Just to follow up on my previous post. I am able to replicate the problem in the problem like in the github post from 2 years ago (https://github.com/epurdom/clusterExperiment/issues/66 <https://github.com/epurdom/clusterExperiment/issues/66>) only now it is not the SummarizedExperiment class but the SingleCellExperiment class that has the problem. [And I was incorrect, the problem does occur in development version 2018-03-22 r74446].
So this is actually a problem with the SingleCellExperiment package — sorry for the incorrect subject line. All of the best, Elizabeth > > library(SingleCellExperiment) > > SingleCellExperiment() > class: SingleCellExperiment > dim: 0 0 > metadata(0): > assays(0): > rownames: NULL > rowData names(0): > colnames: NULL > colData names(0): > reducedDimNames(0): > spikeNames(0): > > library(RNeXML) > Loading required package: ape > > > > SingleCellExperiment() > Found more than one class "Annotated" in cache; using the first, from > namespace 'S4Vectors' > Also defined by ‘RNeXML’ > Found more than one class "Annotated" in cache; using the first, from > namespace 'S4Vectors' > Also defined by ‘RNeXML’ > class: SingleCellExperiment > dim: 0 0 > metadata(0): > assays(0): > rownames: NULL > rowData names(0): > colnames: NULL > colData names(0): > reducedDimNames(0): > spikeNames(0): > > sessionInfo() > R Under development (unstable) (2018-03-22 r74446) > Platform: x86_64-apple-darwin15.6.0 (64-bit) > Running under: OS X El Capitan 10.11.6 > > Matrix products: default > BLAS: > /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib > LAPACK: > /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats4 stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] RNeXML_2.0.8 ape_5.1 > SingleCellExperiment_1.1.2 > [4] SummarizedExperiment_1.9.16 DelayedArray_0.5.30 > BiocParallel_1.13.3 > [7] matrixStats_0.53.1 Biobase_2.39.2 > GenomicRanges_1.31.23 > [10] GenomeInfoDb_1.15.5 IRanges_2.13.28 > S4Vectors_0.17.41 > [13] BiocGenerics_0.25.3 > > loaded via a namespace (and not attached): > [1] Rcpp_0.12.16 pillar_1.2.1 bindr_0.1.1 > compiler_3.5.0 > [5] plyr_1.8.4 XVector_0.19.9 iterators_1.0.9 > bitops_1.0-6 > [9] tools_3.5.0 zlibbioc_1.25.0 uuid_0.1-2 > tibble_1.4.2 > [13] jsonlite_1.5 nlme_3.1-137 lattice_0.20-35 > pkgconfig_2.0.1 > [17] rlang_0.2.0 Matrix_1.2-14 foreach_1.4.4 > crul_0.5.2 > [21] curl_3.2 bindrcpp_0.2.2 GenomeInfoDbData_1.1.0 > dplyr_0.7.4 > [25] httr_1.3.1 stringr_1.3.0 xml2_1.2.0 > grid_3.5.0 > [29] glue_1.2.0 reshape_0.8.7 data.table_1.10.4-3 > R6_2.2.2 > [33] XML_3.98-1.10 purrr_0.2.4 tidyr_0.8.0 > reshape2_1.4.3 > [37] magrittr_1.5 codetools_0.2-15 assertthat_0.2.0 > bold_0.5.0 > [41] taxize_0.9.3 stringi_1.1.7 lazyeval_0.2.1 > RCurl_1.95-4.10 > [45] zoo_1.8-1 > On Apr 11, 2018, at 10:25 AM, Elizabeth Purdom <epur...@stat.berkeley.edu> > wrote: > > Hello, > > Our package clusterExperiment has suddenly started producing errors in the > bioconductor devel branch because our unit tests are failing, even though we > haven’t pushed any changes and they passed previously. We first noticed this > on April 5th. > > I believe the source of these errors likely do to calls to > SummarizedExperiment() creating the following messages due to conflicts in > ‘RNeXML’ and ’S4Vectors’ both defining class ‘Annotated': > >> Found more than one class "Annotated" in cache; using the first, from >> namespace 'S4Vectors' >> Also defined by ‘RNeXML’ > This is killing a vast number of our tests where we repeatedly use > ‘expect_silent’ calls in our unit tests and SummarizedExperiment calls > underlie everything. > > We had this message issue two years ago > (https://github.com/epurdom/clusterExperiment/issues/66 > <https://github.com/epurdom/clusterExperiment/issues/66>), when it appeared > to be a problem with two definitions of the ‘Annotated’ class in two packages > that are both dependencies of packages we call. At that time, Michael > Lawrence posted that he would fix the problem, and it was then fixed in later > versions of bioconductor/R. But it appears to be back. I am unfortunately > unable to get the RNeXML package to compile from source on my computer with > the current Mac OS X development binary which I just downloaded (2018-04-05 > r74542), so I haven’t been able to completely redo the code that we presented > in that earlier github issue to confirm it is the exact same problem. I am > having to rely on the error reports/logs from both Bioconductor and TravisCI > (e.g. 2018-04-07 r74551), where this message shows up everywhere and didn’t > before. Thus I’m guessing that since they are the same messages from before > that the source is again the call to SummarizedExperiment. > > I would note that in development version 2018-03-22 r74446, where I was able > to install all of the packages, I was not getting these messages. > > Thanks, > Elizabeth Purdom [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
