jk86754
commented
5 years ago i was actually able to figure this out. I had to reinstall the package by cloning the git repo.
Closed jk86754 closed 5 years ago
jk86754
commented
5 years ago i was actually able to figure this out. I had to reinstall the package by cloning the git repo.
Hi,
I am trying to follow https://rawgit.com/urrutiag/destin/master/package/vignettes/10xGenomicsPBMC.html
Everyting seems to work all the way until plotting the clusters. At that point I get
Matrix products: default BLAS: /sc/wo/app/R/v3.5.1/lib64/R/lib/libRblas.so LAPACK: /sc/wo/app/R/v3.5.1/lib64/R/lib/libRlapack.so
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats4 parallel grid stats graphics grDevices utils datasets [9] methods base
other attached packages: [1] ClusterR_1.1.8 gtools_3.8.1 Rtsne_0.15 irlba_2.3.3
[5] Matrix_1.2-17 gridExtra_2.3 ggplot2_3.1.0 DelayedArray_0.8.0
[9] BiocParallel_1.14.2 matrixStats_0.54.0 Biobase_2.42.0 data.table_1.12.0
[13] cluster_2.0.7-1 ChIPpeakAnno_3.16.1 VennDiagram_1.6.20 futile.logger_1.4.3 [17] GenomicRanges_1.34.0 GenomeInfoDb_1.18.2 Biostrings_2.48.0 XVector_0.22.0
[21] IRanges_2.16.0 S4Vectors_0.20.1 BiocGenerics_0.28.0
loaded via a namespace (and not attached): [1] nlme_3.1-137 ProtGenerics_1.14.0 bitops_1.0-6
[4] bit64_0.9-7 progress_1.2.0 httr_1.4.0
[7] tools_3.5.1 vegan_2.5-4 R6_2.4.0
[10] mgcv_1.8-28 DBI_1.0.0 lazyeval_0.2.2
[13] colorspace_1.3-2 permute_0.9-5 ade4_1.7-13
[16] withr_2.1.2 tidyselect_0.2.5 prettyunits_1.0.2
[19] bit_1.1-14 curl_3.3 compiler_3.5.1
[22] graph_1.60.0 formatR_1.5 rtracklayer_1.42.2
[25] FD_1.0-12 scales_1.0.0 RBGL_1.58.2
[28] stringr_1.4.0 digest_0.6.18 Rsamtools_1.34.1
[31] pkgconfig_2.0.2 ensembldb_2.6.7 limma_3.38.3
[34] BSgenome_1.50.0 regioneR_1.14.0 rlang_0.3.3
[37] rstudioapi_0.10 RSQLite_2.1.1 bindr_0.1.1
[40] dplyr_0.7.8 RCurl_1.95-4.12 magrittr_1.5
[43] GO.db_3.7.0 GenomeInfoDbData_1.2.0 Rcpp_1.0.1
[46] munsell_0.5.0 abind_1.4-5 ape_5.2
[49] yaml_2.2.0 stringi_1.2.4 MASS_7.3-51.3
[52] SummarizedExperiment_1.12.0 zlibbioc_1.28.0 plyr_1.8.4
[55] blob_1.1.1 crayon_1.3.4 lattice_0.20-38
[58] splines_3.5.1 multtest_2.38.0 GenomicFeatures_1.34.7
[61] hms_0.4.2 pillar_1.3.0 seqinr_3.4-5
[64] biomaRt_2.38.0 magic_1.5-9 futile.options_1.0.1
[67] XML_3.98-1.18 glue_1.3.1 lambda.r_1.2.3
[70] BiocManager_1.30.4 idr_1.2 gtable_0.2.0
[73] purrr_0.3.2 assertthat_0.2.1 AnnotationFilter_1.6.0
[76] survival_2.44-1.1 geometry_0.3-6 tibble_1.4.2
[79] GenomicAlignments_1.18.1 AnnotationDbi_1.44.0 memoise_1.1.0
[82] bindrcpp_0.2.2 gmp_0.5-13.5
Is there anything obvious i am missing?
Thank you,
Joe