[Bioc-devel] Fwd: singscore problems reported in the Multiple platform build/check report for BioC 3.8

[Ruqian Lyu]

That's interesting, thank you for testing it. :)

Regards,
Ruqian

On Tue, Nov 6, 2018 at 5:01 AM Martin Morgan <mtmorgan.bioc using 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-bounces using r-project.org on behalf of grimbough using 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 <
> ruqianl using 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-noreply using 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: <ruqianl using 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
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>     > 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.
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>     >
>     >   * Please check the report again 24h after you've committed your
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>     > to the
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