[R-pkg-devel] [CRAN-pretest-archived] CRAN Submission NMRphasing 1.0.6

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Nice spotting!

Just for fun, I just asked chatgpt if there were any other problems in
that code.  It spotted 3, but not the one you found.  Two of them were
definitely bogus, but this one might not be:

On line 471 kmax is used, but it may not be initialized.

Duncan Murdoch

On 2024-12-17 5:15 a.m., Ivan Krylov via R-package-devel wrote:
> Dear Aixiang,
>
> Welcome to R-package-devel!
>
> ? Tue, 17 Dec 2024 09:47:26 +0000
> Aixiang Jiang <aijiang at bccrc.ca> ?????:
>
>> I am really confused by the error, which did not happen in the
>> previous versions.
>>
>> Since I have not changed my code at all, the possible reason is that
>> the external function is changed.
>
> That's right, you've found a bug in the MassSpecWavelet package. It's
> been introduced more than two years ago:
>
> https://code.bioconductor.org/browse/MassSpecWavelet/commit/ea0f727ffc391fa2643f858844836d8297742433
>
> The code finds out the length of the vector and a pointer to the start
> of its data:
>
>>> double *x;
>
>>> R_xlen_t xlength = Rf_length(s_x);
>
>>> x = REAL(s_x);
>
> Later, the code tries to limit the offset into the array...
>
>>> i2 = i2 >= xlength ? xlength : i2;
>
> ...and accesses the data at this offset:
>
>>> if (xmax > x[i2] && xmax > x[j-1]) {
>
> Unfortunately, it is an error to access data at i2 equal to xlength.
> The correct maximum for i2 must be xlength-1, the last valid element of
> x.
>
> Try reporting this to the maintainer at
> <https://support.bioconductor.org/> or at
> <http://github.com/zeehio/MassSpecWavelet/issues>.
>

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Dear Aixiang,

Thanks for using a Bioconductor package as your dependency.

Please use the maintainer preference to report bugs, as set on the
DESCRIPTION file: Bug Reports
http://github.com/zeehio/MassSpecWavelet/issues
The support site (support.bioconductor.org) is generally set up to
help users with questions about Bioconductor packages (which might
actually come down to be bugs).

I hope MassSpecWavelet's maintainer fixes this on the released version
of the packages soon and you can proceed with your submission to CRAN.
However, I take the occasion to share what CRAN team shared on the
website: "CRAN submission will be offline from Dec 23, 2024 to Jan 07,
2025 (CRAN team vacation and maintenance work)."
So you only have a few more days to submit before they pause the
submission (but I see the time given to fix issues on your package let
you submit after their vacations).

Best wishes,

Llu??s
Bioconductor Community Advisory Board member.

On Tue, 17 Dec 2024 at 11:16, Ivan Krylov via R-package-devel
<r-package-devel at r-project.org> wrote:
>
> Dear Aixiang,
>
> Welcome to R-package-devel!
>
> ?? Tue, 17 Dec 2024 09:47:26 +0000
> Aixiang Jiang <aijiang at bccrc.ca> ??????:
>
> > I am really confused by the error, which did not happen in the
> > previous versions.
> >
> > Since I have not changed my code at all, the possible reason is that
> > the external function is changed.
>
> That's right, you've found a bug in the MassSpecWavelet package. It's
> been introduced more than two years ago:
>
> https://code.bioconductor.org/browse/MassSpecWavelet/commit/ea0f727ffc391fa2643f858844836d8297742433
>
> The code finds out the length of the vector and a pointer to the start
> of its data:
>
> >> double *x;
>
> >> R_xlen_t xlength = Rf_length(s_x);
>
> >> x = REAL(s_x);
>
> Later, the code tries to limit the offset into the array...
>
> >> i2 = i2 >= xlength ? xlength : i2;
>
> ...and accesses the data at this offset:
>
> >> if (xmax > x[i2] && xmax > x[j-1]) {
>
> Unfortunately, it is an error to access data at i2 equal to xlength.
> The correct maximum for i2 must be xlength-1, the last valid element of
> x.
>
> Try reporting this to the maintainer at
> <https://support.bioconductor.org/> or at
> <http://github.com/zeehio/MassSpecWavelet/issues>.
>
> --
> Best regards,
> Ivan
>
> ______________________________________________
> R-package-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

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Dear Aixiang,

Welcome to R-package-devel!

? Tue, 17 Dec 2024 09:47:26 +0000
Aixiang Jiang <aijiang at bccrc.ca> ?????:

> I am really confused by the error, which did not happen in the
> previous versions.
>
> Since I have not changed my code at all, the possible reason is that
> the external function is changed.

That's right, you've found a bug in the MassSpecWavelet package. It's
been introduced more than two years ago:

https://code.bioconductor.org/browse/MassSpecWavelet/commit/ea0f727ffc391fa2643f858844836d8297742433

The code finds out the length of the vector and a pointer to the start
of its data:

>> double *x;

>> R_xlen_t xlength = Rf_length(s_x);

>> x = REAL(s_x);

Later, the code tries to limit the offset into the array...

>> i2 = i2 >= xlength ? xlength : i2;

...and accesses the data at this offset:

>> if (xmax > x[i2] && xmax > x[j-1]) {

Unfortunately, it is an error to access data at i2 equal to xlength.
The correct maximum for i2 must be xlength-1, the last valid element of
x.

Try reporting this to the maintainer at
<https://support.bioconductor.org/> or at
<http://github.com/zeehio/MassSpecWavelet/issues>.

--
Best regards,
Ivan