Great, thanks,
Uwe
On 05.02.2025 02:32, Zhian Kamvar wrote:
Thank you, Uwe for tagging me in. Huge thank you to Ivan for the
detailed analysis. This reflects what Max Coulter found in https://
github.com/thibautjombart/adegenet/issues/363 <https://github.com/
thibautjombart/adegenet/issues/363>. I just merged in https://
github.com/thibautjombart/adegenet/issues/363 <https://github.com/
thibautjombart/adegenet/issues/363> yesterday and I believe that should
fix the issue.
I am going to run a test using the https://hub.docker.com/r/rocker/r-
devel-san/ <https://hub.docker.com/r/rocker/r-devel-san/> to confirm
that this is fixed before I send it off to CRAN.
Best,
Zhian
On Tue, Feb 4, 2025 at 4:01 AM Iñaki Ucar <iu...@fedoraproject.org
<mailto:iu...@fedoraproject.org>> wrote:
On Tue, 4 Feb 2025 at 12:56, Uwe Ligges <lig...@statistik.tu-
dortmund.de <mailto:lig...@statistik.tu-dortmund.de>> wrote:
>
>
>
> On 04.02.2025 12:46, Iñaki Ucar wrote:
> > @Ivan: Excellent anaylsis as always.
> >
> > @Bernd: So what can **you** do about it? You are using adegenet
> > correctly as Ivan pointed out, so IMHO CRAN should have requested
> > adegenet's maintainer to fix this. But since it's your package
that is
> > on the line here, I would put that example inside a dontrun{} chunk
> > for now, to avoid triggering this issue on CRAN, and I would report
> > Ivan's analysis upstream.
>
> Putting it in dontrun is the wrong advise in any case, as we like to
> track whether the underlying issue has been fixed. And both Professor
> Ripley and I already asked to liase with the adegenet maintainer
to get
> this fixed.
Great, we obviously didn't know this, but only that Bernd's package is
scheduled to be archived soon, thus my advice.
Iñaki
> So I wonder why the most relevant person (Zhian N. Kamvar)
> was not included here (CCIng now).
> Ivan's analysis is as always extremely helpful, particularly for the
> adegenet maintainer.
>
> Best,
> Uwe
>
>
>
> > Iñaki
> >
> >
> > On Tue, 4 Feb 2025 at 12:30, Ivan Krylov via R-package-devel
> > <r-package-devel@r-project.org <mailto:r-package-devel@r-
project.org>> wrote:
> >>
> >> В Sun, 2 Feb 2025 22:56:47 +0000
> >> Bernd.Gruber <bernd.gru...@canberra.edu.au
<mailto:bernd.gru...@canberra.edu.au>> пишет:
> >>
> >>> READ of size 16 at 0x518000697ff0 thread T0
> >>> #0 0x7f2e873ccfdf in bytesToDouble
> >>> /tmp/RtmpNNPUz9/R.INSTALL3cef1f2b1bd39c/adegenet/src/
snpbin.c:225:19
> >>> #1 0x7f2e873ceca5 in snpbin2freq
> >>> /tmp/RtmpNNPUz9/R.INSTALL3cef1f2b1bd39c/adegenet/src/
snpbin.c:332:5
> >>> #2 0x7f2e873ceca5 in snpbin_dotprod_freq
> >>> /tmp/RtmpNNPUz9/R.INSTALL3cef1f2b1bd39c/adegenet/src/
snpbin.c:447:5
> >>> #3 0x7f2e873bba42 in GLdotProd
> >>> /tmp/RtmpNNPUz9/R.INSTALL3cef1f2b1bd39c/adegenet/src/
GLfunctions.c:42:14
> >>
> >> Ben Bolker is exactly right; the problem happens in the 'adegenet'
> >> code. Why?
> >>
> >> bytesToDouble() is asked to unpack the bytes from the
'vecbytes' array
> >> (26 bytes) into individual bits stored as doubles in the 'out'
array.
> >> The latter was allocated by the snpbin_dotprod_freq() function to
> >> contain 199 elements [1]. Every byte must be unpacked into 8
bits, and
> >> 199 is less than 26*8 = 208. Where did the values come from?
> >>
> >> The C function GLsumFreq() stores them unchanged from its
arguments
> >> [2], and those come from the SNPbin objects passed by R code
[3] from
> >> nLoc(x) and length(x$gen[[1]]@snp[[1]]). Where do they originate?
> >>
> >> The R traceback at the point of the crash is
dartR.base::gl.pcoa ->
> >> adegenet::glPca -> adegenet::glDotProd. The object 'possums.gl
<http://possums.gl>' of S4
> >> class 'dartR' exported by 'dartR.base' appears valid: its .
$n.loc is
> >> exactly equal to length(.$gen[[1]]@snp[[1]]) * 8, so the
allocation size
> >> matches the packed binary content.
> >>
> >> The subset possums.gl <http://possums.gl>[1:50,] that is used
to perform PCA, on the other
> >> hand, is invalid: length(possums.gl <http://
possums.gl>[1:50,]$gen[[1]]@snp[[1]]) is 26
> >> instead of 25, which later causes bytesToDouble() to try to
write extra
> >> 8 doubles (64 bytes) into the buffer.
> >>
> >> This happens because trying to extract all SNPs from an SNPbin
object
> >> introduces an extra byte:
> >>
> >> possums.gl@gen[[1]] |> _@snp |> lengths()
> >> # [1] 25 25
> >>
> >> possums.gl@gen[[1]][rep(TRUE, nLoc(possums.gl@gen[[1]]))] |>
> >> _@snp |> lengths()
> >> # 26 26
> >>
> >> This can be traced to a bug in adegenet:::.subsetbin:
> >>
> >> .subsetbin(as.raw(0xff), 1:8)
> >> # [1] ff 00 # <-- should be just 'ff'
> >>
> >> xint <- as.integer(rawToBits(x)[i]) # may be not divisible by 8
> >> # so introduce padding: the following line gives 8 bits of padding
> >> # instead of 0 when length(xint) is divisible by 8
> >> zeroes <- 8 - (length(xint)%%8)
> >> # instead use something like:
> >> # zeroes <- (8 - (length(xint)%%8)) * (length(xint)%%8 > 0)
> >> # (could probably be golfed further)
> >> return(packBits(c(xint, rep(0L, zeroes))))
> >>
> >> But we're getting two bugs for the price of one, because even
with a
> >> 25-byte buffer, nLoc(.) == 199 would still result in an 8-byte
> >> overflow. This is solely on the bytesToDouble() C function: it
ought to
> >> know to stop after writing *reslength elements into the
'vecres' array.
> >>
> >> I'm afraid there is no easy way to work around either of the
bugs in
> >> the dartR.base code.
> >>
> >> --
> >> Best regards,
> >> Ivan
> >>
> >> [1]
> >> https://github.com/thibautjombart/adegenet/blob/
c7287597155ab18989d892a72eff33cf8c288958/src/snpbin.c#L443-L444
<https://github.com/thibautjombart/adegenet/blob/
c7287597155ab18989d892a72eff33cf8c288958/src/snpbin.c#L443-L444>
> >>
> >> [2]
> >> https://github.com/thibautjombart/adegenet/blob/
c7287597155ab18989d892a72eff33cf8c288958/src/GLfunctions.c#L124
<https://github.com/thibautjombart/adegenet/blob/
c7287597155ab18989d892a72eff33cf8c288958/src/GLfunctions.c#L124>
> >>
> >> [3]
> >> https://github.com/thibautjombart/adegenet/blob/
c7287597155ab18989d892a72eff33cf8c288958/R/glFunctions.R#L215-L216
<https://github.com/thibautjombart/adegenet/blob/
c7287597155ab18989d892a72eff33cf8c288958/R/glFunctions.R#L215-L216>
> >>
> >> ______________________________________________
> >> R-package-devel@r-project.org <mailto:R-package-devel@r-
project.org> mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
<https://stat.ethz.ch/mailman/listinfo/r-package-devel>
> >>
> >
> >
>
--
Iñaki Úcar
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