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 at r-project.org on behalf of grimbough at 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 at 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,
> successful without errors.
>
> The error message was within the vignette which hasn't been updated
> several months.
>
> Would please help with identifying the problem?
>
> Thanks a lot!
>
> Best regards,
> Ruqian
>
> ---------- Forwarded message ---------
> From: <BBS-noreply at bioconductor.org>
> Date: Fri, Nov 2, 2018 at 12:14 AM
> Subject: singscore problems reported in the Multiple platform
> report for BioC 3.8
> To: <ruqianl at 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:
>
>
>
>
> 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
> you.
> Given that the online report is updated daily (in normal
> 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
> positives,
> either because another package (from CRAN or Bioconductor)
> package (if yours depends on it) or because of a Build System
> If this is the case, then you can ignore this email.
>
> * Please check the report again 24h after you've committed your
> 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
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