[Rd] paste(character(0), collapse="", recycle0=FALSE) should be ""
Hervé Pagès
hp@ge@ @end|ng |rom |redhutch@org
Sat May 23 00:16:09 CEST 2020
Gabe,
It's the current behavior of paste() that is a major source of bugs:
## Add "rs" prefix to SNP ids and collapse them in a
## comma-separated string.
collapse_snp_ids <- function(snp_ids)
paste("rs", snp_ids, sep="", collapse=",")
snp_groups <- list(
group1=c(55, 22, 200),
group2=integer(0),
group3=c(99, 550)
)
vapply(snp_groups, collapse_snp_ids, character(1))
# group1 group2 group3
# "rs55,rs22,rs200" "rs" "rs99,rs550"
This has hit me so many times!
Now with 'collapse0=TRUE', we finally have the opportunity to make it do
the right thing. Let's not miss that opportunity.
Cheers,
H.
On 5/22/20 11:26, Gabriel Becker wrote:
> I understand that this is consistent but it also strikes me as an
> enormous 'gotcha' of a magnitude that 'we' are trying to avoid/smooth
> over at this point in user-facing R space.
>
> For the record I'm not suggesting it should return something other than
> "", and in particular I'm not arguing that any call to paste /that does
> not return an error/ with non-NULL collapse should return a character
> vector of length one.
>
> Rather I'm pointing out that it could (perhaps should, imo) simply be an
> error, which is also consistent, in the strict sense, with
> previous behavior in that it is the developer simply declining to extend
> the recycle0 argument to the full parameter space (there is no rule that
> says we must do so, arguments whose use is incompatible with other
> arguments can be reasonable and called for).
>
> I don't feel feel super strongly that reeturning "" in this and similar
> cases horrible and should never happen, but i'd bet dollars to donuts
> that to the extent that behavior occurs it will be a disproportionately
> major source of bugs, and i think thats at least worth considering in
> addition to pure consistency.
>
> ~G
>
> On Fri, May 22, 2020 at 9:50 AM William Dunlap <wdunlap using tibco.com
> <mailto:wdunlap using tibco.com>> wrote:
>
> I agree with Herve, processing collapse happens last so
> collapse=non-NULL always leads to a single character string being
> returned, the same as paste(collapse=""). See the altPaste function
> I posted yesterday.
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__tibco.com&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Z1o-HO3_OqxOR9LaRguGvnG7X4vF_z1_q13I7zmjcfY&s=7ZT1IjmexPqsDBhrV3NspPTr8M8XiMweEwJWErgAlqw&e=>
>
>
> On Fri, May 22, 2020 at 9:12 AM Hervé Pagès <hpages using fredhutch.org
> <mailto:hpages using fredhutch.org>> wrote:
>
> I think that
>
> paste(c("a", "b"), NULL, c("c", "d"), sep = " ", collapse
> = ",",
> recycle0=TRUE)
>
> should just return an empty string and don't see why it needs to
> emit a
> warning or raise an error. To me it does exactly what the user
> is asking
> for, which is to change how the 3 arguments are recycled
> **before** the
> 'sep' operation.
>
> The 'recycle0' argument has no business in the 'collapse' operation
> (which comes after the 'sep' operation): this operation still
> behaves
> like it always had.
>
> That's all there is to it.
>
> H.
>
>
> On 5/22/20 03:00, Gabriel Becker wrote:
> > Hi Martin et al,
> >
> >
> >
> > On Thu, May 21, 2020 at 9:42 AM Martin Maechler
> > <maechler using stat.math.ethz.ch
> <mailto:maechler using stat.math.ethz.ch>
> <mailto:maechler using stat.math.ethz.ch
> <mailto:maechler using stat.math.ethz.ch>>> wrote:
> >
> > >>>>> Hervé Pagès
> > >>>>> on Fri, 15 May 2020 13:44:28 -0700 writes:
> >
> > > There is still the situation where **both** 'sep' and
> > 'collapse' are
> > > specified:
> >
> > >> paste(integer(0), "nth", sep="", collapse=",")
> > > [1] "nth"
> >
> > > In that case 'recycle0' should **not** be ignored i.e.
> >
> > > paste(integer(0), "nth", sep="", collapse=",",
> recycle0=TRUE)
> >
> > > should return the empty string (and not
> character(0) like it
> > does at the
> > > moment).
> >
> > > In other words, 'recycle0' should only control the
> first
> > operation (the
> > > operation controlled by 'sep'). Which makes plenty
> of sense:
> > the 1st
> > > operation is binary (or n-ary) while the collapse
> operation
> > is unary.
> > > There is no concept of recycling in the context of
> unary
> > operations.
> >
> > Interesting, ..., and sounding somewhat convincing.
> >
> > > On 5/15/20 11:25, Gabriel Becker wrote:
> > >> Hi all,
> > >>
> > >> This makes sense to me, but I would think that
> recycle0 and
> > collapse
> > >> should actually be incompatible and paste should
> throw an
> > error if
> > >> recycle0 were TRUE and collapse were declared in
> the same
> > call. I don't
> > >> think the value of recycle0 should be silently
> ignored if it
> > is actively
> > >> specified.
> > >>
> > >> ~G
> >
> > Just to summarize what I think we should know and agree
> (or be
> > be "disproven") and where this comes from ...
> >
> > 1) recycle0 is a new R 4.0.0 option in paste() / paste0()
> which by
> > default
> > (recycle0 = FALSE) should (and *does* AFAIK) not
> change anything,
> > hence paste() / paste0() behave completely
> back-compatible
> > if recycle0 is kept to FALSE.
> >
> > 2) recycle0 = TRUE is meant to give different behavior,
> notably
> > 0-length arguments (among '...') should result in
> 0-length results.
> >
> > The above does not specify what this means in detail,
> see 3)
> >
> > 3) The current R 4.0.0 implementation (for which I'm
> primarily
> > responsible)
> > and help(paste) are in accordance.
> > Notably the help page (Arguments -> 'recycle0' ;
> Details 1st
> > para ; Examples)
> > says and shows how the 4.0.0 implementation has been
> meant to work.
> >
> > 4) Several provenly smart members of the R community
> argue that
> > both the implementation and the documentation of
> 'recycle0 =
> > TRUE' should be changed to be more logical /
> coherent / sensical ..
> >
> > Is the above all correct in your view?
> >
> > Assuming yes, I read basically two proposals, both agreeing
> > that recycle0 = TRUE should only ever apply to the
> action of 'sep'
> > but not the action of 'collapse'.
> >
> > 1) Bill and Hervé (I think) propose that 'recycle0'
> should have
> > no effect whenever 'collapse = <string>'
> >
> > 2) Gabe proposes that 'collapse = <string>' and 'recycle0
> = TRUE'
> > should be declared incompatible and error. If going
> in that
> > direction, I could also see them to give a warning (and
> > continue as if recycle = FALSE).
> >
> >
> > Herve makes a good point about when sep and collapse are both
> set. That
> > said, if the user explicitly sets recycle0, Personally, I
> don't think it
> > should be silently ignored under any configuration of other
> arguments.
> >
> > If all of the arguments are to go into effect, the question
> then becomes
> > one of ordering, I think.
> >
> > Consider
> >
> > paste(c("a", "b"), NULL, c("c", "d"), sep = " ",
> collapse = ",",
> > recycle0=TRUE)
> >
> > Currently that returns character(0), becuase the logic is
> > essenttially (in pseudo-code)
> >
> > collapse(paste(c("a", "b"), NULL, c("c", "d"), sep = " ",
> > recycle0=TRUE), collapse = ", ", recycle0=TRUE)
> >
> > -> collapse(character(0), collapse = ", " recycle0=TRUE)
> >
> > -> character(0)
> >
> > Now Bill Dunlap argued, fairly convincingly I think, that
> paste(...,
> > collapse=<string>) should /always/ return a character vector
> of length
> > exactly one. With recycle0, though, it will return "" via
> the progression
> >
> > paste(c("a", "b"), NULL, c("c", "d"), sep = " ",
> collapse = ",",
> > recycle0=TRUE)
> >
> > -> collapse(character(0), collapse = ", ")
> >
> > -> ""
> >
> >
> > because recycle0 is still applied to the sep-based operation
> which
> > occurs before collapse, thus leaving a vector of length 0 to
> collapse.
> >
> > That is consistent but seems unlikely to be what the user
> wanted, imho.
> > I think if it does this there should be at least a warning
> when paste
> > collapses to "" this way, if it is allowed at all (ie if mixing
> > collapse=<string>and recycle0=TRUEis not simply made an error).
> >
> > I would like to hear others' thoughts as well though. @Pages,
> Herve
> > <mailto:hpages using fredhutch.org <mailto:hpages using fredhutch.org>>
> @William Dunlap
> > <mailto:wdunlap using tibco.com <mailto:wdunlap using tibco.com>> is ""
> what you envision as thee desired and
> > useful behavior there?
> >
> > Best,
> > ~G
> >
> >
> >
> > I have not yet my mind up but would tend to agree to "you
> guys",
> > but I think that other R Core members should chime in, too.
> >
> > Martin
> >
> > >> On Fri, May 15, 2020 at 11:05 AM Hervé Pagès
> > <hpages using fredhutch.org <mailto:hpages using fredhutch.org>
> <mailto:hpages using fredhutch.org <mailto:hpages using fredhutch.org>>
> > >> <mailto:hpages using fredhutch.org
> <mailto:hpages using fredhutch.org> <mailto:hpages using fredhutch.org
> <mailto:hpages using fredhutch.org>>>>
> > wrote:
> > >>
> > >> Totally agree with that.
> > >>
> > >> H.
> > >>
> > >> On 5/15/20 10:34, William Dunlap via R-devel wrote:
> > >> > I agree: paste(collapse="something", ...)
> should always
> > return a
> > >> single
> > >> > character string, regardless of the value of
> recycle0.
> > This would be
> > >> > similar to when there are no non-NULL arguments
> to paste;
> > >> collapse="."
> > >> > gives a single empty string and collapse=NULL
> gives a zero
> > long
> > >> character
> > >> > vector.
> > >> >> paste()
> > >> > character(0)
> > >> >> paste(collapse=", ")
> > >> > [1] ""
> > >> >
> > >> > Bill Dunlap
> > >> > TIBCO Software
> > >> > wdunlap tibco.com
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__tibco.com&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Z1o-HO3_OqxOR9LaRguGvnG7X4vF_z1_q13I7zmjcfY&s=7ZT1IjmexPqsDBhrV3NspPTr8M8XiMweEwJWErgAlqw&e=>
> >
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__tibco.com&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q5ueyHReS5hHK6TZ0dJ1N7Ro8dx-rsLHys8GrCugOls&s=o9ozvxBK-kVvAUFro7U1RrI5w0U8EPb0uyjQwMvOpt8&e=>
> > >>
> >
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__tibco.com&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cC2qctlVXd0qHMPvCyYvuVMqR8GU3DjTTqKJ0zjIFj8&s=rXIwWqf4U4HZS_bjUT3KfA9ARaV5YTb_kEcXWHnkt-c&e=>
> > >> >
> > >> >
> > >> > On Thu, Apr 30, 2020 at 9:56 PM
> suharto_anggono--- via
> > R-devel <
> > >> > r-devel using r-project.org
> <mailto:r-devel using r-project.org> <mailto:r-devel using r-project.org
> <mailto:r-devel using r-project.org>>
> > <mailto:r-devel using r-project.org
> <mailto:r-devel using r-project.org> <mailto:r-devel using r-project.org
> <mailto:r-devel using r-project.org>>>> wrote:
> > >> >
> > >> >> Without 'collapse', 'paste' pastes
> (concatenates) its
> > arguments
> > >> >> elementwise (separated by 'sep', " " by
> default). New in
> > R devel
> > >> and R
> > >> >> patched, specifying recycle0 = FALSE makes mixing
> > zero-length and
> > >> >> nonzero-length arguments results in length
> zero. The
> > result of
> > >> paste(n,
> > >> >> "th", sep = "", recycle0 = FALSE) always have
> the same
> > length as
> > >> 'n'.
> > >> >> Previously, the result is still as long as the
> longest
> > argument,
> > >> with the
> > >> >> zero-length argument like "". If all og the
> arguments have
> > >> length zero,
> > >> >> 'recycle0' doesn't matter.
> > >> >>
> > >> >> As far as I understand, 'paste' with
> 'collapse' as a
> > character
> > >> string is
> > >> >> supposed to put together elements of a vector
> into a single
> > >> character
> > >> >> string. I think 'recycle0' shouldn't change it.
> > >> >>
> > >> >> In current R devel and R patched,
> paste(character(0),
> > collapse = "",
> > >> >> recycle0 = FALSE) is character(0). I think it
> should be
> > "", like
> > >> >> paste(character(0), collapse="").
> > >> >>
> > >> >> paste(c("4", "5"), "th", sep = "", collapse =
> ", ",
> > recycle0 =
> > >> FALSE)
> > >> >> is
> > >> >> "4th, 5th".
> > >> >> paste(c("4" ), "th", sep = "", collapse =
> ", ",
> > recycle0 =
> > >> FALSE)
> > >> >> is
> > >> >> "4th".
> > >> >> I think
> > >> >> paste(c( ), "th", sep = "", collapse =
> ", ",
> > recycle0 =
> > >> FALSE)
> > >> >> should be
> > >> >> "",
> > >> >> not character(0).
> > >> >>
> > >> >> ______________________________________________
> > >> >> R-devel using r-project.org
> <mailto:R-devel using r-project.org> <mailto:R-devel using r-project.org
> <mailto:R-devel using r-project.org>>
> > <mailto:R-devel using r-project.org
> <mailto:R-devel using r-project.org> <mailto:R-devel using r-project.org
> <mailto:R-devel using r-project.org>>>
> > mailing list
> > >> >>
> > >>
> >
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> > >> >>
> > >> >
> > >> > [[alternative HTML version deleted]]
> > >> >
> > >> > ______________________________________________
> > >> > R-devel using r-project.org
> <mailto:R-devel using r-project.org> <mailto:R-devel using r-project.org
> <mailto:R-devel using r-project.org>>
> > <mailto:R-devel using r-project.org
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> > >> >
> > >>
> >
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> > >> >
> > >>
> > >> --
> > >> Hervé Pagès
> > >>
> > >> Program in Computational Biology
> > >> Division of Public Health Sciences
> > >> Fred Hutchinson Cancer Research Center
> > >> 1100 Fairview Ave. N, M1-B514
> > >> P.O. Box 19024
> > >> Seattle, WA 98109-1024
> > >>
> > >> E-mail: hpages using fredhutch.org
> <mailto:hpages using fredhutch.org> <mailto:hpages using fredhutch.org
> <mailto:hpages using fredhutch.org>>
> > <mailto:hpages using fredhutch.org
> <mailto:hpages using fredhutch.org> <mailto:hpages using fredhutch.org
> <mailto:hpages using fredhutch.org>>>
> > >> Phone: (206) 667-5791
> > >> Fax: (206) 667-1319
> > >>
> > >> ______________________________________________
> > >> R-devel using r-project.org
> <mailto:R-devel using r-project.org> <mailto:R-devel using r-project.org
> <mailto:R-devel using r-project.org>>
> > <mailto:R-devel using r-project.org
> <mailto:R-devel using r-project.org> <mailto:R-devel using r-project.org
> <mailto:R-devel using r-project.org>>>
> > mailing list
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> > >>
> >
> > > --
> > > Hervé Pagès
> >
> > > Program in Computational Biology
> > > Division of Public Health Sciences
> > > Fred Hutchinson Cancer Research Center
> > > 1100 Fairview Ave. N, M1-B514
> > > P.O. Box 19024
> > > Seattle, WA 98109-1024
> >
> > > E-mail: hpages using fredhutch.org
> <mailto:hpages using fredhutch.org> <mailto:hpages using fredhutch.org
> <mailto:hpages using fredhutch.org>>
> > > Phone: (206) 667-5791
> > > Fax: (206) 667-1319
> >
> > > ______________________________________________
> > > R-devel using r-project.org
> <mailto:R-devel using r-project.org> <mailto:R-devel using r-project.org
> <mailto:R-devel using r-project.org>> mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-devel
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Z1o-HO3_OqxOR9LaRguGvnG7X4vF_z1_q13I7zmjcfY&s=CDOaP2RJnAyhpbHe6-O752uc4IPMugypbcgdYzhoF_8&e=>
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> >
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages using fredhutch.org <mailto:hpages using fredhutch.org>
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages using fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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