[Bioc-devel] Problems with MACPET package

[Vincent Carey]

It should be possible to get stringdist as a binary package for mac.
provide your sessionInfo().

> BiocManager::install("stringdist")

*Bioconductor version 3.10 (BiocManager 1.30.4), R 3.6.0 Patched
(2019-05-06*

*  r76460)*

*Installing package(s) 'stringdist'*

*trying URL
'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/stringdist_0.9.5.2.tgz
<https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/stringdist_0.9.5.2.tgz>'*

*Content type 'application/x-gzip' length 567740 bytes (554 KB)*

*==================================================*

*downloaded 554 KB*

On Fri, Jul 12, 2019 at 10:13 AM Ioannis Vardaxis <ioannis.vardaxis using ntnu.no>
wrote:

> I have changed the S4methods now and the Rcheck is working fine locally on
> my machine.
>
> I cannot run BiocCheck because I cannot install it on my Mac anymore. It
> depends on a package named stringdist, which cannot be installed in my Mac.
> I get an error:
> clang: error: unsupported option '-fopenmp'
>
> However I have pushed the changes to the repository now and we will see if
> the devel version gets fixed.
>
> Best,
> Ioannis
>
>
> > 8. jul. 2019 kl. 11:20 skrev Martin Morgan <mtmorgan.bioc using gmail.com>:
> >
> > Under bioc-devel, I ran
> >
> >  MACPET/vignettes$ R CMD Stangle MACPET.Rmd
> >
> > and then in R
> >
> >  source("MACPET.R", echo = TRUE)
> >
> > where the problem manifests as
> >
> >> summary(MACPET_pintraData,heatmap=TRUE)
> >  Error in .Vector_summary(object, ...) : unused argument (heatmap = TRUE)
> >
> > You have the S4 class
> >
> >> getClass(class(MACPET_pintraData))
> > Class "PIntra" [package "MACPET"]
> >
> > Slots:
> >
> > Name:            anchor1           anchor2           regions
>  NAMES
> > Class:           integer           integer           GRanges
> character_OR_NULL
> >
> > Name:    elementMetadata          metadata
> > Class:         DataFrame              list
> >
> > Extends:
> > Class "GInteractions", directly
> > Class "Vector", by class "GInteractions", distance 2
> > Class "Annotated", by class "GInteractions", distance 3
> > Class "vector_OR_Vector", by class "GInteractions", distance 3
> >
> > that extends 'Vector'.
> >
> > You have an S3 generic summary.PIntra, but I guess recently S4Vectors
> introduced an S4 method summary,Vector-method. Probably the dispatch system
> sees the inherited S4 method before your S3 method, and the solution is to
> change your S3 method to S4. Best practice would do this for all S3 methods
> defined on S4 classes.
> >
> > Martin
> >
> > On 7/8/19, 10:46 AM, "Bioc-devel on behalf of Ioannis Vardaxis" <
> bioc-devel-bounces using r-project.org on behalf of ioannis.vardaxis using ntnu.no>
> wrote:
> >
> >    Hey,
> >
> >    My package (MACPET) has been crashing lately. The error I get is from
> the vignette:
> >
> >
> >    Error in .Vector_summary(object, ...) : unused argument (heatmap =
> TRUE)
> >    Calls: <Anonymous> ... withCallingHandlers -> withVisible -> eval ->
> eval -> summary -> summary
> >    Execution halted
> >
> >    When I call the summary function which is specified on one of my
> classes.
> >
> >    I realised that for some reason all the methods that I had created
> and worked fine for every class, they just don’t work anymore.
> >
> >    I have no idea what causes the error..
> >
> >
> >    Best,
> >
> >    Ioannis
> >
> >       [[alternative HTML version deleted]]
> >
> >    _______________________________________________
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> >    https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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