
Can't create output index file c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind.
Usage: makeindex [-ilqrcgLT] [-s sty] [-o ind] [-t log] [-p num] [idx0 idx1 ...]
Collected error summary (may duplicate other messages):
  makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx: Command for 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx' gave return code 1
      Refer to 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ilg' for details
Latexmk: Use the -f option to force complete processing,
 unless error was exceeding maximum runs, or warnings treated as errors.
.
[21:04:45] The environment variable $PATH: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Windows\System32\OpenSSH\;C:\rtools40\usr\bin;C:\Program Files\MiKTeX\miktex\bin\x64\;C:\Users\victo\AppData\Local\Programs\Python\Python39\Scripts\;C:\Users\victo\AppData\Local\Programs\Python\Python39\;C:\Users\victo\AppData\Local\Microsoft\WindowsApps;;C:\Users\victo\AppData\Local\Programs\Microsoft VS Code\bin
[21:04:45] The environment variable $SHELL: undefined
[21:04:45] Cleaning auxiliary files and retrying build after toolchain error.
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\1-mrf.aux
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\3-bayes-mixed-models.aux
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\apendices.aux
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\2-bayesian-mrf.aux
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\considfinais.aux
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\introducao.aux
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\resumos.aux
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.aux
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.bbl
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.blg
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.ind
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.idx
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.lof
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.lot
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.toc
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.fls
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.log
[21:04:45] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.fdb_latexmk
[21:04:45] Recipe step 1: latexmk, --max-print-line=10000,-synctex=1,-interaction=nonstopmode,-file-line-error,-pdf,-outdir=c:/Users/victo/Documents/phd-thesis-master/tese,c:/Users/victo/Documents/phd-thesis-master/tese/trabalho
[21:04:45] cwd: c:\Users\victo\Documents\phd-thesis-master\tese
[21:04:45] LaTeX build process spawned. PID: 10552.
[21:04:46] File watcher - file deleted: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.ind
[21:04:51] LaTeX log parsed with 79 messages.
[21:04:51] Recipe returns with error: 12/null. PID: 10552. message: Rc files read:
  NONE
Latexmk: This is Latexmk, John Collins, 29 September 2020, version: 4.70b.
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  --max-print-line=10000 -synctex=1 -interaction=nonstopmode -file-line-error -recorder -output-directory="c:/Users/victo/Documents/phd-thesis-master/tese"  "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.tex"'
------------
Latexmk: Index file 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx' was written
Latexmk: Non-existent bbl file 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.bbl in line'
 No file trabalho.bbl.
Latexmk: Missing input file: 'trabalho.ind' from line
  'No file trabalho.ind.'
Latexmk: References changed.
Latexmk: References changed.
Latexmk: Log file says output to 'trabalho.pdf'
Latexmk: List of undefined refs and citations:
  Citation `arnold1991pseudolikelihood' on page 20 undefined on input line 161
  Citation `atchade2013bayesian' on page 29 undefined on input line 21
  Citation `besag1974spatial' on page 16 undefined on input line 52
  Citation `besag1975statistical' on page 20 undefined on input line 145
  Citation `besag1982point' on page 17 undefined on input line 68
  Citation `bouranis2017efficient' on page 29 undefined on input line 31
  Citation `cliff1981spatial' on page 16 undefined on input line 52
  Citation `cross1983markov' on page 16 undefined on input line 52
  Citation `freguglia2020hidden' on page 17 undefined on input line 76
  Citation `friedli2017statistical' on page 15 undefined on input line 39
  Citation `geman1984stochastic' on page 16 undefined on input line 52
  Citation `georgii2011gibbs' on page 15 undefined on input line 39
  Citation `geyer1992constrained' on page 24 undefined on input line 329
  Citation `gimel1996texture' on page 16 undefined on input line 52
  Citation `gimel1996texture' on page 17 undefined on input line 76
  Citation `green1995reversible' on page 31 undefined on input line 73
  Citation `hammersley1971markov' on page 14 undefined on input line 33
  Citation `hastings1970monte' on page 29 undefined on input line 15
  Citation `jensen1993asymptotic' on page 20 undefined on input line 159
  Citation `mccoy2014two' on page 16 undefined on input line 52
  Citation `moller2003statistical' on page 17 undefined on input line 68
  Citation `pauli2011bayesian' on page 29 undefined on input line 25
  Citation `propp1996exact' on page 22 undefined on input line 287
  Citation `robbins1951stochastic' on page 22 undefined on input line 297
  Citation `robins2007introduction' on page 17 undefined on input line 68
  Citation `snijders2006new' on page 17 undefined on input line 68
  Citation `strauss1975model' on page 17 undefined on input line 68
  Citation `varin2008composite' on page 20 undefined on input line 145
  Citation `varin2011overview' on page 20 undefined on input line 145
  Citation `wang1990cluster' on page 22 undefined on input line 287
  Citation `wu1982potts' on page 16 undefined on input line 52
  Reference `eq:exponential_family_mrf' on page 16 undefined on input line 52
  Reference `eq:exponential_family_mrf' on page 17 undefined on input line 64
  Reference `eq:exponential_family_mrf' on page 17 undefined on input line 70
  Reference `eq:exponential_family_mrf' on page 17 undefined on input line 74
  Reference `eq:exponential_family_mrf' on page 18 undefined on input line 109
  Reference `eq:exponential_family_mrf' on page 22 undefined on input line 299
  Reference `eq:exponential_family_mrf' on page 24 undefined on input line 307
  Reference `eq:exponential_family_mrf' on page 24 undefined on input line 332
  Reference `eq:exponential_family_mrf' on page 25 undefined on input line 356
  Reference `eq:identifiability' on page 19 undefined on input line 122
  Reference `eq:ising_original' on page 19 undefined on input line 122
  Reference `eq:ising_original' on page 19 undefined on input line 131
  Reference `eq:lhat_gradient' on page 25 undefined on input line 384
  Reference `eq:lhat_gradient' on page 25 undefined on input line 395
  Reference `eq:markov_property' on page 14 undefined on input line 20
  Reference `eq:markov_property' on page 14 undefined on input line 33
  Reference `eq:mrf_factorized' on page 15 undefined on input line 39
  Reference `eq:mrf_factorized' on page 16 undefined on input line 41
  Reference `eq:mrf_factorized' on page 16 undefined on input line 43
  Reference `eq:mrf_factorized' on page 17 undefined on input line 63
  Reference `eq:mrf_pairs' on page 18 undefined on input line 98
  Reference `eq:pl_definition' on page 20 undefined on input line 151
  Reference `ex:pl_gaussian' on page 20 undefined on input line 161
  Reference `ex:pl_gaussian' on page 21 undefined on input line 232
  Reference `ex:pl_ising' on page 20 undefined on input line 161
  Reference `ex:pl_ising' on page 22 undefined on input line 278
  Reference `example:ising_original' on page 19 undefined on input line 120
  Reference `example_mcl' on page 25 undefined on input line 410
  Reference `fig:interactions' on page 18 undefined on input line 89
  Reference `fig:ising_example' on page 22 undefined on input line 282
  Reference `fig:pl_example' on page 21 undefined on input line 227
  Reference `prop:expected_gt' on page 25 undefined on input line 364
  Reference `prop:mcl_convergence' on page 25 undefined on input line 387
  Reference `tab:ising_parameters' on page 19 undefined on input line 122
Latexmk: Found bibliography file(s) [biblio.bib]
Rule 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx'
------------
Run number 1 of rule 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx'
------------
------------
Running 'makeindex  -o "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind" "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx"'
------------

makeindex.exe: file not writable for security reasons: c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind
Can't create output index file c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind.
Usage: makeindex [-ilqrcgLT] [-s sty] [-o ind] [-t log] [-p num] [idx0 idx1 ...]
Latexmk: Summary of warnings from last run of *latex:
  Latex failed to resolve 38 reference(s)
  Latex failed to resolve 31 citation(s)
Collected error summary (may duplicate other messages):
  makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx: Command for 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx' gave return code 1
      Refer to 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ilg' for details
Latexmk: Use the -f option to force complete processing,
 unless error was exceeding maximum runs, or warnings treated as errors.
.
[21:04:51] The environment variable $PATH: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Windows\System32\OpenSSH\;C:\rtools40\usr\bin;C:\Program Files\MiKTeX\miktex\bin\x64\;C:\Users\victo\AppData\Local\Programs\Python\Python39\Scripts\;C:\Users\victo\AppData\Local\Programs\Python\Python39\;C:\Users\victo\AppData\Local\Microsoft\WindowsApps;;C:\Users\victo\AppData\Local\Programs\Microsoft VS Code\bin
[21:04:51] The environment variable $SHELL: undefined
[21:04:53] Current workspace folders: ["file:///c:/Users/victo/Documents/phd-thesis-master"]
[21:04:53] Current workspaceRootDir: c:\Users\victo\Documents\phd-thesis-master
[21:04:53] Found root file from active editor: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:04:53] Keep using the same root file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:14:51] LOG command invoked.
[21:14:51] Current workspace folders: ["file:///c:/Users/victo/Documents/phd-thesis-master"]
[21:14:51] Current workspaceRootDir: c:\Users\victo\Documents\phd-thesis-master
[21:14:51] Found root file from active editor: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:14:51] Keep using the same root file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:20:27] RECIPES command invoked.
[21:20:27] BUILD command invoked.
[21:20:27] The document of the active editor: output:extension-output-%232
[21:20:27] The languageId of the document: Log
[21:20:27] Cannot find LaTeX root file.
[21:20:31] Current workspace folders: ["file:///c:/Users/victo/Documents/phd-thesis-master"]
[21:20:31] Current workspaceRootDir: c:\Users\victo\Documents\phd-thesis-master
[21:20:31] Found root file from active editor: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:20:31] Keep using the same root file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:20:33] CLEAN command invoked.
[21:20:33] Current workspace folders: ["file:///c:/Users/victo/Documents/phd-thesis-master"]
[21:20:33] Current workspaceRootDir: c:\Users\victo\Documents\phd-thesis-master
[21:20:33] Found root file from active editor: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:20:33] Keep using the same root file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:20:33] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\1-mrf.aux
[21:20:33] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\3-bayes-mixed-models.aux
[21:20:33] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\apendices.aux
[21:20:33] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\2-bayesian-mrf.aux
[21:20:33] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\considfinais.aux
[21:20:33] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\introducao.aux
[21:20:33] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\resumos.aux
[21:20:33] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.aux
[21:20:33] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.idx
[21:20:33] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.lof
[21:20:33] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.lot
[21:20:33] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.toc
[21:20:33] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.fls
[21:20:33] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.log
[21:20:33] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.fdb_latexmk
[21:20:34] CLEAN command invoked.
[21:20:34] Current workspace folders: ["file:///c:/Users/victo/Documents/phd-thesis-master"]
[21:20:34] Current workspaceRootDir: c:\Users\victo\Documents\phd-thesis-master
[21:20:34] Found root file from active editor: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:20:34] Keep using the same root file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:20:34] CLEAN command invoked.
[21:20:34] Current workspace folders: ["file:///c:/Users/victo/Documents/phd-thesis-master"]
[21:20:34] Current workspaceRootDir: c:\Users\victo\Documents\phd-thesis-master
[21:20:34] Found root file from active editor: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:20:34] Keep using the same root file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:20:35] RECIPES command invoked.
[21:20:35] BUILD command invoked.
[21:20:35] The document of the active editor: file:///c%3A/Users/victo/Documents/phd-thesis-master/tese/trabalho.tex
[21:20:35] The languageId of the document: latex
[21:20:35] Current workspace folders: ["file:///c:/Users/victo/Documents/phd-thesis-master"]
[21:20:35] Current workspaceRootDir: c:\Users\victo\Documents\phd-thesis-master
[21:20:35] Found root file from active editor: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:20:35] Keep using the same root file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:20:35] Building root file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:20:35] Build root file c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:20:35] Recipe step 1: latexmk, --max-print-line=10000,-synctex=1,-interaction=nonstopmode,-file-line-error,-pdf,-outdir=c:/Users/victo/Documents/phd-thesis-master/tese,c:/Users/victo/Documents/phd-thesis-master/tese/trabalho
[21:20:35] cwd: c:\Users\victo\Documents\phd-thesis-master\tese
[21:20:35] LaTeX build process spawned. PID: 8168.
[21:20:35] RECIPES command invoked.
[21:20:35] BUILD command invoked.
[21:20:35] The document of the active editor: file:///c%3A/Users/victo/Documents/phd-thesis-master/tese/trabalho.tex
[21:20:35] The languageId of the document: latex
[21:20:35] Current workspace folders: ["file:///c:/Users/victo/Documents/phd-thesis-master"]
[21:20:35] Current workspaceRootDir: c:\Users\victo\Documents\phd-thesis-master
[21:20:35] Found root file from active editor: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:20:35] Keep using the same root file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:20:35] Building root file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:20:43] LaTeX log parsed with 79 messages.
[21:20:43] Recipe returns with error: 12/null. PID: 8168. message: Rc files read:
  NONE
Latexmk: This is Latexmk, John Collins, 29 September 2020, version: 4.70b.
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  --max-print-line=10000 -synctex=1 -interaction=nonstopmode -file-line-error -recorder -output-directory="c:/Users/victo/Documents/phd-thesis-master/tese"  "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.tex"'
------------
Latexmk: Index file 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx' was written
Latexmk: Non-existent bbl file 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.bbl in line'
 No file trabalho.bbl.
Latexmk: Missing input file: 'trabalho.ind' from line
  'No file trabalho.ind.'
Latexmk: References changed.
Latexmk: References changed.
Latexmk: Log file says output to 'trabalho.pdf'
Latexmk: List of undefined refs and citations:
  Citation `arnold1991pseudolikelihood' on page 20 undefined on input line 161
  Citation `atchade2013bayesian' on page 29 undefined on input line 21
  Citation `besag1974spatial' on page 16 undefined on input line 52
  Citation `besag1975statistical' on page 20 undefined on input line 145
  Citation `besag1982point' on page 17 undefined on input line 68
  Citation `bouranis2017efficient' on page 29 undefined on input line 31
  Citation `cliff1981spatial' on page 16 undefined on input line 52
  Citation `cross1983markov' on page 16 undefined on input line 52
  Citation `freguglia2020hidden' on page 17 undefined on input line 76
  Citation `friedli2017statistical' on page 15 undefined on input line 39
  Citation `geman1984stochastic' on page 16 undefined on input line 52
  Citation `georgii2011gibbs' on page 15 undefined on input line 39
  Citation `geyer1992constrained' on page 24 undefined on input line 329
  Citation `gimel1996texture' on page 16 undefined on input line 52
  Citation `gimel1996texture' on page 17 undefined on input line 76
  Citation `green1995reversible' on page 31 undefined on input line 73
  Citation `hammersley1971markov' on page 14 undefined on input line 33
  Citation `hastings1970monte' on page 29 undefined on input line 15
  Citation `jensen1993asymptotic' on page 20 undefined on input line 159
  Citation `mccoy2014two' on page 16 undefined on input line 52
  Citation `moller2003statistical' on page 17 undefined on input line 68
  Citation `pauli2011bayesian' on page 29 undefined on input line 25
  Citation `propp1996exact' on page 22 undefined on input line 287
  Citation `robbins1951stochastic' on page 22 undefined on input line 297
  Citation `robins2007introduction' on page 17 undefined on input line 68
  Citation `snijders2006new' on page 17 undefined on input line 68
  Citation `strauss1975model' on page 17 undefined on input line 68
  Citation `varin2008composite' on page 20 undefined on input line 145
  Citation `varin2011overview' on page 20 undefined on input line 145
  Citation `wang1990cluster' on page 22 undefined on input line 287
  Citation `wu1982potts' on page 16 undefined on input line 52
  Reference `eq:exponential_family_mrf' on page 16 undefined on input line 52
  Reference `eq:exponential_family_mrf' on page 17 undefined on input line 64
  Reference `eq:exponential_family_mrf' on page 17 undefined on input line 70
  Reference `eq:exponential_family_mrf' on page 17 undefined on input line 74
  Reference `eq:exponential_family_mrf' on page 18 undefined on input line 109
  Reference `eq:exponential_family_mrf' on page 22 undefined on input line 299
  Reference `eq:exponential_family_mrf' on page 24 undefined on input line 307
  Reference `eq:exponential_family_mrf' on page 24 undefined on input line 332
  Reference `eq:exponential_family_mrf' on page 25 undefined on input line 356
  Reference `eq:identifiability' on page 19 undefined on input line 122
  Reference `eq:ising_original' on page 19 undefined on input line 122
  Reference `eq:ising_original' on page 19 undefined on input line 131
  Reference `eq:lhat_gradient' on page 25 undefined on input line 384
  Reference `eq:lhat_gradient' on page 25 undefined on input line 395
  Reference `eq:markov_property' on page 14 undefined on input line 20
  Reference `eq:markov_property' on page 14 undefined on input line 33
  Reference `eq:mrf_factorized' on page 15 undefined on input line 39
  Reference `eq:mrf_factorized' on page 16 undefined on input line 41
  Reference `eq:mrf_factorized' on page 16 undefined on input line 43
  Reference `eq:mrf_factorized' on page 17 undefined on input line 63
  Reference `eq:mrf_pairs' on page 18 undefined on input line 98
  Reference `eq:pl_definition' on page 20 undefined on input line 151
  Reference `ex:pl_gaussian' on page 20 undefined on input line 161
  Reference `ex:pl_gaussian' on page 21 undefined on input line 232
  Reference `ex:pl_ising' on page 20 undefined on input line 161
  Reference `ex:pl_ising' on page 22 undefined on input line 278
  Reference `example:ising_original' on page 19 undefined on input line 120
  Reference `example_mcl' on page 25 undefined on input line 410
  Reference `fig:interactions' on page 18 undefined on input line 89
  Reference `fig:ising_example' on page 22 undefined on input line 282
  Reference `fig:pl_example' on page 21 undefined on input line 227
  Reference `prop:expected_gt' on page 25 undefined on input line 364
  Reference `prop:mcl_convergence' on page 25 undefined on input line 387
  Reference `tab:ising_parameters' on page 19 undefined on input line 122
Latexmk: Found bibliography file(s) [biblio.bib]
Rule 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx'
------------
Run number 1 of rule 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx'
------------
------------
Running 'makeindex  -o "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind" "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx"'
------------

makeindex.exe: file not writable for security reasons: c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind
Can't create output index file c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind.
Usage: makeindex [-ilqrcgLT] [-s sty] [-o ind] [-t log] [-p num] [idx0 idx1 ...]
Latexmk: Summary of warnings from last run of *latex:
  Latex failed to resolve 38 reference(s)
  Latex failed to resolve 31 citation(s)
Collected error summary (may duplicate other messages):
  makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx: Command for 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx' gave return code 1
      Refer to 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ilg' for details
Latexmk: Use the -f option to force complete processing,
 unless error was exceeding maximum runs, or warnings treated as errors.
.
[21:20:43] The environment variable $PATH: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Windows\System32\OpenSSH\;C:\rtools40\usr\bin;C:\Program Files\MiKTeX\miktex\bin\x64\;C:\Users\victo\AppData\Local\Programs\Python\Python39\Scripts\;C:\Users\victo\AppData\Local\Programs\Python\Python39\;C:\Users\victo\AppData\Local\Microsoft\WindowsApps;;C:\Users\victo\AppData\Local\Programs\Microsoft VS Code\bin
[21:20:43] The environment variable $SHELL: undefined
[21:20:43] Cleaning auxiliary files and retrying build after toolchain error.
[21:20:43] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\1-mrf.aux
[21:20:43] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\2-bayesian-mrf.aux
[21:20:43] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\3-bayes-mixed-models.aux
[21:20:43] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\considfinais.aux
[21:20:43] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\introducao.aux
[21:20:43] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\resumos.aux
[21:20:43] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\apendices.aux
[21:20:43] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.aux
[21:20:43] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.idx
[21:20:43] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.lof
[21:20:43] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.lot
[21:20:43] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.toc
[21:20:43] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.fls
[21:20:43] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.log
[21:20:43] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.fdb_latexmk
[21:20:43] Recipe step 1: latexmk, --max-print-line=10000,-synctex=1,-interaction=nonstopmode,-file-line-error,-pdf,-outdir=c:/Users/victo/Documents/phd-thesis-master/tese,c:/Users/victo/Documents/phd-thesis-master/tese/trabalho
[21:20:43] cwd: c:\Users\victo\Documents\phd-thesis-master\tese
[21:20:43] LaTeX build process spawned. PID: 7436.
[21:20:48] LaTeX log parsed with 79 messages.
[21:20:48] Recipe returns with error: 12/null. PID: 7436. message: Rc files read:
  NONE
Latexmk: This is Latexmk, John Collins, 29 September 2020, version: 4.70b.
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  --max-print-line=10000 -synctex=1 -interaction=nonstopmode -file-line-error -recorder -output-directory="c:/Users/victo/Documents/phd-thesis-master/tese"  "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.tex"'
------------
Latexmk: Index file 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx' was written
Latexmk: Non-existent bbl file 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.bbl in line'
 No file trabalho.bbl.
Latexmk: Missing input file: 'trabalho.ind' from line
  'No file trabalho.ind.'
Latexmk: References changed.
Latexmk: References changed.
Latexmk: Log file says output to 'trabalho.pdf'
Latexmk: List of undefined refs and citations:
  Citation `arnold1991pseudolikelihood' on page 20 undefined on input line 161
  Citation `atchade2013bayesian' on page 29 undefined on input line 21
  Citation `besag1974spatial' on page 16 undefined on input line 52
  Citation `besag1975statistical' on page 20 undefined on input line 145
  Citation `besag1982point' on page 17 undefined on input line 68
  Citation `bouranis2017efficient' on page 29 undefined on input line 31
  Citation `cliff1981spatial' on page 16 undefined on input line 52
  Citation `cross1983markov' on page 16 undefined on input line 52
  Citation `freguglia2020hidden' on page 17 undefined on input line 76
  Citation `friedli2017statistical' on page 15 undefined on input line 39
  Citation `geman1984stochastic' on page 16 undefined on input line 52
  Citation `georgii2011gibbs' on page 15 undefined on input line 39
  Citation `geyer1992constrained' on page 24 undefined on input line 329
  Citation `gimel1996texture' on page 16 undefined on input line 52
  Citation `gimel1996texture' on page 17 undefined on input line 76
  Citation `green1995reversible' on page 31 undefined on input line 73
  Citation `hammersley1971markov' on page 14 undefined on input line 33
  Citation `hastings1970monte' on page 29 undefined on input line 15
  Citation `jensen1993asymptotic' on page 20 undefined on input line 159
  Citation `mccoy2014two' on page 16 undefined on input line 52
  Citation `moller2003statistical' on page 17 undefined on input line 68
  Citation `pauli2011bayesian' on page 29 undefined on input line 25
  Citation `propp1996exact' on page 22 undefined on input line 287
  Citation `robbins1951stochastic' on page 22 undefined on input line 297
  Citation `robins2007introduction' on page 17 undefined on input line 68
  Citation `snijders2006new' on page 17 undefined on input line 68
  Citation `strauss1975model' on page 17 undefined on input line 68
  Citation `varin2008composite' on page 20 undefined on input line 145
  Citation `varin2011overview' on page 20 undefined on input line 145
  Citation `wang1990cluster' on page 22 undefined on input line 287
  Citation `wu1982potts' on page 16 undefined on input line 52
  Reference `eq:exponential_family_mrf' on page 16 undefined on input line 52
  Reference `eq:exponential_family_mrf' on page 17 undefined on input line 64
  Reference `eq:exponential_family_mrf' on page 17 undefined on input line 70
  Reference `eq:exponential_family_mrf' on page 17 undefined on input line 74
  Reference `eq:exponential_family_mrf' on page 18 undefined on input line 109
  Reference `eq:exponential_family_mrf' on page 22 undefined on input line 299
  Reference `eq:exponential_family_mrf' on page 24 undefined on input line 307
  Reference `eq:exponential_family_mrf' on page 24 undefined on input line 332
  Reference `eq:exponential_family_mrf' on page 25 undefined on input line 356
  Reference `eq:identifiability' on page 19 undefined on input line 122
  Reference `eq:ising_original' on page 19 undefined on input line 122
  Reference `eq:ising_original' on page 19 undefined on input line 131
  Reference `eq:lhat_gradient' on page 25 undefined on input line 384
  Reference `eq:lhat_gradient' on page 25 undefined on input line 395
  Reference `eq:markov_property' on page 14 undefined on input line 20
  Reference `eq:markov_property' on page 14 undefined on input line 33
  Reference `eq:mrf_factorized' on page 15 undefined on input line 39
  Reference `eq:mrf_factorized' on page 16 undefined on input line 41
  Reference `eq:mrf_factorized' on page 16 undefined on input line 43
  Reference `eq:mrf_factorized' on page 17 undefined on input line 63
  Reference `eq:mrf_pairs' on page 18 undefined on input line 98
  Reference `eq:pl_definition' on page 20 undefined on input line 151
  Reference `ex:pl_gaussian' on page 20 undefined on input line 161
  Reference `ex:pl_gaussian' on page 21 undefined on input line 232
  Reference `ex:pl_ising' on page 20 undefined on input line 161
  Reference `ex:pl_ising' on page 22 undefined on input line 278
  Reference `example:ising_original' on page 19 undefined on input line 120
  Reference `example_mcl' on page 25 undefined on input line 410
  Reference `fig:interactions' on page 18 undefined on input line 89
  Reference `fig:ising_example' on page 22 undefined on input line 282
  Reference `fig:pl_example' on page 21 undefined on input line 227
  Reference `prop:expected_gt' on page 25 undefined on input line 364
  Reference `prop:mcl_convergence' on page 25 undefined on input line 387
  Reference `tab:ising_parameters' on page 19 undefined on input line 122
Latexmk: Found bibliography file(s) [biblio.bib]
Rule 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx'
------------
Run number 1 of rule 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx'
------------
------------
Running 'makeindex  -o "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind" "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx"'
------------

makeindex.exe: file not writable for security reasons: c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind
Can't create output index file c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind.
Usage: makeindex [-ilqrcgLT] [-s sty] [-o ind] [-t log] [-p num] [idx0 idx1 ...]
Latexmk: Summary of warnings from last run of *latex:
  Latex failed to resolve 38 reference(s)
  Latex failed to resolve 31 citation(s)
Collected error summary (may duplicate other messages):
  makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx: Command for 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx' gave return code 1
      Refer to 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ilg' for details
Latexmk: Use the -f option to force complete processing,
 unless error was exceeding maximum runs, or warnings treated as errors.
.
[21:20:48] The environment variable $PATH: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Windows\System32\OpenSSH\;C:\rtools40\usr\bin;C:\Program Files\MiKTeX\miktex\bin\x64\;C:\Users\victo\AppData\Local\Programs\Python\Python39\Scripts\;C:\Users\victo\AppData\Local\Programs\Python\Python39\;C:\Users\victo\AppData\Local\Microsoft\WindowsApps;;C:\Users\victo\AppData\Local\Programs\Microsoft VS Code\bin
[21:20:48] The environment variable $SHELL: undefined
[21:20:48] Build root file c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:20:48] Recipe step 1: latexmk, --max-print-line=10000,-synctex=1,-interaction=nonstopmode,-file-line-error,-pdf,-outdir=c:/Users/victo/Documents/phd-thesis-master/tese,c:/Users/victo/Documents/phd-thesis-master/tese/trabalho
[21:20:48] cwd: c:\Users\victo\Documents\phd-thesis-master\tese
[21:20:48] LaTeX build process spawned. PID: 9940.
[21:20:49] Recipe returns with error: 12/null. PID: 9940. message: Rc files read:
  NONE
Latexmk: This is Latexmk, John Collins, 29 September 2020, version: 4.70b.
Rule 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx': The following rules & subrules became out-of-date:
      'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx'
------------
Run number 1 of rule 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx'
------------
------------
Running 'makeindex  -o "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind" "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx"'
------------

makeindex.exe: file not writable for security reasons: c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind
Can't create output index file c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind.
Usage: makeindex [-ilqrcgLT] [-s sty] [-o ind] [-t log] [-p num] [idx0 idx1 ...]
Collected error summary (may duplicate other messages):
  makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx: Command for 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx' gave return code 1
      Refer to 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ilg' for details
Latexmk: Use the -f option to force complete processing,
 unless error was exceeding maximum runs, or warnings treated as errors.
.
[21:20:49] The environment variable $PATH: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Windows\System32\OpenSSH\;C:\rtools40\usr\bin;C:\Program Files\MiKTeX\miktex\bin\x64\;C:\Users\victo\AppData\Local\Programs\Python\Python39\Scripts\;C:\Users\victo\AppData\Local\Programs\Python\Python39\;C:\Users\victo\AppData\Local\Microsoft\WindowsApps;;C:\Users\victo\AppData\Local\Programs\Microsoft VS Code\bin
[21:20:49] The environment variable $SHELL: undefined
[21:20:49] Cleaning auxiliary files and retrying build after toolchain error.
[21:20:49] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\2-bayesian-mrf.aux
[21:20:49] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\1-mrf.aux
[21:20:49] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\apendices.aux
[21:20:49] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\3-bayes-mixed-models.aux
[21:20:49] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\considfinais.aux
[21:20:49] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\introducao.aux
[21:20:49] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\resumos.aux
[21:20:49] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.aux
[21:20:49] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.idx
[21:20:49] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.lof
[21:20:49] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.lot
[21:20:49] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.toc
[21:20:49] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.fls
[21:20:49] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.log
[21:20:49] File cleaned: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.fdb_latexmk
[21:20:49] Recipe step 1: latexmk, --max-print-line=10000,-synctex=1,-interaction=nonstopmode,-file-line-error,-pdf,-outdir=c:/Users/victo/Documents/phd-thesis-master/tese,c:/Users/victo/Documents/phd-thesis-master/tese/trabalho
[21:20:49] cwd: c:\Users\victo\Documents\phd-thesis-master\tese
[21:20:49] LaTeX build process spawned. PID: 1548.
[21:20:55] LaTeX log parsed with 79 messages.
[21:20:55] Recipe returns with error: 12/null. PID: 1548. message: Rc files read:
  NONE
Latexmk: This is Latexmk, John Collins, 29 September 2020, version: 4.70b.
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  --max-print-line=10000 -synctex=1 -interaction=nonstopmode -file-line-error -recorder -output-directory="c:/Users/victo/Documents/phd-thesis-master/tese"  "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.tex"'
------------
Latexmk: Index file 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx' was written
Latexmk: Non-existent bbl file 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.bbl in line'
 No file trabalho.bbl.
Latexmk: Missing input file: 'trabalho.ind' from line
  'No file trabalho.ind.'
Latexmk: References changed.
Latexmk: References changed.
Latexmk: Log file says output to 'trabalho.pdf'
Latexmk: List of undefined refs and citations:
  Citation `arnold1991pseudolikelihood' on page 20 undefined on input line 161
  Citation `atchade2013bayesian' on page 29 undefined on input line 21
  Citation `besag1974spatial' on page 16 undefined on input line 52
  Citation `besag1975statistical' on page 20 undefined on input line 145
  Citation `besag1982point' on page 17 undefined on input line 68
  Citation `bouranis2017efficient' on page 29 undefined on input line 31
  Citation `cliff1981spatial' on page 16 undefined on input line 52
  Citation `cross1983markov' on page 16 undefined on input line 52
  Citation `freguglia2020hidden' on page 17 undefined on input line 76
  Citation `friedli2017statistical' on page 15 undefined on input line 39
  Citation `geman1984stochastic' on page 16 undefined on input line 52
  Citation `georgii2011gibbs' on page 15 undefined on input line 39
  Citation `geyer1992constrained' on page 24 undefined on input line 329
  Citation `gimel1996texture' on page 16 undefined on input line 52
  Citation `gimel1996texture' on page 17 undefined on input line 76
  Citation `green1995reversible' on page 31 undefined on input line 73
  Citation `hammersley1971markov' on page 14 undefined on input line 33
  Citation `hastings1970monte' on page 29 undefined on input line 15
  Citation `jensen1993asymptotic' on page 20 undefined on input line 159
  Citation `mccoy2014two' on page 16 undefined on input line 52
  Citation `moller2003statistical' on page 17 undefined on input line 68
  Citation `pauli2011bayesian' on page 29 undefined on input line 25
  Citation `propp1996exact' on page 22 undefined on input line 287
  Citation `robbins1951stochastic' on page 22 undefined on input line 297
  Citation `robins2007introduction' on page 17 undefined on input line 68
  Citation `snijders2006new' on page 17 undefined on input line 68
  Citation `strauss1975model' on page 17 undefined on input line 68
  Citation `varin2008composite' on page 20 undefined on input line 145
  Citation `varin2011overview' on page 20 undefined on input line 145
  Citation `wang1990cluster' on page 22 undefined on input line 287
  Citation `wu1982potts' on page 16 undefined on input line 52
  Reference `eq:exponential_family_mrf' on page 16 undefined on input line 52
  Reference `eq:exponential_family_mrf' on page 17 undefined on input line 64
  Reference `eq:exponential_family_mrf' on page 17 undefined on input line 70
  Reference `eq:exponential_family_mrf' on page 17 undefined on input line 74
  Reference `eq:exponential_family_mrf' on page 18 undefined on input line 109
  Reference `eq:exponential_family_mrf' on page 22 undefined on input line 299
  Reference `eq:exponential_family_mrf' on page 24 undefined on input line 307
  Reference `eq:exponential_family_mrf' on page 24 undefined on input line 332
  Reference `eq:exponential_family_mrf' on page 25 undefined on input line 356
  Reference `eq:identifiability' on page 19 undefined on input line 122
  Reference `eq:ising_original' on page 19 undefined on input line 122
  Reference `eq:ising_original' on page 19 undefined on input line 131
  Reference `eq:lhat_gradient' on page 25 undefined on input line 384
  Reference `eq:lhat_gradient' on page 25 undefined on input line 395
  Reference `eq:markov_property' on page 14 undefined on input line 20
  Reference `eq:markov_property' on page 14 undefined on input line 33
  Reference `eq:mrf_factorized' on page 15 undefined on input line 39
  Reference `eq:mrf_factorized' on page 16 undefined on input line 41
  Reference `eq:mrf_factorized' on page 16 undefined on input line 43
  Reference `eq:mrf_factorized' on page 17 undefined on input line 63
  Reference `eq:mrf_pairs' on page 18 undefined on input line 98
  Reference `eq:pl_definition' on page 20 undefined on input line 151
  Reference `ex:pl_gaussian' on page 20 undefined on input line 161
  Reference `ex:pl_gaussian' on page 21 undefined on input line 232
  Reference `ex:pl_ising' on page 20 undefined on input line 161
  Reference `ex:pl_ising' on page 22 undefined on input line 278
  Reference `example:ising_original' on page 19 undefined on input line 120
  Reference `example_mcl' on page 25 undefined on input line 410
  Reference `fig:interactions' on page 18 undefined on input line 89
  Reference `fig:ising_example' on page 22 undefined on input line 282
  Reference `fig:pl_example' on page 21 undefined on input line 227
  Reference `prop:expected_gt' on page 25 undefined on input line 364
  Reference `prop:mcl_convergence' on page 25 undefined on input line 387
  Reference `tab:ising_parameters' on page 19 undefined on input line 122
Latexmk: Found bibliography file(s) [biblio.bib]
Rule 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx'
------------
Run number 1 of rule 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx'
------------
------------
Running 'makeindex  -o "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind" "c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx"'
------------

makeindex.exe: file not writable for security reasons: c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind
Can't create output index file c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ind.
Usage: makeindex [-ilqrcgLT] [-s sty] [-o ind] [-t log] [-p num] [idx0 idx1 ...]
Latexmk: Summary of warnings from last run of *latex:
  Latex failed to resolve 38 reference(s)
  Latex failed to resolve 31 citation(s)
Collected error summary (may duplicate other messages):
  makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx: Command for 'makeindex c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.idx' gave return code 1
      Refer to 'c:/Users/victo/Documents/phd-thesis-master/tese/trabalho.ilg' for details
Latexmk: Use the -f option to force complete processing,
 unless error was exceeding maximum runs, or warnings treated as errors.
.
[21:20:55] The environment variable $PATH: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Windows\System32\OpenSSH\;C:\rtools40\usr\bin;C:\Program Files\MiKTeX\miktex\bin\x64\;C:\Users\victo\AppData\Local\Programs\Python\Python39\Scripts\;C:\Users\victo\AppData\Local\Programs\Python\Python39\;C:\Users\victo\AppData\Local\Microsoft\WindowsApps;;C:\Users\victo\AppData\Local\Programs\Microsoft VS Code\bin
[21:20:55] The environment variable $SHELL: undefined
[21:21:16] LOG command invoked.
[21:21:16] Current workspace folders: ["file:///c:/Users/victo/Documents/phd-thesis-master"]
[21:21:16] Current workspaceRootDir: c:\Users\victo\Documents\phd-thesis-master
[21:21:16] Found root file from active editor: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex
[21:21:16] Keep using the same root file: c:\Users\victo\Documents\phd-thesis-master\tese\trabalho.tex

Developer Tools Console [Required]

Nothing suspicious.

Desktop [Required]

• OS: Windows 10
• VS Code version: 1.51.1 (user setup)
• Extension version: 8.14.0
• TeX distribution version: MiKTeX 2.9.7250

Additional questions

Are you using VSCodium?

No

Are you using LaTeX Workshop with VS Code Remote?

No

Additional context

Works as expected in Linux.