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 > _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel The information in this e-mail is intended only for the person to whom it is addressed. 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