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Your call to R_unif_index in

leads to undefined symbol: R_unif_index error since this function is only defined in R 3.4 and publicly introduced as API in R 3.5. In my case, this causes the CI of my package (which depend on Rdpack for creating the documentation) on R 3.3 to fail. This will also cause problems for all package developers that use the Github action workflow in https://github.com/r-lib/actions/blob/master/examples/check-full.yaml for their CI which tests on R 3.3.

You could use the following workaround:

#include <Rversion.h> 
// ...
#if defined(R_VERSION) && R_VERSION >= R_Version(3, 4, 0)
  return floor + ( (int) R_unif_index((double) RAND_MAX)) ) % len;
#else
  return  floor + ( (int) floor(RAND_MAX * unif_rand()) ) % len;
#endif

Note that your solution and my workaround will probably be biased (see section 3 in https://isocpp.org/files/papers/n3551.pdf). A better solution might be the following which should produce random integers in [floor, floor+len) and is consistent with R's way to sample a random integer on R< 3.4 and R >= 3.4:

#include <Rversion.h> 
// ...
#if defined(R_VERSION) && R_VERSION >= R_Version(3, 4, 0)
  return floor + ( (int) R_unif_index((double) len)) );
#else
  return  floor + ( (int) floor(len * unif_rand()) );
#endif

I have an pubmed xml file with more than 500 references.
I tried to convert to bib file using this code:

bibConvert(infile = fn_med, #fn_med: route to my xml file
outfile = "export.bib",
informat = "med",
outformat = "bib")

But I got only 3 references:
$nref_in
[1] 3

$nref_out
[1] 3

How to set the number of references to read from the input file (nref_in) and number of references to write to the output file (nref_out)?

How to read and write all the references from the source file?

Thanks

Hi,

In the latest version 2.2.7, one test is failing on archs other than amd64 and i386 in debian, as can be seen here

It chokes on

more specifically, in the resultant bib file, the last U is missing on two lines:

readLines(tmp_ads) has changed from known value recorded in 'xampl_bib2ads.rds'.
2/313 mismatches
x[293]: "%R ..................."
y[293]: "%R ..................U"

x[300]: "%R 1988..............."
y[300]: "%R 1988..............U"

Could you please fix the problem?

====================================================================================================

CC: @GeoBosh

@misc{x,
author = "P{\'\i}{\'i}"
}

rbibutils::readBib("test.bib", direct=TRUE, encoding = "UTF-8")

produces:

Pí\'i (????).

but it should produce:

Píí (????).

This may be a bug in R itself: https://bugs.r-project.org/show_bug.cgi?id=18208

In case of bibtex entries with italicized codes specified using \emph{}, rbibuitils is converting backslash in \emph to \backslash, resulting in \backslashemph leading to a unknown macro '\backslashemph' error.

bib1 <- "@article{burton_quantitative_1951,
	title = {Quantitative inheritance in pearl millet (\\emph{{Pennisetum} glaucum})},
	volume = {43},
	number = {9},
	journal = {Agronomy Journal},
	author = {Burton, Glenn W.},
	year = {1951},
	pages = {409--417}
}"


bib2 <- "@article{diwan_methods_1995,
  title = {Methods of developing a core collection of annual \\emph{{Medicago}} species},
  volume = {90},
  language = {en},
  number = {6},
  journal = {Theoretical and Applied Genetics},
  author = {Diwan, N. and McIntosh, M. S. and Bauchan, G. R.},
  month = may,
  year = {1995},
  keywords = {Annual Medicago species, Core collection, Germplasm collection, Relative Diversity method},
  pages = {755--761}
}"

rbibutils::charToBib(bib1)
#> Burton GW (1951). "Quantitative inheritance in pearl millet
#> (\backslashemph{{Pennisetum} glaucum})." _Agronomy Journal_, *43*(9),
#> 409-417.
rbibutils::charToBib(bib2)
#> Diwan N, McIntosh MS, Bauchan GR (1995). "Methods of developing a core
#> collection of annual \backslashemph{{Medicago}} species." _Theoretical
#> and Applied Genetics_, *90*(6), 755-761.

@misc{x,
author = "P{\i}{\'\i}{\'i}",
}
@misc{y,
  author = "L P{\i}{\'\i}{\'i}",
}

Save into bug.bib

rbibutils::readBib("test.bib", direct=TRUE, encoding = "UTF-8")

gives:

Pıí\'i (????).

P\i}'i\'i L (????).
Warning messages:
1: In parseLatex(x) : x:1: unexpected END_OF_INPUT 'i'
2: In parseLatex(x) : x:1: unexpected END_OF_INPUT 'i'
3: In withCallingHandlers(.External2(C_parseRd, tcon, srcfile, "UTF-8",  :
  <connection>:2: unexpected END_OF_INPUT ' L (????).
'

Something is removing one opening brace when the author has "firstname lastname".

test.bib:

@misc{x,
author = "P{\'\i}{\'i}"
}
@misc{y,
  author = "L. P{\'\i}{\'i}"
}
@misc{z,
  author = "P{\'\i}{\'i}, L."
}

rbibutils::readBib("test.bib", direct=TRUE, encoding = "UTF-8")

gives:

Pí\'i (????).

P\'i\'i L (????).

P\'i\'i L (????).

that is, having firstname lastname fails to process "'\i" into "í".