Re: [Rd] bug in utils:::format.person
> Achim Zeileis writes:
Thanks---Ivan's fix committed now with c84497.
Best
-k
> Apologies, I missed Ivan's fix to the problem (my day was too long...)
> which is, of course, better than mine.
> On Sat, 3 Jun 2023, Achim Zeileis wrote:
>> Thierry,
>>
>> thanks for this, this is a bug in utils:::.format_person_as_R_code(). This
>> calls deparse() on the elements of the person object with the default
>> width.cutoff = 60. As your comment exceeds this width, the erroneous
>> formatting is produced. The simplest reproducible example I could come up
>> with was:
>>
>> p <- person(".", comment = c(foo = ".",
>> bar = "."))
>> writeLines(format(p, style = "R"))
>>
>> This can be fixed in line 1017 of utils/R/citation.R either by increasing
>> the
>> width.cutoff, e.g.,
>>
>> sprintf("%s = %s", names(e), sapply(e, deparse, width.cutoff = 500L))
>>
>> but, of course, this still has an arbitrary cutoff. So maybe better
>>
>> sprintf("%s = %s", names(e), sapply(e,
>> function(x) paste(deparse(x), collapse = "")))
>>
>> which should work.
>>
>> I'll ping Kurt about this and try to coordinate a fix.
>>
>> Best wishes,
>> Achim
>>
>>
>> On Fri, 2 Jun 2023, Thierry Onkelinx via R-devel wrote:
>>
>>> Dear all,
>>>
>>> I think I found a bug in utils::format.person when using style = "R" with a
>>> vector of comments. The comment section is not parsed properly. Please find
>>> below the mwe and the session info.
>>>
>>> Best regards,
>>>
>>> Thierry
>>>
>>> maintainer <- person(
>>> given = "Thierry", family = "Onkelinx", role = c("aut", "cre"),
>>> email = "thierry.onkel...@inbo.be",
>>> comment = c(
>>> ORCID = "-0001-8804-4216",
>>> affiliation = "Research Institute for Nature and Forest (INBO)"
>>> )
>>> )
>>> format(maintainer, style = "R") |>
>>> cat(sep = "\n")
>>> # output
>>> person(given = "Thierry",
>>> family = "Onkelinx",
>>> role = c("aut", "cre"),
>>> email = "thierry.onkel...@inbo.be",
>>> comment = c("c(ORCID = \"-0001-8804-4216\", affiliation =
>>> \"Research Institute for Nature and Forest (INBO)\"", ")"))
>>>
>>> ─ Session info
>>> ──
>>> setting value
>>> version R version 4.3.0 (2023-04-21)
>>> os Ubuntu 22.04.2 LTS
>>> system x86_64, linux-gnu
>>> ui X11
>>> language nl_BE:nl
>>> collate nl_BE.UTF-8
>>> ctypenl_BE.UTF-8
>>> tz Europe/Brussels
>>> date 2023-06-02
>>> pandoc NA
>>>
>>> ─ Packages
>>> ──
>>> package * version date (UTC) lib source
>>> cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0)
>>> fortunes 1.5-4 2016-12-29 [1] CRAN (R 4.3.0)
>>> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0)
>>>
>>>
>>>
>>> ir. Thierry Onkelinx
>>> Statisticus / Statistician
>>>
>>> Vlaamse Overheid / Government of Flanders
>>> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
>>> FOREST
>>> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
>>> thierry.onkel...@inbo.be
>>> Havenlaan 88 bus 73, 1000 Brussel
>>> www.inbo.be
>>>
>>> ///
>>> To call in the statistician after the experiment is done may be no more
>>> than asking him to perform a post-mortem examination: he may be able to say
>>> what the experiment died of. ~ Sir Ronald Aylmer Fisher
>>> The plural of anecdote is not data. ~ Roger Brinner
>>> The combination of some data and an aching desire for an answer does not
>>> ensure that a reasonable answer can be extracted from a given body of data.
>>> ~ John Tukey
>>> ///
>>>
>>>
>>>
>>> [[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
>>
> __
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Re: [Rd] bug in utils:::format.person
Apologies, I missed Ivan's fix to the problem (my day was too long...)
which is, of course, better than mine.
On Sat, 3 Jun 2023, Achim Zeileis wrote:
Thierry,
thanks for this, this is a bug in utils:::.format_person_as_R_code(). This
calls deparse() on the elements of the person object with the default
width.cutoff = 60. As your comment exceeds this width, the erroneous
formatting is produced. The simplest reproducible example I could come up
with was:
p <- person(".", comment = c(foo = ".",
bar = "."))
writeLines(format(p, style = "R"))
This can be fixed in line 1017 of utils/R/citation.R either by increasing the
width.cutoff, e.g.,
sprintf("%s = %s", names(e), sapply(e, deparse, width.cutoff = 500L))
but, of course, this still has an arbitrary cutoff. So maybe better
sprintf("%s = %s", names(e), sapply(e,
function(x) paste(deparse(x), collapse = "")))
which should work.
I'll ping Kurt about this and try to coordinate a fix.
Best wishes,
Achim
On Fri, 2 Jun 2023, Thierry Onkelinx via R-devel wrote:
Dear all,
I think I found a bug in utils::format.person when using style = "R" with a
vector of comments. The comment section is not parsed properly. Please find
below the mwe and the session info.
Best regards,
Thierry
maintainer <- person(
given = "Thierry", family = "Onkelinx", role = c("aut", "cre"),
email = "thierry.onkel...@inbo.be",
comment = c(
ORCID = "-0001-8804-4216",
affiliation = "Research Institute for Nature and Forest (INBO)"
)
)
format(maintainer, style = "R") |>
cat(sep = "\n")
# output
person(given = "Thierry",
family = "Onkelinx",
role = c("aut", "cre"),
email = "thierry.onkel...@inbo.be",
comment = c("c(ORCID = \"-0001-8804-4216\", affiliation =
\"Research Institute for Nature and Forest (INBO)\"", ")"))
─ Session info
──
setting value
version R version 4.3.0 (2023-04-21)
os Ubuntu 22.04.2 LTS
system x86_64, linux-gnu
ui X11
language nl_BE:nl
collate nl_BE.UTF-8
ctypenl_BE.UTF-8
tz Europe/Brussels
date 2023-06-02
pandoc NA
─ Packages
──
package * version date (UTC) lib source
cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0)
fortunes 1.5-4 2016-12-29 [1] CRAN (R 4.3.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0)
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be
///
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
///
[[alternative HTML version deleted]]
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Re: [Rd] bug in utils:::format.person
Thierry,
thanks for this, this is a bug in utils:::.format_person_as_R_code(). This
calls deparse() on the elements of the person object with the default
width.cutoff = 60. As your comment exceeds this width, the erroneous
formatting is produced. The simplest reproducible example I could come up
with was:
p <- person(".", comment = c(foo = ".",
bar = "."))
writeLines(format(p, style = "R"))
This can be fixed in line 1017 of utils/R/citation.R either by increasing
the width.cutoff, e.g.,
sprintf("%s = %s", names(e), sapply(e, deparse, width.cutoff = 500L))
but, of course, this still has an arbitrary cutoff. So maybe better
sprintf("%s = %s", names(e), sapply(e,
function(x) paste(deparse(x), collapse = "")))
which should work.
I'll ping Kurt about this and try to coordinate a fix.
Best wishes,
Achim
On Fri, 2 Jun 2023, Thierry Onkelinx via R-devel wrote:
Dear all,
I think I found a bug in utils::format.person when using style = "R" with a
vector of comments. The comment section is not parsed properly. Please find
below the mwe and the session info.
Best regards,
Thierry
maintainer <- person(
given = "Thierry", family = "Onkelinx", role = c("aut", "cre"),
email = "thierry.onkel...@inbo.be",
comment = c(
ORCID = "-0001-8804-4216",
affiliation = "Research Institute for Nature and Forest (INBO)"
)
)
format(maintainer, style = "R") |>
cat(sep = "\n")
# output
person(given = "Thierry",
family = "Onkelinx",
role = c("aut", "cre"),
email = "thierry.onkel...@inbo.be",
comment = c("c(ORCID = \"-0001-8804-4216\", affiliation =
\"Research Institute for Nature and Forest (INBO)\"", ")"))
─ Session info
──
setting value
version R version 4.3.0 (2023-04-21)
os Ubuntu 22.04.2 LTS
system x86_64, linux-gnu
ui X11
language nl_BE:nl
collate nl_BE.UTF-8
ctypenl_BE.UTF-8
tz Europe/Brussels
date 2023-06-02
pandoc NA
─ Packages
──
package * version date (UTC) lib source
cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0)
fortunes 1.5-4 2016-12-29 [1] CRAN (R 4.3.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0)
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be
///
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
///
[[alternative HTML version deleted]]
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Re: [Rd] bug in utils:::format.person
On Fri, 2 Jun 2023 16:55:59 +0200
Thierry Onkelinx via R-devel wrote:
> I think I found a bug in utils::format.person when using style = "R"
> with a vector of comments. The comment section is not parsed
> properly.
Good catch! This looks like another occasion of deparse() suddenly
returning a multi-element character vector where the caller expects a
single string:
format(person(c('J.', 'Random'), 'Hacker', comment = c(ORCID =
'---', foo = 'bar bar bar bar bar')), style = 'R')
# [1] "person(given = c(\"J.\", \"Random\"),"
# [2] " family = \"Hacker\","
# [3] " comment = c(ORCID = \"---\", foo = \"bar
# bar bar bar bar\"))"
format(person(c('J.', 'Random'), 'Hacker', comment = c(ORCID =
'---', foo = 'bar bar bar bar bar bar')), style = 'R')
# [1] "person(given = c(\"J.\", \"Random\"),"
# [2] " family = \"Hacker\","
# [3] " comment = c(\"c(ORCID = \\\"---\\\", foo =
# \\\"bar bar bar bar bar bar\\\"\", \")\"))"
The following seems to fix it:
--- src/library/utils/R/citation.R (revision 84486)
+++ src/library/utils/R/citation.R (working copy)
@@ -1014,7 +1014,7 @@
function(e) {
e <- e[!vapply(e, is.null, NA)]
cargs <-
-sprintf("%s = %s", names(e), sapply(e, deparse))
+sprintf("%s = %s", names(e), sapply(e, deparse1))
.format_call_RR("person", cargs)
})
if(length(s) > 1L)
A regression test could be along the lines of:
p <- person(
'foo', 'bar', comment = c(
comment = 'just enough to deparse into multiple lines',
needs = 'multiple entries'
)
)
stopifnot(all.equal(
eval(parse(text = format(p, style = 'R')))$comment,
p$comment
))
--
Best regards,
Ivan
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[Rd] bug in utils:::format.person
Dear all,
I think I found a bug in utils::format.person when using style = "R" with a
vector of comments. The comment section is not parsed properly. Please find
below the mwe and the session info.
Best regards,
Thierry
maintainer <- person(
given = "Thierry", family = "Onkelinx", role = c("aut", "cre"),
email = "thierry.onkel...@inbo.be",
comment = c(
ORCID = "-0001-8804-4216",
affiliation = "Research Institute for Nature and Forest (INBO)"
)
)
format(maintainer, style = "R") |>
cat(sep = "\n")
# output
person(given = "Thierry",
family = "Onkelinx",
role = c("aut", "cre"),
email = "thierry.onkel...@inbo.be",
comment = c("c(ORCID = \"-0001-8804-4216\", affiliation =
\"Research Institute for Nature and Forest (INBO)\"", ")"))
─ Session info
──
setting value
version R version 4.3.0 (2023-04-21)
os Ubuntu 22.04.2 LTS
system x86_64, linux-gnu
ui X11
language nl_BE:nl
collate nl_BE.UTF-8
ctypenl_BE.UTF-8
tz Europe/Brussels
date 2023-06-02
pandoc NA
─ Packages
──
package * version date (UTC) lib source
cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0)
fortunes 1.5-4 2016-12-29 [1] CRAN (R 4.3.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0)
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be
///
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
///
[[alternative HTML version deleted]]
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