[Rd] Strange behaviour of do.call()
The knitr::kable() function does some internal setup, including
determining the target format, and then calls an internal function using
do.call(paste("kable", format, sep = "_"), list(x = x,
caption = caption, escape = escape, ...))
I was interested in setting the `vlign` argument to knitr:::kable_latex,
using this code:
knitr::kable(head(mtcars), format="latex", align = "c", vlign="")
If I debug knitr::kable, I can see that `vlign = ""` is part of
list(...). However, if I debug knitr:::kable_latex, I get weird results:
> debug(knitr:::kable_latex)
> knitr::kable(head(mtcars), format="latex", align = "c", vlign="")
debugging in: kable_latex(x = c("Mazda RX4", "Mazda RX4 Wag", "Datsun
710",
"Hornet 4 Drive", "Hornet Sportabout", "Valiant", "21.0", "21.0",
"22.8", "21.4", "18.7", "18.1", "6", "6", "4", "6", "8", "6",
"160", "160", "108", "258", "360", "225", "110", "110", "93",
"110", "175", "105", "3.90", "3.90", "3.85", "3.08", "3.15",
"2.76", "2.620", "2.875", "2.320", "3.215", "3.440", "3.460",
"16.46", "17.02", "18.61", "19.44", "17.02", "20.22", "0", "0",
"1", "1", "0", "1", "1", "1", "1", "0", "0", "0", "4", "4", "4",
"3", "3", "3", "4", "4", "1", "1", "2", "1"), caption = NULL,
escape = TRUE, vlign = "")
debug: {
[rest of function display omitted]
I see here that vlign = "" is being shown as an argument. However, when
I print vlign, sometimes I get "object not found", and somethings I get
Browse[2]> vline
debug: [1] "|"
(which is what the default value would be). In the latter case, I also see
Browse[2]> list(...)
$vlign
[1] ""
i.e. vlign remains part of the ... list, it wasn't bound to the argument
named vlign.
I can't spot anything particularly strange in the way knitr is handling
this; can anyone else? My sessionInfo() is below.
Duncan Murdoch
> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6.9
Matrix products: default
BLAS:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;
LAPACK version 3.11.0
locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
time zone: America/Toronto
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.3.1 tools_4.3.1knitr_1.44 xfun_0.40
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Re: [Rd] Strange behaviour of do.call()
Sorry, it's a silly thinko. I misspelled the vline argument. Thanks
Ivan for the gentle nudge!
Duncan Murdoch
On 19/09/2023 10:44 a.m., Duncan Murdoch wrote:
The knitr::kable() function does some internal setup, including
determining the target format, and then calls an internal function using
do.call(paste("kable", format, sep = "_"), list(x = x,
caption = caption, escape = escape, ...))
I was interested in setting the `vlign` argument to knitr:::kable_latex,
using this code:
knitr::kable(head(mtcars), format="latex", align = "c", vlign="")
If I debug knitr::kable, I can see that `vlign = ""` is part of
list(...). However, if I debug knitr:::kable_latex, I get weird results:
> debug(knitr:::kable_latex)
> knitr::kable(head(mtcars), format="latex", align = "c", vlign="")
debugging in: kable_latex(x = c("Mazda RX4", "Mazda RX4 Wag", "Datsun
710",
"Hornet 4 Drive", "Hornet Sportabout", "Valiant", "21.0", "21.0",
"22.8", "21.4", "18.7", "18.1", "6", "6", "4", "6", "8", "6",
"160", "160", "108", "258", "360", "225", "110", "110", "93",
"110", "175", "105", "3.90", "3.90", "3.85", "3.08", "3.15",
"2.76", "2.620", "2.875", "2.320", "3.215", "3.440", "3.460",
"16.46", "17.02", "18.61", "19.44", "17.02", "20.22", "0", "0",
"1", "1", "0", "1", "1", "1", "1", "0", "0", "0", "4", "4", "4",
"3", "3", "3", "4", "4", "1", "1", "2", "1"), caption = NULL,
escape = TRUE, vlign = "")
debug: {
[rest of function display omitted]
I see here that vlign = "" is being shown as an argument. However, when
I print vlign, sometimes I get "object not found", and somethings I get
Browse[2]> vline
debug: [1] "|"
(which is what the default value would be). In the latter case, I also see
Browse[2]> list(...)
$vlign
[1] ""
i.e. vlign remains part of the ... list, it wasn't bound to the argument
named vlign.
I can't spot anything particularly strange in the way knitr is handling
this; can anyone else? My sessionInfo() is below.
Duncan Murdoch
> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6.9
Matrix products: default
BLAS:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;
LAPACK version 3.11.0
locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
time zone: America/Toronto
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.3.1 tools_4.3.1knitr_1.44 xfun_0.40
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Re: [Rd] Strange behaviour of do.call()
Le 19/09/2023 à 16:44, Duncan Murdoch a écrit :
The knitr::kable() function does some internal setup, including
determining the target format, and then calls an internal function using
do.call(paste("kable", format, sep = "_"), list(x = x,
caption = caption, escape = escape, ...))
I was interested in setting the `vlign` argument to
knitr:::kable_latex, using this code:
knitr::kable(head(mtcars), format="latex", align = "c", vlign="")
If I debug knitr::kable, I can see that `vlign = ""` is part of
list(...). However, if I debug knitr:::kable_latex, I get weird results:
> debug(knitr:::kable_latex)
> knitr::kable(head(mtcars), format="latex", align = "c", vlign="")
If I do this in my R v4.3.1 on linux, I get:
> debug(knitr:::kable_latex)
> knitr::kable(head(mtcars), format="latex", align = "c", vlign="")
Error in kable_latex(x = c("Mazda RX4", "Mazda RX4 Wag", "Datsun 710", :
unused argument (vlign = "")
By looking at args(knitr:::kable_latex), I see 2 similar arguments
'valign' and 'vline' but no 'vlign'.
Can it be just a typo in your code?
debugging in: kable_latex(x = c("Mazda RX4", "Mazda RX4 Wag", "Datsun
710",
"Hornet 4 Drive", "Hornet Sportabout", "Valiant", "21.0", "21.0",
"22.8", "21.4", "18.7", "18.1", "6", "6", "4", "6", "8", "6",
"160", "160", "108", "258", "360", "225", "110", "110", "93",
"110", "175", "105", "3.90", "3.90", "3.85", "3.08", "3.15",
"2.76", "2.620", "2.875", "2.320", "3.215", "3.440", "3.460",
"16.46", "17.02", "18.61", "19.44", "17.02", "20.22", "0", "0",
"1", "1", "0", "1", "1", "1", "1", "0", "0", "0", "4", "4", "4",
"3", "3", "3", "4", "4", "1", "1", "2", "1"), caption = NULL,
escape = TRUE, vlign = "")
debug: {
[rest of function display omitted]
I see here that vlign = "" is being shown as an argument. However,
when I print vlign, sometimes I get "object not found", and somethings
I get
Browse[2]> vline
debug: [1] "|"
Here again, 'vline' is used on purpose instead of 'vlign'?
Best,
Serguei.
(which is what the default value would be). In the latter case, I
also see
Browse[2]> list(...)
$vlign
[1] ""
i.e. vlign remains part of the ... list, it wasn't bound to the
argument named vlign.
I can't spot anything particularly strange in the way knitr is
handling this; can anyone else? My sessionInfo() is below.
Duncan Murdoch
> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6.9
Matrix products: default
BLAS:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;
LAPACK version 3.11.0
locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
time zone: America/Toronto
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.3.1 tools_4.3.1 knitr_1.44 xfun_0.40
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--
Serguei Sokol
Ingenieur de recherche INRAE
Cellule Mathématiques
TBI, INSA/INRAE UMR 792, INSA/CNRS UMR 5504
135 Avenue de Rangueil
31077 Toulouse Cedex 04
tel: +33 5 61 55 98 49
email: so...@insa-toulouse.fr
https://www.toulouse-biotechnology-institute.fr/en/plateformes-plateaux/cellule-mathematiques/
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