[Bioc-devel] Problems with MACPET package

Ioannis Vardaxis |o@nn|@@v@rd@x|@ @end|ng |rom ntnu@no
Mon Jul 15 09:53:44 CEST 2019


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 <stvjc using channing.harvard.edu<mailto:stvjc using 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.vardaxis using ntnu.no<mailto: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<mailto: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<mailto:bioc-devel-bounces using r-project.org> on behalf of ioannis.vardaxis using ntnu.no<mailto: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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