fatal flex scanner internal error--end of buffer missed about bibtex HOT 19 CLOSED

# PR 47 https://github.com/ropensci/bibtex/pull/47

library(bibtex)

# File 1 ----

f1 <- tempfile("file1", fileext = ".txt")

download.file(
  "https://github.com/romainfrancois/bibtex/files/1120203/long_field.txt",
  f1
)

ex1 <- read.bib(f1)
ex1
#> Batzill M (2012). "The Surface Science of Graphene: Metal Interfaces,
#> CVD Synthesis, Nanoribbons, Chemical Modifications, and Defects."
#> _SURFACE SCIENCE REPORTS_, *67*(3-4), 83-115. ISSN 0167-5729, doi:
#> 10.1016/j.surfrep.2011.12.001 (URL:
#> https://doi.org/10.1016/j.surfrep.2011.12.001).

# File 2 ----
f2 <- tempfile("file2", fileext = ".txt")

download.file(
  "https://github.com/romainfrancois/bibtex/files/1120229/jabref_comment.txt",
  f2
)

ex2 <- read.bib(f2)
ex2
#> Gómez RL (2002). "Variability and Detection of Invariant Structure."
#> _Psychological Science_, *13*(5), 431-436. ISSN 0956-7976, 1467-9280,
#> doi: 10.1111/1467-9280.00476 (URL:
#> https://doi.org/10.1111/1467-9280.00476), <URL: 2015-01-20>.

# File 3 -----
f3 <- tempfile("file3", fileext = ".zip")
download.file(
  "https://github.com/romainfrancois/bibtex/files/1229495/soil.health_healthy.soil_1to500.bib.zip",
  f3
)


unzip(f3, junkpaths = TRUE, exdir = tempdir())
ex3 <- read.bib(
  file.path(
    tempdir(),
    "soil.health_healthy.soil_1to500.bib"
  )
)
#> ignoring entry 'ISI:000268383100002' (line 34779) because :
#>  A bibentry of bibtype 'InCollection' has to specify the field: author
#> ignoring entry 'ISI:000268383100003' (line 34853) because :
#>  A bibentry of bibtype 'InCollection' has to specify the field: author
#> ignoring entry 'ISI:000268383100004' (line 34928) because :
#>  A bibentry of bibtype 'InCollection' has to specify the field: author
#> ignoring entry 'ISI:000268383100005' (line 34999) because :
#>  A bibentry of bibtype 'InCollection' has to specify the field: author
#> ignoring entry 'ISI:000268383100006' (line 35080) because :
#>  A bibentry of bibtype 'InCollection' has to specify the field: author
#> ignoring entry 'ISI:000268383100008' (line 35134) because :
#>  A bibentry of bibtype 'InCollection' has to specify the field: author
#> ignoring entry 'ISI:000268383100010' (line 35192) because :
#>  A bibentry of bibtype 'InCollection' has to specify the field: author

length(ex3)
#> [1] 493

# Small sample of entries, since the file has 500 (493 read)

ex3[1:5]
#> FORMAN J (1951). "SOIL, HEALTH, AND THE DENTAL PROFESSION." _JOURNAL OF
#> PROSTHETIC DENTISTRY_, *1*(5), 508-522. ISSN 0022-3913, doi:
#> 10.1016/0022-3913(51)90037-6 (URL:
#> https://doi.org/10.1016/0022-3913(51)90037-6).
#> 
#> SHARMA N, MADAN M (1983). "EARTHWORMS FOR SOIL HEALTH AND
#> POLLUTION-CONTROL." _JOURNAL OF SCIENTIFIC \& INDUSTRIAL RESEARCH_,
#> *42*(10), 575-583. ISSN 0022-4456.
#> 
#> HABERERN J (1992). "A SOIL HEALTH INDEX." _JOURNAL OF SOIL AND WATER
#> CONSERVATION_, *47*(1), 6. ISSN 0022-4561.
#> 
#> [Anonymous] (1993). "THE BREAD CORNER - NO BREAD WITHOUT HEALTHY SOIL."
#> _ALIMENTA_, *32*(3), 45. ISSN 0002-5402.
#> 
#> Watts M (1994). "Pesticide residues in food: The views of the Soil \&
#> Health Association of New Zealand." In Savage, GP (ed.), _PROCEEDINGS
#> OF THE NUTRITION SOCIETY OF NEW ZEALAND, VOL 19_, volume 19 number 0
#> series PROCEEDINGS OF THE NUTRITION SOCIETY OF NEW ZEALAND, 58-63. Nutr
#> Soc New Zealand, ANIMAL \& VETERINARY SCI GROUP, LINCOLN UNIVERSITY, PO
#> BOX 84, CANTERBURY, NEW ZEALAND. 29th Annual Conference of the
#> Nutrition-Society-of-New-Zealand, CHRISTCHURCH, NEW ZEALAND, AUG, 1994.

# From gist ----
gist <- tempfile(fileext = ".bib")

download.file(
  url = "https://gist.githubusercontent.com/kguidonimartins/6ca03106109cef5a891c67748b895e6a/raw/32c0e203de7875a1d13db6705aa9b507914a9fd9/library.bib",
  destfile = gist
)

bibtex::read.bib(file = gist)
#> Vellend M (2001). "Do commonly used indices of $\beta$ -diversity
#> measure species turnover ?" _Journal of Vegetation Science_, *12*,
#> 545-552.
#> 
#> López-Mart\'inez JO, Sanaphre-Villanueva L, Dupuy JM,
#> Hernández-Stefanoni JL, Meave JA, Gallardo-Cruz JA (2013).
#> "$\beta$-Diversity of functional groups of woody plants in a tropical
#> dry forest in Yucatan." _PloS one_, *8*(9), e73660. ISSN 1932-6203,
#> doi: 10.1371/journal.pone.0073660 (URL:
#> https://doi.org/10.1371/journal.pone.0073660), <URL:
#> http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3769343{\&}tool=pmcentrez{\&}rendertype=abstract>.
#> 
#> Swenson NG, Stegen JC, Davies SJ, Erickson DL, Forero-Montaña J,
#> Hurlbert AH, Kress WJ, Thompson J, Uriarte M, Wright SJ, Zimmerman JK
#> (2012). "Temporal turnover in the composition of tropical tree
#> communities: functional determinism and phylogenetic stochasticity."
#> _Ecology_, *93*(3), 490-499. ISSN 0012-9658, doi: 10.1890/11-1180.1
#> (URL: https://doi.org/10.1890/11-1180.1), <URL:
#> http://doi.wiley.com/10.1890/11-1180.1>.

bibtex::read.bib("long_field.txt")
#> Error: lex fatal error:
#> input buffer overflow, can't enlarge buffer because scanner uses REJECT

bibtex::read.bib("jabref_comment.txt")
#> Error: lex fatal error:
#> input buffer overflow, can't enlarge buffer because scanner uses REJECT

download.file(url = "https://gist.githubusercontent.com/kguidonimartins/6ca03106109cef5a891c67748b895e6a/raw/32c0e203de7875a1d13db6705aa9b507914a9fd9/library.bib", 
              destfile = "library.bib")

bibtex::read.bib(file = "library.bib")

RefManageR::ReadBib(file = "library.bib")

download.file(url = "https://gist.githubusercontent.com/kguidonimartins/6ca03106109cef5a891c67748b895e6a/raw/32c0e203de7875a1d13db6705aa9b507914a9fd9/library.bib", 
              destfile = "library.bib")
bibtex::read.bib(file = "library.bib")
#> Vellend M (2001). "Do commonly used indices of $\beta$ -diversity
#> measure species turnover ?" _Journal of Vegetation Science_, *12*,
#> pp. 545-552.
#> 
#> López-Mart\'inez JO, Sanaphre-Villanueva L, Dupuy JM,
#> Hernández-Stefanoni JL, Meave JA and Gallardo-Cruz JA (2013).
#> "$\beta$-Diversity of functional groups of woody plants in a
#> tropical dry forest in Yucatan." _PloS one_, *8*(9), pp. e73660.
#> ISSN 1932-6203, doi: 10.1371/journal.pone.0073660 (URL:
#> http://doi.org/10.1371/journal.pone.0073660), <URL:
#> http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3769343{\&}tool=pmcentrez{\&}rendertype=abstract>.
#> 
#> Swenson NG, Stegen JC, Davies SJ, Erickson DL, Forero-Montaña J,
#> Hurlbert AH, Kress WJ, Thompson J, Uriarte M, Wright SJ and
#> Zimmerman JK (2012). "Temporal turnover in the composition of
#> tropical tree communities: functional determinism and phylogenetic
#> stochasticity." _Ecology_, *93*(3), pp. 490-499. ISSN 0012-9658,
#> doi: 10.1890/11-1180.1 (URL: http://doi.org/10.1890/11-1180.1),
#> <URL: http://doi.wiley.com/10.1890/11-1180.1>.

RefManageR::ReadBib(file = "library.bib")
#> Warning in parse_Rd(Rd, encoding = encoding, fragment = fragment, ...):
#> <connection>:3: unknown macro '\beta'
#> Warning in parse_Rd(Rd, encoding = encoding, fragment = fragment, ...):
#> <connection>:3: unknown macro '\beta'
#> [1] J. O. López-Mart\'inez, L. Sanaphre-Villanueva, J. M. Dupuy,
#> et al. "$\beta$-Diversity of functional groups of woody plants in
#> a tropical dry forest in Yucatan.". In: _PloS one_ 8.9 (Jan.
#> 2013), p. e73660. ISSN: 1932-6203. DOI:
#> 10.1371/journal.pone.0073660. <URL:
#> http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3769343{\&}tool=pmcentrez{\&}rendertype=abstract>.
#> 
#> [2] N. G. Swenson, J. C. Stegen, S. J. Davies, et al. "Temporal
#> turnover in the composition of tropical tree communities:
#> functional determinism and phylogenetic stochasticity". In:
#> _Ecology_ 93.3 (Mar. 2012), pp. 490-499. ISSN: 0012-9658. DOI:
#> 10.1890/11-1180.1. <URL: http://doi.wiley.com/10.1890/11-1180.1>.
#> 
#> [3] M. Vellend. "Do commonly used indices of $\beta$ -diversity
#> measure species turnover ?". In: _Journal of Vegetation Science_
#> 12 (2001), pp. 545-552.