thr3ads.net - R devel - [Rd] Control statements with condition with greater than one should give error (not just warning) [PATCH] [Mar 2017]

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Henrik Bengtsson

2017-Mar-03 17:43 UTC

[Rd] Control statements with condition with greater than one should give error (not just warning) [PATCH]

On Fri, Mar 3, 2017 at 9:22 AM, Martin Maechler
<maechler at stat.math.ethz.ch> wrote:>>>>>> Henrik Bengtsson <henrik.bengtsson at gmail.com>
>>>>>>     on Fri, 3 Mar 2017 00:52:16 -0800 writes:
>
>     > I'd like to propose that the whenever the length of condition
passed
>     > to an if or a while statement differs from one, an error is
produced
>     > rather than just a warning as today:
>
>     >> x <- 1:2
>     >> if (x == 1) message("x == 1")
>     > x == 1
>     > Warning message:
>     > In if (x == 1) message("x == 1") :
>     > the condition has length > 1 and only the first element will be
used
>
>     > There are probably legacy reasons for why this is accepted by R in
the
>     > first place, but I cannot imagine than anyone wants to use an
if/while
>     > statement this way on purpose.  The warning about this misuse, was
>     > introduced in November 2002 (R-devel thread 'vector arguments
to
>     > if()';
https://stat.ethz.ch/pipermail/r-devel/2002-November/025537.html).
>
> yes, before, there was *no* warning at all and so the problem existed
> in several partly important R packages.
>
> Now is a different time, I agree, and I even tend to agree we
> should make this an error... probably however not for the
> upcoming R 3.4.0 (in April which is somewhat soon) but rather
> for the next version.
>
>
>     > Below is patch (also attached) that introduces option
>     > 'check.condition' such that when TRUE,
>
> ouch ouch ouch!   There are many sayings starting with
>   "The way to hell ...."
>
> Here:
>
> The way to R hell starts (or "widens", your choice) by
> introducing options() that influence basic language semantics
>
> !!
>
> For robust code you will start to test all code of R for all
> different possible combinations of these options set ---- I am
> sure you would not want this.
You only want to test with check.condition = TRUE.  No new code,
package updates etc should be allowed to only pass if they have to use
check.condition = FALSE.
>
> No --- don't even think of allowing an option for something such basic!
But, how you propose a warning-to-error transition should be made
without wreaking havoc?  Just flip the switch in R-devel and see CRAN
and Bioconductor packages break overnight?  Particularly Bioconductor
devel might become non-functional (since at times it requires
R-devel).  For my own code / packages, I would be able to handle such
a change, but I'm completely out of control if one of the package I'm
depending on does not provide a quick fix (with the only option to
remove package tests for those dependencies).

My idea is that with this option, then this can be tested at runtime
locally by users and developers (cf. warnPartialMatchArgs), but also
via R CMD check.  It would also provide CRAN with a way to check it on
incoming submissions as on the test farm - eventually all CRAN
packages pass without errors.  This option would only exist for a
number of R releases (first default to FALSE, then TRUE) and then
eventually be deprecated and removed.  Does this clarify my design?

As an alternative to an option, one could use an environment variable
R_CHECK_CONDITION that is a bit "hidden" from misuse.

/Henrik
>
> Martin Maechler
> ETH Zurich (and R Core)
>
>     > it will generate an error
>     > rather than a warning (default).  This option allows for a smooth
>     > migration as it can be added to 'R CMD check --as-cran'
and developers
>     > can give time to check and fix their packages.  Eventually,
>     > check.condition=TRUE can become the new default.
>
>     > With options(check.condition = TRUE), one gets:
>
>     >> x <- 1:2
>     >> if (x == 1) message("x == 1")
>     > Error in if (x == 1) message("x == 1") : the condition
has length > 1
>
>     > and
>
>     >> while (x < 2) message("x < 2")
>     > Error in while (x < 2) message("x < 2") : the
condition has length > 1
>
>
>     > Index: src/library/base/man/options.Rd
>     >
==================================================================>     >
--- src/library/base/man/options.Rd (revision 72298)
>     > +++ src/library/base/man/options.Rd (working copy)
>     > @@ -86,6 +86,11 @@
>     > vector (atomic or \code{\link{list}}) is extended, by something
>     > like \code{x <- 1:3; x[5] <- 6}.}
>
>     > +    \item{\code{check.condition}:}{logical, defaulting to
\code{FALSE}.  If
>     > +      \code{TRUE}, an error is produced whenever the condition to
an
>     > +      \code{if} or a \code{while} control statement is of length
greater
>     > +      than one.  If \code{FALSE}, a \link{warning} is produced.}
>     > +
>     > \item{\code{CBoundsCheck}:}{logical, controlling whether
>     > \code{\link{.C}} and \code{\link{.Fortran}} make copies to check
for
>     > array over-runs on the atomic vector arguments.
>     > @@ -445,6 +450,7 @@
>     > \tabular{ll}{
>     > \code{add.smooth} \tab \code{TRUE}\cr
>     > \code{check.bounds} \tab \code{FALSE}\cr
>     > +    \code{check.condition} \tab \code{FALSE}\cr
>     > \code{continue} \tab \code{"+ "}\cr
>     > \code{digits} \tab \code{7}\cr
>     > \code{echo} \tab \code{TRUE}\cr
>     > Index: src/library/utils/R/completion.R
>     >
==================================================================>     >
--- src/library/utils/R/completion.R (revision 72298)
>     > +++ src/library/utils/R/completion.R (working copy)
>     > @@ -1304,8 +1304,8 @@
>     > "plt", "ps", "pty", "smo",
"srt", "tck", "tcl", "usr",
>     > "xaxp", "xaxs", "xaxt",
"xpd", "yaxp", "yaxs", "yaxt")
>
>     > -    options <- c("add.smooth", "browser",
"check.bounds", "continue",
>     > - "contrasts", "defaultPackages",
"demo.ask", "device",
>     > +    options <- c("add.smooth", "browser",
"check.bounds", "check.condition",
>     > +        "continue", "contrasts",
"defaultPackages", "demo.ask", "device",
>     > "digits", "dvipscmd", "echo",
"editor", "encoding",
>     > "example.ask", "expressions",
"help.search.types",
>     > "help.try.all.packages", "htmlhelp",
"HTTPUserAgent",
>     > Index: src/main/eval.c
>     >
==================================================================>     >
--- src/main/eval.c (revision 72298)
>     > +++ src/main/eval.c (working copy)
>     > @@ -1851,9 +1851,13 @@
>     > Rboolean cond = NA_LOGICAL;
>
>     > if (length(s) > 1) {
>     > + int check =
asInteger(GetOption1(install("check.condition")));
>     > PROTECT(s); /* needed as per PR#15990.  call gets protected by
>     > warningcall() */
>     > - warningcall(call,
>     > -    _("the condition has length > 1 and only the first
element will be used"));
>     > + if(check != NA_INTEGER && check > 0)
>     > +    errorcall(call, _("the condition has length >
1"));
>     > + else
>     > +    warningcall(call,
>     > + _("the condition has length > 1 and only the first
element will be used"));
>     > UNPROTECT(1);
>     > }
>     > if (length(s) > 0) {
>     > Index: src/main/options.c
>     >
==================================================================>     >
--- src/main/options.c (revision 72298)
>     > +++ src/main/options.c (working copy)
>     > @@ -65,6 +65,7 @@
>     > * "timeout" ./connections.c
>
>     > * "check.bounds"
>     > + * "check.condition"
>     > * "error"
>     > * "error.messages"
>     > * "show.error.messages"
>     > @@ -248,9 +249,9 @@
>     > char *p;
>
>     > #ifdef HAVE_RL_COMPLETION_MATCHES
>     > +    PROTECT(v = val = allocList(22));
>     > +#else
>     > PROTECT(v = val = allocList(21));
>     > -#else
>     > -    PROTECT(v = val = allocList(20));
>     > #endif
>
>     > SET_TAG(v, install("prompt"));
>     > @@ -289,6 +290,10 @@
>     > SETCAR(v, ScalarLogical(0)); /* no checking */
>     > v = CDR(v);
>
>     > +    SET_TAG(v, install("check.condition"));
>     > +    SETCAR(v, ScalarLogical(0)); /* no checking */
>     > +    v = CDR(v);
>     > +
>     > p = getenv("R_KEEP_PKG_SOURCE");
>     > R_KeepSource = (p && (strcmp(p, "yes") == 0)) ?
1 : 0;
>
>
>     > I'm happy to file this via https://bugs.r-project.org, if
preferred.
>
>     > /Henrik
>
>     >
----------------------------------------------------------------------
>     > Index: src/library/base/man/options.Rd
>     >
==================================================================>     >
--- src/library/base/man/options.Rd       (revision 72298)
>     > +++ src/library/base/man/options.Rd       (working copy)
>     > @@ -86,6 +86,11 @@
>     > vector (atomic or \code{\link{list}}) is extended, by something
>     > like \code{x <- 1:3; x[5] <- 6}.}
>
>     > +    \item{\code{check.condition}:}{logical, defaulting to
\code{FALSE}.  If
>     > +      \code{TRUE}, an error is produced whenever the condition to
an
>     > +      \code{if} or a \code{while} control statement is of length
greater
>     > +      than one.  If \code{FALSE}, a \link{warning} is produced.}
>     > +
>     > \item{\code{CBoundsCheck}:}{logical, controlling whether
>     > \code{\link{.C}} and \code{\link{.Fortran}} make copies to check
for
>     > array over-runs on the atomic vector arguments.
>     > @@ -445,6 +450,7 @@
>     > \tabular{ll}{
>     > \code{add.smooth} \tab \code{TRUE}\cr
>     > \code{check.bounds} \tab \code{FALSE}\cr
>     > +    \code{check.condition} \tab \code{FALSE}\cr
>     > \code{continue} \tab \code{"+ "}\cr
>     > \code{digits} \tab \code{7}\cr
>     > \code{echo} \tab \code{TRUE}\cr
>     > Index: src/library/utils/R/completion.R
>     >
==================================================================>     >
--- src/library/utils/R/completion.R      (revision 72298)
>     > +++ src/library/utils/R/completion.R      (working copy)
>     > @@ -1304,8 +1304,8 @@
>     > "plt", "ps", "pty", "smo",
"srt", "tck", "tcl", "usr",
>     > "xaxp", "xaxs", "xaxt",
"xpd", "yaxp", "yaxs", "yaxt")
>
>     > -    options <- c("add.smooth", "browser",
"check.bounds", "continue",
>     > - "contrasts", "defaultPackages",
"demo.ask", "device",
>     > +    options <- c("add.smooth", "browser",
"check.bounds", "check.condition",
>     > +        "continue", "contrasts",
"defaultPackages", "demo.ask", "device",
>     > "digits", "dvipscmd", "echo",
"editor", "encoding",
>     > "example.ask", "expressions",
"help.search.types",
>     > "help.try.all.packages", "htmlhelp",
"HTTPUserAgent",
>     > Index: src/main/eval.c
>     >
==================================================================>     >
--- src/main/eval.c       (revision 72298)
>     > +++ src/main/eval.c       (working copy)
>     > @@ -1851,9 +1851,13 @@
>     > Rboolean cond = NA_LOGICAL;
>
>     > if (length(s) > 1) {
>     > + int check =
asInteger(GetOption1(install("check.condition")));
>     > PROTECT(s);        /* needed as per PR#15990.  call gets protected
by warningcall() */
>     > - warningcall(call,
>     > -             _("the condition has length > 1 and only the
first element will be used"));
>     > + if(check != NA_INTEGER && check > 0)
>     > +     errorcall(call, _("the condition has length >
1"));
>     > + else
>     > +     warningcall(call,
>     > +                 _("the condition has length > 1 and only
the first element will be used"));
>     > UNPROTECT(1);
>     > }
>     > if (length(s) > 0) {
>     > Index: src/main/options.c
>     >
==================================================================>     >
--- src/main/options.c    (revision 72298)
>     > +++ src/main/options.c    (working copy)
>     > @@ -65,6 +65,7 @@
>     > * "timeout"               ./connections.c
>
>     > * "check.bounds"
>     > + *       "check.condition"
>     > * "error"
>     > * "error.messages"
>     > * "show.error.messages"
>     > @@ -248,9 +249,9 @@
>     > char *p;
>
>     > #ifdef HAVE_RL_COMPLETION_MATCHES
>     > +    PROTECT(v = val = allocList(22));
>     > +#else
>     > PROTECT(v = val = allocList(21));
>     > -#else
>     > -    PROTECT(v = val = allocList(20));
>     > #endif
>
>     > SET_TAG(v, install("prompt"));
>     > @@ -289,6 +290,10 @@
>     > SETCAR(v, ScalarLogical(0));      /* no checking */
>     > v = CDR(v);
>
>     > +    SET_TAG(v, install("check.condition"));
>     > +    SETCAR(v, ScalarLogical(0)); /* no checking */
>     > +    v = CDR(v);
>     > +
>     > p = getenv("R_KEEP_PKG_SOURCE");
>     > R_KeepSource = (p && (strcmp(p, "yes") == 0)) ?
1 : 0;
>
>
>     >
----------------------------------------------------------------------
>     > ______________________________________________
>     > R-devel at r-project.org mailing list
>     > https://stat.ethz.ch/mailman/listinfo/r-devel

Hadley Wickham

2017-Mar-03 17:55 UTC

head link

[Rd] Control statements with condition with greater than one should give error (not just warning) [PATCH]

> But, how you propose a warning-to-error transition should be made
> without wreaking havoc?  Just flip the switch in R-devel and see CRAN
> and Bioconductor packages break overnight?  Particularly Bioconductor
> devel might become non-functional (since at times it requires
> R-devel).  For my own code / packages, I would be able to handle such
> a change, but I'm completely out of control if one of the package
I'm
> depending on does not provide a quick fix (with the only option to
> remove package tests for those dependencies).
Generally, a package can not be on CRAN if it has any warnings, so I
don't think this change would have any impact on CRAN packages.  Isn't
this also true for bioconductor?

Hadley

-- 
http://hadley.nz

Henrik Bengtsson

2017-Mar-03 18:10 UTC

head link

[Rd] Control statements with condition with greater than one should give error (not just warning) [PATCH]

On Fri, Mar 3, 2017 at 9:55 AM, Hadley Wickham <h.wickham at gmail.com>
wrote:>> But, how you propose a warning-to-error transition should be made
>> without wreaking havoc?  Just flip the switch in R-devel and see CRAN
>> and Bioconductor packages break overnight?  Particularly Bioconductor
>> devel might become non-functional (since at times it requires
>> R-devel).  For my own code / packages, I would be able to handle such
>> a change, but I'm completely out of control if one of the package
I'm
>> depending on does not provide a quick fix (with the only option to
>> remove package tests for those dependencies).
>
> Generally, a package can not be on CRAN if it has any warnings, so I
> don't think this change would have any impact on CRAN packages. 
Isn't
> this also true for bioconductor?
Having a tests/warn.R file with:

warning("boom")

passes through R CMD check --as-cran unnoticed.  Same with:

if (sample(2) == 1) message("It's your lucky day today!")

/Henrik

PS. Does testthat signal that?
>
> Hadley
>
> --
> http://hadley.nz

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