That's interesting, thank you for testing it. :)
Regards,
Ruqian
On Tue, Nov 6, 2018 at 5:01 AM Martin Morgan <mtmorgan.b...@gmail.com>
wrote:
> Further to this it is helpful to ensure that you are using the correct
> version of Bioconductor and that your packages are up-to-date
>
> BiocManager::version() == "3.8"
> BiocManager::valid()
>
> Martin
>
> On 11/5/18, 12:11 PM, "Bioc-devel on behalf of Mike Smith" <
> bioc-devel-boun...@r-project.org on behalf of grimbo...@gmail.com> wrote:
>
> Hi Ruqian,
>
> I think this is a consequence of your internal data.frames have column
> names that include the minus sign i.e. "-". The code clearly tries to
> deal
> with this by wrapping them in back-ticks at certain points, but I
> think it
> doesn't do this successfully in projectScoreLandscape()
>
> First, consider this example, which I think is a simplified version of
> what
> happens in plotScoreLandscape()
>
> df <- data.frame(x = 1:10, y = 1:10)
> colnames(df) <- c("tgca-EPI","tgca-MES")
> ggplot(df, aes_string("`tgca-EPI`", "`tgca-MES`")) +
> geom_point()
>
> For me this works & produces a plot where the axis labels include the
> backticks i.e. `tgca-EPI` and `tgca-EPI`
>
> Now we rename the columns of our data.frame to include the back-ticks,
> which is what happens when plabs = c(plotObj$labels$x,
> plotObj$labels$y) is
> called within projectScoreLandscape(). We plot in the same fashion and
> get
> an error similar to what you're seeing.
>
> colnames(df) <- c("`tgca-EPI`","`tgca-MES`")
> ggplot(df, aes_string("`tgca-EPI`", "`tgca-MES`")) +
> geom_point()
>
> Error in FUN(X[[i]], ...) : object 'tgca-EPI' not found
>
> Why this behavior would change I don't know, but presumably something
> in
> one of the tidyverse packages has led to this. You should probably
> investigate more, but if this is the problem then you can modify that
> plabs
> line in projectScoreLandscape() to strip the back-ticks. However,
> perhaps a
> more robust solution is to enforce the use of "_" rather than "-" in
> column
> names, that way you don't have to worry about using back-ticks to
> quote the
> non-syntactic names.
>
> Best regards,
>
> Mike
>
> On Mon, 5 Nov 2018 at 14:21, Ruqian Lyu <
> ruqi...@student.unimelb.edu.au>
> wrote:
>
> > Hi Bioconductor,
> >
> > I received a notification email regarding the building error for our
> > package 'singscore'.
> >
> > I pull the RELEASE_3_8 branch and checked/built on my local machine,
> it was
> > successful without errors.
> >
> > The error message was within the vignette which hasn't been updated
> for
> > several months.
> >
> > Would please help with identifying the problem?
> >
> > Thanks a lot!
> >
> > Best regards,
> > Ruqian
> >
> > ---------- Forwarded message ---------
> > From: <bbs-nore...@bioconductor.org>
> > Date: Fri, Nov 2, 2018 at 12:14 AM
> > Subject: singscore problems reported in the Multiple platform
> build/check
> > report for BioC 3.8
> > To: <ruqi...@student.unimelb.edu.au>
> >
> >
> > [This is an automatically generated email. Please don't reply.]
> >
> > Hi singscore maintainer,
> >
> > According to the Multiple platform build/check report for BioC 3.8,
> > the singscore package has the following problem(s):
> >
> > o ERROR for 'R CMD build' on malbec1. See the details here:
> >
> >
> >
> https://master.bioconductor.org/checkResults/3.8/bioc-LATEST/singscore/malbec1-buildsrc.html
> >
> > Please take the time to address this by committing and pushing
> > changes to your package at git.bioconductor.org
> >
> > Notes:
> >
> > * This was the status of your package at the time this email was
> sent to
> > you.
> > Given that the online report is updated daily (in normal
> conditions)
> > you
> > could see something different when you visit the URL(s) above,
> > especially if
> > you do so several days after you received this email.
> >
> > * It is possible that the problems reported in this report are
> false
> > positives,
> > either because another package (from CRAN or Bioconductor)
> breaks your
> > package (if yours depends on it) or because of a Build System
> problem.
> > If this is the case, then you can ignore this email.
> >
> > * Please check the report again 24h after you've committed your
> changes
> > to the
> > package and make sure that all the problems have gone.
> >
> > * If you have questions about this report or need help with the
> > maintenance of your package, please use the Bioc-devel mailing
> list:
> >
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