On 11/22/2017 09:51 AM, Mattia Chiesa wrote:
Dear all,
we looked at the traceback():
7: array(STATS, dims[perm])
6: aperm(array(STATS, dims[perm]), order(perm))
5: sweep(WW[, 1:opt.comp], 2, Q2TT, "*")
4: apply(sweep(WW[, 1:opt.comp], 2, Q2TT, "*"), 1, sum)
3: VIP(pls.fit, opt.comp = opt.comp)
2: bve_pls(df$class, as.matrix(data), ncomp = num_PC, VIP.threshold =
th.VIP)
1: DaMiR.FSelect(data_clean <http://data_clean.mx>, df = df, th.corr = 0.6)
and it seems that the problem is the forth point (apply(sweep(WW[,
1:opt.comp], 2, Q2TT, "*"), 1, sum) when*opt.comp = 1*.
In this case, WW is a object with NULL dimensions (it is not a matrix
anymore), which gives problems to 'sweep()' function (it needs a matrix
with at least 1 column). We have already advised the authors and
suggested them a possible solution (i.e. WW[, 1:opt.comp, drop=FALSE])
that can fix this bug.
Notably, this happens only with 'plsVarSel version = 0.9.2' (released
on November 11th ,2017 !!!), which embeds the modified "filter.R" source
code, but not with the previous ones.
For this reason, in the meantime, we would modify the DESCRIPTION file
(both in devel and RELEASE 3_6), forcing the usage of 'plsVarSel
version = 0.9.1'.
Since this version is not available in the main CRAN repository, your
package will simply fail because the specified version cannot be loaded.
The best solution is simply to wait for the authors to fix the bug. Note
also that 1:opt.comp causes problems, much like omitting drop=FALSE,
when opt.comp == 0 and it is always better to use seq_len() (or its
compatriot seq_along()).
> 1:opt.comp
[1] 1 0
> seq_len(opt.comp)
integer(0)
Martin
Mattia
------------------------------------------------------------------------
*Da:* Martin Morgan <martin.mor...@roswellpark.org>
*Inviato:* lunedì 20 novembre 2017 15:48
*A:* Shepherd, Lori; Mattia Chiesa; bioc-devel@r-project.org
*Oggetto:* Re: [Bioc-devel] DaMiRseq in ERROR in the stable release
On 11/20/2017 08:54 AM, Shepherd, Lori wrote:
It is quite possible that it could be because of a dependent package.
Unfortunately the only way to tell would be to see if any of those packages are
producing a similar ERROR on the build report or to investigate your code to
see where and how this ERROR is occurring.
Another place to start is to simply reproduce the error on your own
system. Usually this requires running the version of R and Bioconductor
on the build system (noted at the top of the multi-platform build /
check report page), and making sure that dependencies are current, e.g.,
by BiocInstaller::biocValid().
For vignettes, it can be helpful to 'Stangle' them and step through the
R code chunks in the resulting file
R CMD Stangle DaMiRseq.Rnw
Martin
It is possible that it is a bug in one of the dependencies' code or that it is
an intended change that your package would now need to adjust for but you need
to better understand where it is coming from.
Normally we hope that the release stays fairly stable and only bug fixes are
pushed to code in that branch; the devel branch is intended to implement
changes to give other maintainers a chance to adapt (or point out bugs to
correct).
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Mattia Chiesa
<mattia.chi...@hotmail.it>
Sent: Monday, November 20, 2017 6:12:45 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] DaMiRseq in ERROR in the stable release
Dear Bioc team,
I�m the mantainer of the DaMiRseq package. About a week ago, the BUILD ended up
in ERROR in the stable release (3.6).
The error occurs in each platform during the creation of the vignette.
Here the Build/Check report:
http://bioconductor.org/checkResults/release/bioc-LATEST/DaMiRseq/
In addition, I noted that the devel release fails, as well; however, here the
reason seems to be different:
http://bioconductor.org/checkResults/devel/bioc-LATEST/DaMiRseq/
Actually, I didn�t push any changes since the last new Bioc release.
Can errors in dependencies be the reason of this BUILD failure?
What could I do to solve these issues?
Thanks in advance,
Mattia
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