[Rd] Rd parser throws error for user macros invoked with empty argument
Bug or feature?
I get the following error from parse_Rd() when a user Rd macro (including
system ones) is invoked with empty argument {},
eg \mymacro{}:
Error in tools::parse_Rd(fn) :
Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'NULL'
A full example is further below with the system macro \CRANpkg{}. In this
example it doesn't make sense to use empty argument but the error is not
specific to this particular macro.
--
Georgi Boshnakov
Create an Rd file containing system macro \CRANpkg{bibtex}, parse_Rd() is ok:
=
fn <- tempfile()
writeLines("\\name{dummyfun}
\\alias{dummyfun}
\\title{Dummy title}
\\description{Dummy description}
\\usage{
dummyfun(x, ...)
}
\\arguments{
\\item{x}{a value.}
\\item{\\dots}{further arguments.}
}
\\details{
\\CRANpkg{bibtex}
}
", fn)
> tools::parse_Rd(fn)
...
\details{
\href{{https://CRAN.R-project.org/package=bibtex}{\pkg{bibtex}}}
}
With empty argument - \CRANpkg{} - Rd parser throws error. Of course it is
silly in this example but I have used it with other user defined macros where
it may make sense to have empty argument.
> writeLines("\\name{dummyfun}
\\alias{dummyfun}
\\title{Dummy title}
\\description{Dummy description}
\\usage{
dummyfun(x, ...)
}
\\arguments{
\\item{x}{a value.}
\\item{\\dots}{further arguments.}
}
\\details{
\\CRANpkg{}
}
", fn)
> tools::parse_Rd(fn)
Error in tools::parse_Rd(fn) :
Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'NULL'
[[alternative HTML version deleted]]
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Re: [Rd] readLines() behaves differently for gzfile connection
I haven't been able to reproduce the empty lines issue on my Mac or Linux laptop, but I have yet to try that container. The warning is because of a SEEK_SET to -1, which apparently is unsupported by zlib. Maybe the zlib version in that container is getting confused. I'm not sure why readLines() wants to seek to -1 instead of 0, but it only does that on non-blocking connections. The compressed file connections are effectively blocking but are marked as non-blocking. Marking them as blocking removes the warning. I will get that into devel and release soon. Hopefully that fixes the empty lines issue also. Michael On Thu, May 10, 2018 at 4:21 PM, Ben Heavner wrote: > You bet - it's available on github at > https://github.com/UW-GAC/wgsaparsr/blob/master/tests/testthat/1k_annotation.gz > > -Ben > > On Thu, May 10, 2018 at 4:17 PM, Michael Lawrence > wrote: >> >> Would it be possible to get that file or a representative subset of it >> somewhere so that I can reproduce this? >> >> Thanks, >> Michael >> >> On Thu, May 10, 2018 at 3:31 PM, Ben Heavner wrote: >> > When I read a .gz file with readLines() in 3.4.3, it returns text (and a >> > warning). In 3.5.0, it gives a warning, but no text. Is this expected >> > behavior or a bug? >> > >> > 3.4.3: >> >> source_file = "1k_annotation.gz" >> >> readfile_con <- gzfile(source_file, "r") >> >> readLines(readfile_con, n = 5) >> > [1] "#chr\tpos\tref\talt\t >> > >> > >> > >> > Warning message: >> > In readLines(readfile_con, n = 5) : >> > seek on a gzfile connection returned an internal error >> > >> >> close(readfile_con) >> > >> >> sessionInfo() >> > R version 3.4.3 (2017-11-30) >> > Platform: x86_64-apple-darwin15.6.0 (64-bit) >> > Running under: macOS Sierra 10.12.6 >> > >> > Matrix products: default >> > BLAS: >> > >> > /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib >> > LAPACK: >> > >> > /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib >> > >> > locale: >> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> > >> > attached base packages: >> > [1] stats graphics grDevices utils datasets methods base >> > >> > loaded via a namespace (and not attached): >> > [1] compiler_3.4.3 >> > >> > - >> > >> > 3.5.0: >> >> source_file = "1k_annotation.gz" >> >> readfile_con <- gzfile(source_file, "r") >> >> readLines(readfile_con, n = 5) >> > [1] "" "" "" "" "" >> > Warning message: >> > In readLines(readfile_con, n = 5) : >> > seek on a gzfile connection returned an internal error >> >> close(readfile_con) >> >> sessionInfo() >> > R version 3.5.0 (2018-04-23) >> > Platform: x86_64-pc-linux-gnu (64-bit) >> > Running under: Debian GNU/Linux 9 (stretch) >> > >> > Matrix products: default >> > BLAS: /usr/lib/openblas-base/libblas.so.3 >> > LAPACK: /usr/lib/libopenblasp-r0.2.19.so >> > >> > locale: >> > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> > [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 >> > [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=C >> > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> > [9] LC_ADDRESS=C LC_TELEPHONE=C >> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> > >> > attached base packages: >> > [1] stats graphics grDevices utils datasets methods base >> > >> > loaded via a namespace (and not attached): >> > [1] compiler_3.5.0 >> > >> > >> > (note: I'm running 3.5.0 via the docker rocker/tidyverse:3.5 container, >> > and >> > 3.4.3 on my mac desktop machine) >> > >> > Thanks! >> > Ben Heavner >> > >> > [[alternative HTML version deleted]] >> > >> > __ >> > R-devel@r-project.org mailing list >> > https://stat.ethz.ch/mailman/listinfo/r-devel >> > > > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] access an element with empty name
Le 14/05/2018 à 15:55, Kurt Hornik a écrit :
Serguei Sokol writes:
Hi,
I came across a case where I cannot access a list element by its empty name.
Minimal example can be constructed as
x=list("A", 1)
names(x)=c("a", "")
x[["a"]]
#[1] "A"
x[[""]]
#NULL
x$`a`
#[1] "A"
x$``
# Error: attempt to use zero-length variable name
# but we can still access the second element by its index
x[[2]]
#[1] 1
To my mind, it should be perfectly legal to access an element by an
empty name as we can have for example
match("", names(x))
#[1] 2
Hence a traditional question: is it a bug or feature?
A feature according to the docs: ? Extract says
Neither empty (‘""’) nor ‘NA’ indices match any names, not even
empty nor missing names.
Thanks Kurt, I missed that one.
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Re: [Rd] access an element with empty name
> Serguei Sokol writes:
> Hi,
> I came across a case where I cannot access a list element by its empty name.
> Minimal example can be constructed as
> x=list("A", 1)
> names(x)=c("a", "")
> x[["a"]]
> #[1] "A"
> x[[""]]
> #NULL
> x$`a`
> #[1] "A"
> x$``
> # Error: attempt to use zero-length variable name
> # but we can still access the second element by its index
> x[[2]]
> #[1] 1
> To my mind, it should be perfectly legal to access an element by an
> empty name as we can have for example
> match("", names(x))
> #[1] 2
> Hence a traditional question: is it a bug or feature?
A feature according to the docs: ? Extract says
Neither empty (‘""’) nor ‘NA’ indices match any names, not even
empty nor missing names.
-k
> Best,
> Serguei.
>> sessionInfo()
> R version 3.5.0 (2018-04-23)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Mageia 6
> Matrix products: default
> BLAS/LAPACK: /home/opt/OpenBLAS/lib/libopenblas_sandybridge-r0.3.0.dev.so
> locale:
> [1] C
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
> loaded via a namespace (and not attached):
> [1] compiler_3.5.0
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
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[Rd] access an element with empty name
Hi,
I came across a case where I cannot access a list element by its empty name.
Minimal example can be constructed as
x=list("A", 1)
names(x)=c("a", "")
x[["a"]]
#[1] "A"
x[[""]]
#NULL
x$`a`
#[1] "A"
x$``
# Error: attempt to use zero-length variable name
# but we can still access the second element by its index
x[[2]]
#[1] 1
To my mind, it should be perfectly legal to access an element by an
empty name as we can have for example
match("", names(x))
#[1] 2
Hence a traditional question: is it a bug or feature?
Best,
Serguei.
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Mageia 6
Matrix products: default
BLAS/LAPACK: /home/opt/OpenBLAS/lib/libopenblas_sandybridge-r0.3.0.dev.so
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.0
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