LTLA
commented
5 years ago You're not BiocManager::valid(), DelayedMatrixStats is an odd middle number while everything else is even (as is a few other packages, e.g., GenomicAlignments). Correct your installation and try again.
Hi
I am trying to follow the tutorial
https://master.bioconductor.org/packages/release/workflows/vignettes/simpleSingleCell/inst/doc/work-3-tenx.html
everything works fine except when I ran this line
sce <- denoisePCA(sce, technical=new.trend, approximate=TRUE)
Giving me this error
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object 'get_default_block_maxlength' not found
Can you help me pleae?
Thanks
**R version 3.5.2 (2018-12-20) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.6 LTS
Matrix products: default BLAS: /usr/lib/openblas-base/libblas.so.3 LAPACK: /usr/lib/libopenblasp-r0.2.18.so
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=es_ES.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=es_ES.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] scran_1.10.2 EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.5.3 AnnotationFilter_1.5.2
[5] GenomicFeatures_1.34.1 AnnotationDbi_1.44.0 scater_1.10.1 ggplot2_3.1.0
[9] dplyr_0.8.0.1 BiocFileCache_1.6.0 dbplyr_1.3.0 DropletUtils_1.2.2
[13] SingleCellExperiment_1.4.1 SummarizedExperiment_1.12.0 DelayedArray_0.8.0 matrixStats_0.54.0
[17] Biobase_2.42.0 GenomicRanges_1.34.0 GenomeInfoDb_1.18.2 IRanges_2.16.0
[21] S4Vectors_0.20.1 BiocGenerics_0.28.0 BiocParallel_1.16.6
loaded via a namespace (and not attached): [1] ProtGenerics_1.14.0 bitops_1.0-6 bit64_0.9-7 progress_1.2.0
[5] httr_1.3.1 dynamicTreeCut_1.63-1 tools_3.5.2 irlba_2.3.3
[9] R6_2.4.0 HDF5Array_1.10.1 vipor_0.4.5 DBI_1.0.0
[13] lazyeval_0.2.1 colorspace_1.4-0 withr_2.1.2 tidyselect_0.2.5
[17] gridExtra_2.3 prettyunits_1.0.2 bit_1.1-14 curl_3.3
[21] compiler_3.5.2 BiocNeighbors_1.0.0 rtracklayer_1.41.3 labeling_0.3
[25] scales_1.0.0 rappdirs_0.3.1 stringr_1.4.0 digest_0.6.18
[29] Rsamtools_1.33.3 XVector_0.22.0 pkgconfig_2.0.2 limma_3.38.3
[33] rlang_0.3.1 rstudioapi_0.9.0 RSQLite_2.1.1 DelayedMatrixStats_1.3.4 [37] RCurl_1.95-4.12 magrittr_1.5 GenomeInfoDbData_1.2.0 Matrix_1.2-16
[41] Rcpp_1.0.0 ggbeeswarm_0.6.0 munsell_0.5.0 Rhdf5lib_1.4.2
[45] viridis_0.5.1 stringi_1.4.3 yaml_2.2.0 edgeR_3.24.3
[49] zlibbioc_1.28.0 rhdf5_2.26.2 plyr_1.8.4 grid_3.5.2
[53] blob_1.1.1 crayon_1.3.4 lattice_0.20-38 cowplot_0.9.4
[57] Biostrings_2.50.2 hms_0.4.2 locfit_1.5-9.1 pillar_1.3.1
[61] igraph_1.2.4 reshape2_1.4.3 biomaRt_2.37.3 XML_3.98-1.19
[65] glue_1.3.1 gtable_0.2.0 purrr_0.3.1 assertthat_0.2.0
[69] viridisLite_0.3.0 tibble_2.0.1 GenomicAlignments_1.17.3 beeswarm_0.2.3
[73] memoise_1.1.0 statmod_1.4.30**