Well, it's not really SingleCellExperiment's problem, either. library(S4Vectors) DataFrame(1:5) # Silent, okay. library(RNeXML) DataFrame(1:5) # Prints out the message ## Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors' ## Also defined by ‘RNeXML’
Session information attached below. -Aaron > sessionInfo() R Under development (unstable) (2018-03-26 r74466) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.4 LTS Matrix products: default BLAS: /home/cri.camres.org/lun01/Software/R/trunk/lib/libRblas.so LAPACK: /home/cri.camres.org/lun01/Software/R/trunk/lib/libRlapack.so locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] RNeXML_2.0.8 ape_5.1 S4Vectors_0.17.41 [4] BiocGenerics_0.25.3 loaded via a namespace (and not attached): [1] Rcpp_0.12.16 compiler_3.6.0 pillar_1.2.1 [4] plyr_1.8.4 bindr_0.1.1 iterators_1.0.9 [7] tools_3.6.0 uuid_0.1-2 jsonlite_1.5 [10] tibble_1.4.2 nlme_3.1-137 lattice_0.20-35 [13] pkgconfig_2.0.1 rlang_0.2.0 foreach_1.4.4 [16] crul_0.5.2 curl_3.2 bindrcpp_0.2.2 [19] httr_1.3.1 stringr_1.3.0 dplyr_0.7.4 [22] xml2_1.2.0 grid_3.6.0 reshape_0.8.7 [25] glue_1.2.0 data.table_1.10.4-3 R6_2.2.2 [28] XML_3.98-1.10 purrr_0.2.4 reshape2_1.4.3 [31] tidyr_0.8.0 magrittr_1.5 codetools_0.2-15 [34] assertthat_0.2.0 bold_0.5.0 taxize_0.9.3 [37] stringi_1.1.7 lazyeval_0.2.1 zoo_1.8-1 On Thu, 2018-04-12 at 17:40 +0200, Elizabeth Purdom wrote: > 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 (http > s://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/Framewor > > ks/vecLib.framework/Versions/A/libBLAS.dylib > > LAPACK: > > /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapa > > ck.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 SingleCellE > > xperiment_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 GenomicRang > > es_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 reshape > > 2_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 <epurdom@stat.Berkel > > ey.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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel