Fails to install dependencies after running dynwrap::infer_trajectories with umap

[PGuen]

Hi, i'm running a dynwrap command infer_trajectories as follows:

model_gng <- infer_trajectory(dataset, parameters = list(dimred="umap", ndim=2), method = "gng")

and get the following error message:

Loading required package: dynutils Installing uwot Warning in download.packages(x$name, destdir = dest_dir, repos = x$repos, : no package ‘uwot’ at the repositories Installation failed: subscript out of bounds Installed uwot Loading required namespace: uwot Failed with error: ‘there is no package called ‘uwot’’ Error in loadNamespace(name) : there is no package called ‘uwot’ Calls: ... tryCatch -> tryCatchList -> tryCatchOne -> Execution halted Error traceback: 2: 1: Error: Error during trajectory inference

Obviously, dynoutils cannot install the rpackage uwot. I can install uwot without any issue. Interestingly, when calling dynutils::install_packages(dependencies = "uwot", package = "dyndimred") directly I do get a NULL response. Can you think of any issue, which leads to this?

Thanks and I highly appreciate your fantastic package!

R version 3.5.1 (2018-07-02) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default attached base packages: [1] splines parallel stats4 stats graphics grDevices utils
[8] datasets methods base
other attached packages: [1] scales_1.0.0 uwot_0.0.0.9005
[3] shiny_1.1.0 bindrcpp_0.2.2
[5] forcats_0.3.0 purrr_0.2.5
[7] tidyr_0.8.1 tibble_1.4.2
[9] tidyverse_1.2.1.9000 dyno_0.1.0
[11] dynwrap_0.1.0 dynplot_0.1.0
[13] dynmethods_0.1.0 dynguidelines_0.1.0
[15] dynfeature_0.1.0 slingshot_0.99.12
[17] princurve_2.1.3 VGAM_1.0-5
[19] monocle_2.99.1 DDRTree_0.1.5
[21] irlba_2.3.2 igraph_1.2.2
[23] Matrix.utils_0.9.7 Seurat_2.3.4
[25] Matrix_1.2-14 cowplot_0.9.3
[27] DESeq2_1.20.0 SummarizedExperiment_1.10.1 [29] DelayedArray_0.6.6 BiocParallel_1.14.2
[31] matrixStats_0.54.0 Biobase_2.40.0
[33] GenomicRanges_1.32.7 GenomeInfoDb_1.16.0
[35] IRanges_2.14.12 S4Vectors_0.18.3
[37] BiocGenerics_0.26.0 tximport_1.8.0
[39] dplyr_0.7.7 reshape2_1.4.3
[41] stringr_1.3.1 useful_1.2.6
[43] ggplot2_3.0.0 readr_1.1.1
[45] RevoUtils_11.0.1 RevoUtilsMath_11.0.0
loaded via a namespace (and not attached): [1] mixtools_1.1.0 pbapply_1.3-4
[3] lattice_0.20-35 haven_1.1.2
[5] dyndimred_0.1.0 expm_0.999-3
[7] fastICA_1.2-1 usethis_1.4.0
[9] mgcv_1.8-24 blob_1.1.1
[11] survival_2.42-6 dynutils_1.0.1.9000
[13] later_0.7.5 DBI_1.0.0
[15] R.utils_2.7.0 SingleCellExperiment_1.2.0 [17] L1Graph_0.1.1 bindr_0.1.1
[19] zlibbioc_1.26.0 SDMTools_1.1-221
[21] htmlwidgets_1.3 mvtnorm_1.0-8
[23] future_1.10.0 hdf5r_1.0.1
[25] laeken_0.4.6 DEoptimR_1.0-8
[27] tidygraph_1.1.0 lars_1.2
[29] Rcpp_0.12.19 KernSmooth_2.23-15
[31] promises_1.0.1 gdata_2.18.0
[33] limma_3.36.5 pkgload_1.0.1
[35] locfdr_1.1-8 RcppParallel_4.4.1
[37] Hmisc_4.1-1 RSpectra_0.13-1
[39] fs_1.2.6 fastmatch_1.1-0
[41] ranger_0.10.1 digest_0.6.18
[43] png_0.1-7 rncl_0.8.3
[45] qlcMatrix_0.9.7 LearnBayes_2.15.1
[47] glmnet_2.0-16 ggraph_1.0.2
[49] pkgconfig_2.0.2 docopt_0.6.1
[51] gridBase_0.4-7 DelayedMatrixStats_1.2.0
[53] iterators_1.0.10 reticulate_1.9
[55] modeltools_0.2-22 zoo_1.8-4
[57] tidyselect_0.2.5 kernlab_0.9-27
[59] GA_3.1.1 ica_1.0-2
[61] viridisLite_0.3.0 snow_0.4-3
[63] pkgbuild_1.0.2 rlang_0.2.2
[65] manipulateWidget_0.10.0 dyneval_0.1.0
[67] glue_1.3.0 metap_1.0
[69] RColorBrewer_1.1-2 registry_0.5
[71] modelr_0.1.2 fpc_2.1-11.1
[73] pkgmaker_0.27 labeling_0.3
[75] gbRd_0.4-11 httpuv_1.4.5
[77] class_7.3-14 pbmcapply_1.2.5
[79] grr_0.9.5 annotate_1.58.0
[81] webshot_0.5.1 jsonlite_1.5
[83] XVector_0.20.0 bit_1.1-14
[85] mime_0.6 gridExtra_2.3
[87] gplots_3.0.1 stringi_1.2.4
[89] gmodels_2.18.1 processx_3.2.0
[91] bitops_1.0-6 cli_1.0.1
[93] Rdpack_0.10-1 RSQLite_2.1.1
[95] pheatmap_1.0.10 data.table_1.11.8
[97] rsconnect_0.8.8 ParamHelpers_1.11
[99] spData_0.2.9.4 rstudioapi_0.8
[101] units_0.6-1 nlme_3.1-137
[103] locfit_1.5-9.1 listenv_0.7.0
[105] ggthemes_4.0.1 miniUI_0.1.1.1
[107] R.oo_1.22.0 prabclus_2.2-6
[109] segmented_0.5-3.0 TTR_0.23-4
[111] sessioninfo_1.1.0 readxl_1.1.0
[113] howmany_0.3-1 munsell_0.5.0
[115] cellranger_1.1.0 R.methodsS3_1.7.1
[117] caTools_1.17.1.1 codetools_0.2-15
[119] shades_1.2.0 coda_0.19-2
[121] lmtest_0.9-36 shinyWidgets_0.4.3
[123] htmlTable_1.12 lsei_1.2-0
[125] xtable_1.8-3 ROCR_1.0-7
[127] diptest_0.75-7 scatterplot3d_0.3-41
[129] abind_1.4-5 farver_1.0
[131] FNN_1.1.2.1 RANN_2.6
[133] BBmisc_1.11 sparsesvd_0.1-4
[135] bibtex_0.4.2 rgl_0.99.16
[137] patchwork_0.0.1 cluster_2.0.7-1
[139] dendextend_1.9.0 prettyunits_1.0.2
[141] lubridate_1.7.4 ggridges_0.5.1
[143] mclust_5.4.1 RcppEigen_0.3.3.4.0
[145] shinyjs_1.0 remotes_2.0.1
[147] slam_0.1-43 destiny_2.10.2
[149] VIM_4.7.0 testthat_2.0.1
[151] doSNOW_1.0.16 htmltools_0.3.6
[153] yaml_2.2.0 NMF_0.21.0
[155] utf8_1.1.4 XML_3.98-1.16
[157] e1071_1.7-0 foreign_0.8-71
[159] withr_2.1.2 fitdistrplus_1.0-11
[161] bit64_0.9-7 rngtools_1.3.1
[163] foreach_1.5.0 robustbase_0.93-3
[165] devtools_2.0.0 memoise_1.1.0
[167] rio_0.5.10 geneplotter_1.58.0
[169] callr_3.0.0 ps_1.2.0
[171] curl_3.2 fansi_0.4.0
[173] xts_0.11-1 rje_1.9
[175] trimcluster_0.1-2.1 acepack_1.4.1
[177] checkmate_1.8.5 desc_1.2.0
[179] npsurv_0.4-0 deldir_0.1-15
[181] openxlsx_4.1.0 ggrepel_0.8.0
[183] ade4_1.7-13 dtw_1.20-1
[185] rprojroot_1.3-2 tools_3.5.1
[187] magrittr_1.5 RCurl_1.95-4.11
[189] proxy_0.4-22 car_3.0-2
[191] ape_5.2 xml2_1.2.0
[193] httr_1.3.1 assertthat_0.2.0
[195] boot_1.3-20 globals_0.12.4
[197] R6_2.3.0 Rhdf5lib_1.2.1
[199] nnet_7.3-12 progress_1.2.0
[201] genefilter_1.62.0 gtools_3.8.1
[203] HDF5Array_1.8.1 rhdf5_2.24.0
[205] carData_3.0-2 colorspace_1.3-2
[207] base64enc_0.1-3 smoother_1.1
[209] pillar_1.3.0 clusterExperiment_2.0.2
[211] tweenr_1.0.0 sp_1.3-1
[213] HSMMSingleCell_0.114.0 uuid_0.1-2
[215] GenomeInfoDbData_1.1.0 plyr_1.8.4
[217] gtable_0.2.0 pdist_1.2
[219] rvest_0.3.2 zip_1.0.0
[221] lpSolveAPI_5.5.2.0-17 knitr_1.20
[223] latticeExtra_0.6-28 crosstalk_1.0.0
[225] doParallel_1.0.14 spdep_0.7-9
[227] flexmix_2.3-14 AnnotationDbi_1.42.1
[229] vcd_1.4-4 broom_0.5.0
[231] babelwhale_0.0.0.9000 backports_1.1.2
[233] RNeXML_2.1.2 densityClust_0.3
[235] hms_0.4.2 ggforce_0.1.3
[237] Rtsne_0.13 grid_3.5.1
[239] lazyeval_0.2.1 Formula_1.2-3
[241] tsne_0.1-3 whisker_0.3-2
[243] phylobase_0.8.4 crayon_1.3.4
[245] MASS_7.3-51 viridis_0.5.1
[247] rpart_4.1-13 compiler_3.5.1

[rcannood]

Hello PGuen,

I've just pushed an update to dynwrap which would solve this issue. The containers for each of the methods will need to be rebuilt, which might take a while. I'll keep you up to date.

Robrecht

[rcannood]

I updated all of the dockers, including ti_gng. After updating dynmethods (devtools::install_github("dynverse/dynmethods", upgr = TRUE)), could you confirm whether your issue has been resolved?

[rcannood]

Hello @PGuen ,

I'm assuming your issue has been fixed. Please create a new issue if the problem persists.

Kind regards, Robrecht