My seesionInfo:
> sessionInfo()
R Under development (unstable) (2019-07-11 r76823)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5
And
> BiocManager::install("stringdist")
Bioconductor version 3.10 (BiocManager 1.30.4), R Under development (unstable)
(2019-07-11 r76823)
Installing package(s) 'stringdist'
Warning: unable to access index for repository
https://bioconductor.org/packages/3.10/data/annotation/bin/macosx/el-capitan/contrib/3.7:
cannot open URL
'https://bioconductor.org/packages/3.10/data/annotation/bin/macosx/el-capitan/contrib/3.7/PACKAGES'
Warning: unable to access index for repository
https://bioconductor.org/packages/3.10/data/experiment/bin/macosx/el-capitan/contrib/3.7:
cannot open URL
'https://bioconductor.org/packages/3.10/data/experiment/bin/macosx/el-capitan/contrib/3.7/PACKAGES'
Warning: unable to access index for repository
https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.7:
cannot open URL
'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.7/PACKAGES'
Package which is only available in source form, and may need compilation of
C/C++/Fortran: ‘stringdist’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
Also, I cannot such to RELEASE_3_10 because I get error:
$git checkout RELEASE_3_10
error: pathspec 'RELEASE_3_10' did not match any file(s) known to git
12. jul. 2019 kl. 16:20 skrev Vincent Carey
<st...@channing.harvard.edu<mailto:st...@channing.harvard.edu>>:
It should be possible to get stringdist as a binary package for mac. provide
your sessionInfo().
> BiocManager::install("stringdist")
Bioconductor version 3.10 (BiocManager 1.30.4), R 3.6.0 Patched (2019-05-06
r76460)
Installing package(s) 'stringdist'
trying URL
'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/stringdist_0.9.5.2.tgz'
Content type 'application/x-gzip' length 567740 bytes (554 KB)
==================================================
downloaded 554 KB
On Fri, Jul 12, 2019 at 10:13 AM Ioannis Vardaxis
<ioannis.varda...@ntnu.no<mailto:ioannis.varda...@ntnu.no>> wrote:
I have changed the S4methods now and the Rcheck is working fine locally on my
machine.
I cannot run BiocCheck because I cannot install it on my Mac anymore. It
depends on a package named stringdist, which cannot be installed in my Mac. I
get an error:
clang: error: unsupported option '-fopenmp'
However I have pushed the changes to the repository now and we will see if the
devel version gets fixed.
Best,
Ioannis
> 8. jul. 2019 kl. 11:20 skrev Martin Morgan
> <mtmorgan.b...@gmail.com<mailto:mtmorgan.b...@gmail.com>>:
>
> Under bioc-devel, I ran
>
> MACPET/vignettes$ 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-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org> on
> behalf of ioannis.varda...@ntnu.no<mailto:ioannis.varda...@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]]
>
> _______________________________________________
> Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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