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

[Martin Morgan]

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
    > you.
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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
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