Hi Martin and Hervé, The problem lies in the pre-built binaries. Installing SGSeq from source fixes the installation. I bumped the version number for SGSeq to trigger a rebuild, but I guess other packages are affected as well. Among SGSeq dependencies it looks like Rsamtools needs a version bump too.
Thanks, Leonard On Thu, Feb 9, 2017 at 4:19 AM, Martin Morgan <martin.mor...@roswellpark.org > wrote: > On 02/09/2017 06:25 AM, Hervé Pagès wrote: > >> Hi Leonard, >> >> mmh... I can't reproduce this and it doesn't show up on the build report >> either. But I got another strange error when I tried to *install* >> SGSeq: something about TxFeatures not being able to extend GenomicRanges >> because of incompatible type for the elementMetadata slot. >> >> I got rid of it by re-installing GenomicRanges from svn. >> I guess I had some stalled class definition somewhere in a cache. >> >> Looks like maybe you also have a stalled class definition somewhere >> in a cache for one of SGFeatureCounts's parent classes. Not sure which >> one though :-/ >> >> Maybe I forgot to bump a package version somewhere after I renamed >> characterORNULL -> character_OR_NULL? Re-installing S4Vectors, IRanges, >> GenomicRanges, and SummarizedExperiment directly from svn might help. >> > > See also https://support.bioconductor.org/p/92201/#92205 where > > GeneSetCollection extends 'list', which extends 'vector' > > GSEABase Depends: on annotate which Depends: on AnnotationDbi which > Imports: S4Vectors. > > S4Vectors defines a class union on vector_OR_factor (previously > vectorORfactor). Consequently, GeneSetCollection extends vector_OR_factor. > > Class definitions are cached at package installation time, so GSEABase > class definitions became out-of-date when S4Vectors was updated. > > A conservative approach is to bump the version of all packages that depend > on S4Vectors, even GSEABase which is three steps away from S4Vectors. I > believe that this involves > > db = available.packages(repos=BiocInstaller::biocinstallRepos()[1]) > revdeps = tools::package_dependencies("S4Vectors", db, recursive=TRUE, > reverse=TRUE) > > which is > > > length(revdeps$S4Vectors) > [1] 662 > > packages! > > Leonard could find candidates for re-installation with > > > mydep = tools::package_dependencies("SGSeq", db, recursive=TRUE) > > mydep$SGSeq[mydep$SGSeq %in% revdeps$S4Vectors] > [1] "IRanges" "GenomicRanges" "Rsamtools" > [4] "SummarizedExperiment" "AnnotationDbi" "Biostrings" > [7] "GenomicAlignments" "GenomicFeatures" "GenomeInfoDb" > [10] "rtracklayer" "XVector" "biomaRt" > [13] "DelayedArray" > > Martin > > > >> Cheers, >> H. >> >> On 02/08/2017 04:18 PM, Leonard Goldstein wrote: >> >>> Hi Hervé, >>> >>> It looks like there have been some changes in bioc-devel (S4Vectors etc.) >>> that break the SGSeq package (see below). I'm not sure whether this is >>> something that needs to be addressed in SGSeq or its dependencies. I'd be >>> grateful for any pointers. Thanks for your help. >>> >>> Leonard >>> >>> -- >>> >>>> example(makeSGFeatureCounts, "SGSeq") >>>> >>> >>> mkSGFC> sgfc <- makeSGFeatureCounts(sgf_pred, si, >>> mkSGFC+ matrix(0L, length(sgf_pred), nrow(si))) >>> Error in checkSlotAssignment(object, name, value) : >>> assignment of an object of class "NULL" is not valid for slot >>> 'NAMES' in >>> an object of class "SGFeatureCounts"; is(value, "characterORNULL") is not >>> TRUE >>> >>>> >>>> sessionInfo() >>>> >>> R Under development (unstable) (2017-02-06 r72129) >>> Platform: x86_64-apple-darwin13.4.0 (64-bit) >>> Running under: OS X El Capitan 10.11.6 >>> >>> locale: >>> [1] C >>> >>> attached base packages: >>> [1] stats4 parallel stats graphics grDevices utils datasets >>> [8] methods base >>> >>> other attached packages: >>> [1] SGSeq_1.9.1 SummarizedExperiment_1.5.5 >>> [3] DelayedArray_0.1.4 Biobase_2.35.0 >>> [5] Rsamtools_1.27.12 Biostrings_2.43.4 >>> [7] XVector_0.15.2 GenomicRanges_1.27.22 >>> [9] GenomeInfoDb_1.11.9 IRanges_2.9.18 >>> [11] S4Vectors_0.13.13 BiocGenerics_0.21.3 >>> >>> loaded via a namespace (and not attached): >>> [1] igraph_1.0.1 Rcpp_0.12.9 >>> AnnotationDbi_1.37.2 >>> >>> [4] magrittr_1.5 zlibbioc_1.21.0 >>> GenomicAlignments_1.11.9 >>> [7] BiocParallel_1.9.5 lattice_0.20-34 tools_3.4.0 >>> >>> [10] grid_3.4.0 DBI_0.5-1 digest_0.6.12 >>> >>> [13] Matrix_1.2-8 GenomeInfoDbData_0.99.0 rtracklayer_1.35.5 >>> >>> [16] bitops_1.0-6 RUnit_0.4.31 biomaRt_2.31.4 >>> >>> [19] RCurl_1.95-4.8 memoise_1.0.0 RSQLite_1.1-2 >>> >>> [22] compiler_3.4.0 GenomicFeatures_1.27.6 XML_3.98-1.5 >>> >>> >>>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >>> >> > > This email message may contain legally privileged and/or confidential > information. 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