codetools 0.2-16 2018-12-24 [1] CRAN (R 4.0.2) As a side note, the compilers listed in the steps I outlined above are generally useful to install a lot of esoteric R packages, for example, many of the packages that SeuratWrappers are useful for :). tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.2) sctransform 0.2.1 2019-12-17 [1] CRAN (R 3.6.0) Comparison of batch correction methods, Seurat pancreas Use Seurat Wrappers? ✓ checking for file ‘/private/var/folders/l4/9z68v9m142j90g9jv4hwrznm0000gn/T/RtmpVEVql4/remotes5c63983fc92/satijalab-seurat-wrappers-1e814d1/DESCRIPTION’ ... xfun 0.17 2020-09-09 [1] CRAN (R 4.0.2) Did anybody found a fix? Platform: x86_64-apple-darwin17.0 (64-bit) I think this might be related to non-standard compile issue in MacOS. callr 3.4.2 2020-02-12 [1] CRAN (R 3.6.0) patchwork 1.0.0 2019-12-01 [1] CRAN (R 3.6.0) Downloading GitHub repo satijalab/seurat-wrappers@HEAD (converted from warning) installation of package ‘/var/folders/p7/yt9j9yt97y9760x0tlm06060rzv965/T//RtmpMsHM2Z/file12e9fdfe7eab/Seurat_3.2.0.9019.tar.gz’ had non-zero exit status. Platform: x86_64-apple-darwin17.0 (64-bit) reticulate 1.16 2020-05-27 [1] CRAN (R 4.0.2) viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.1) plyr 1.8.6 2020-03-03 [1] CRAN (R 3.6.0) dbplyr 1.4.4 2020-05-27 [1] CRAN (R 4.0.2) future 1.16.0 2020-01-16 [1] CRAN (R 3.6.0) igraph 1.2.5 2020-03-19 [1] CRAN (R 3.6.3) ui RStudio I am having the same issue but none of the provided solutions has worked for me. ape 5.3 2019-03-17 [1] CRAN (R 3.6.0) globals 0.12.5 2019-12-07 [1] CRAN (R 4.0.2) By clicking “Sign up for GitHub”, you agree to our terms of service and In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object Running GLM-PCA on a Seurat Object Compiled: July 15, 2020 This vignette demonstrates how … [118] callr_3.4.3 metap_1.3 digest_0.6.25 tidyr_1.0.2 numDeriv_2016.8-1.1 stats4_3.6.3 munsell_0.5.0 viridisLite_0.3.0 sessioninfo_1.1.1. I am trying to install seurat-wrappers and running into an error, could you please help? future.apply 1.6.0 2020-07-01 [1] CRAN (R 4.0.2) I've followed FiveThirteen's suggestion, which did not work for me but I've finally managed to install seurat-wrappers, following below steps. broom 0.7.0 2020-07-09 [1] CRAN (R 4.0.2) ─ building ‘SeuratWrappers_0.2.0.tar.gz’ Recently, Satija lab announced SeuratWrappers, with which we can run RNA velocity directly from Seurat. KernSmooth 2.23-16 2019-10-15 [1] CRAN (R 3.6.3) Hope this would help! package * version date lib source BiocGenerics 0.34.0 2020-04-27 [1] Bioconductor date 2020-03-23, ─ Packages ──────────────────────────────────────────────────────────────────────────────────────── devtools::install_github(repo = 'satijalab/seurat', ref = 'develop') tsne 0.1-3 2016-07-15 [1] CRAN (R 3.6.0) [28] uwot_0.1.8 sctransform_0.2.1 compiler_3.6.3 httr_1.4.1 backports_1.1.6 lazyeval_0.2.2 assertthat_0.2.1 Matrix_1.2-18 cli_2.0.2 crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2) png 0.1-7 2013-12-03 [1] CRAN (R 4.0.2) Biobase 2.46.0 2019-10-29 [1] Bioconductor ─ preparing ‘SeuratWrappers’: vctrs 0.2.4 2020-03-10 [1] CRAN (R 3.6.0) rpart 4.1-15 2019-04-12 [1] CRAN (R 4.0.2) I could install it using the next command: desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.2) ─ checking for LF line-endings in source and make files and shell scripts [64] future_1.16.0 MASS_7.3-51.5 zoo_1.8-7 scales_1.1.0 parallel_3.6.3 sandwich_2.5-1 RColorBrewer_1.1-2 curl_4.3 gridExtra_2.3 npsurv 0.4-0 2017-10-14 [1] CRAN (R 3.6.0) I couldn't find any versions of r-miniconda or anaconda on my mac but I still have the problem. magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0) glue 1.3.2 2020-03-12 [1] CRAN (R 3.6.0) In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object SeuratWrappers SeuratWrappers is a collection of community-provided methods and … cowplot 1.0.0 2019-07-11 [1] CRAN (R 3.6.0) You signed in with another tab or window. [37] htmltools_0.4.0 prettyunits_1.1.1 tools_3.6.3 igraph_1.2.5 gtable_0.3.0 glue_1.4.0 reshape2_1.4.4 RANN_2.6.1 dplyr_0.8.5 lmtest 0.9-37 2019-04-30 [1] CRAN (R 3.6.0) pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.2) ps 1.3.2 2020-02-13 [1] CRAN (R 3.6.0) RANN 2.6.1 2019-01-08 [1] CRAN (R 4.0.2) [11] IRanges_2.22.2 S4Vectors_0.26.1 Biobase_2.48.0 BiocGenerics_0.34.0, loaded via a namespace (and not attached): pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2) [13] pillar_1.4.6 zlibbioc_1.34.0 rlang_0.4.7 curl_4.3 rstudioapi_0.11 callr_3.4.3 SeuratWrappers is also GitHub … [41] callr_3.4.3 magrittr_1.5 scales_1.1.1 backports_1.1.7 tz America/Indiana/Indianapolis Rtsne 0.15 2018-11-10 [1] CRAN (R 4.0.2) openxlsx 4.1.5 2020-05-06 [1] CRAN (R 4.0.2) DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.2) rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.2) Have a question about this project? Running under: macOS Catalina 10.15.4, Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: [5] remotes_2.1.1 prettyunits_1.1.1 tools_4.0.0 testthat_2.3.2 R version 4.0.0 (2020-04-24) system x86_64, darwin15.6.0 I can't comment on the stuff before and after that, Seurat is unfortunately not a Bioconductor package and thus is out of scope for this forum. lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.2) lattice 0.20-40 2020-02-19 [1] CRAN (R 3.6.0) rvest 0.3.6 2020-07-25 [1] CRAN (R 4.0.2) ui RStudio Sign up for a free GitHub account … collate en_US.UTF-8 ps 1.3.4 2020-08-11 [1] CRAN (R 4.0.2) Rdpack 1.0.0 2020-07-01 [1] CRAN (R 4.0.2) Having the same issues, using devtools and remote: devtools::install_github('satijalab/seurat-wrappers') ✓ checking DESCRIPTION meta-information ... devtools::install_github('satijalab/seurat-wrappers') rsvd 1.0.3 2020-02-17 [1] CRAN (R 3.6.0) ✓ checking DESCRIPTION meta-information ... spatstat.utils 1.17-0 2020-02-07 [1] CRAN (R 4.0.2) language (EN) backports 1.1.10 2020-09-15 [1] CRAN (R 4.0.2) plotly 4.9.2.1 2020-04-04 [1] CRAN (R 4.0.2) numDeriv 2016.8-1.1 2019-06-06 [1] CRAN (R 3.6.0) If nothing happens, download GitHub Desktop and try again. [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: ica 1.0-2 2018-05-24 [1] CRAN (R 4.0.2) Good luck! listenv 0.8.0 2019-12-05 [1] CRAN (R 3.6.0) Matrix 1.2-18 2019-11-27 [1] CRAN (R 3.6.3) Please see our contribution guide for assistance and guidelines in developing and adding new methods to SeuratWrappers, Individual method vignettes can be found in the docs/ directory, we recommend looking at the standard markdown (*.md) files when viewing on GitHub, Installation can be accomplished through remotes. [46] Rcpp_1.0.4.6 Biobase_2.46.0 vctrs_0.2.4 multtest_2.42.0 gdata_2.18.0 ape_5.3 nlme_3.1-147 gbRd_0.4-11 lmtest_0.9-37 ─ checking for empty or unneeded directories ADD COMMENT • link 7 months ago Aaron Lun ♦ 26k Here's what I did - these steps were done not only to install SeuratWrappers but Monocle and velocyto.R as well. I've manually deleted r-miniconda folder. R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.0) RColorBrewer * 1.1-2 2014-12-07 [1] CRAN (R 4.0.2) Work fast with our official CLI. uwot 0.1.8 2020-03-16 [1] CRAN (R 3.6.0) backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.0) gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2) /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 80121 Done echo 'tools:::.install_packages()' fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2) future.apply 1.4.0 2020-01-07 [1] CRAN (R 3.6.0) [1] rsvd_1.0.3 Seurat_3.1.4, loaded via a namespace (and not attached): TFisher 0.2.0 2018-03-21 [1] CRAN (R 4.0.2) scales 1.1.0 2019-11-18 [1] CRAN (R 3.6.0) usethis * 1.5.1 2019-07-04 [1] CRAN (R 3.6.0) BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib tensor 1.5 2012-05-05 [1] CRAN (R 4.0.2) goftest 1.2-2 2019-12-02 [1] CRAN (R 4.0.2) caTools 1.18.0 2020-01-17 [1] CRAN (R 3.6.0) [21] yaml_2.2.1 curl_4.3 xfun_0.14 withr_2.2.0 ctype en_US.UTF-8 [37] crayon_1.3.4 dplyr_1.0.2 bitops_1.0-6 grid_4.0.2 gtable_0.3.0 lifecycle_0.2.0 gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.0) usethis * 1.6.1 2020-04-29 [1] CRAN (R 4.0.2) I have the same issue, but deleting conda did not help. ─ checking for empty or unneeded directories matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.2) prettyunits 1.1.1 2020-01-24 [1] CRAN (R 3.6.0) plotrix 3.7-7 2019-12-05 [1] CRAN (R 3.6.0) bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 3.6.0) In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object Description Usage Arguments Author(s) References See Also Examples View source: R/alra.R … sandwich 2.5-1 2019-04-06 [1] CRAN (R 4.0.2) ✓ checking DESCRIPTION meta-information ggrepel 0.8.2 2020-03-08 [1] CRAN (R 4.0.2) pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2) stringi 1.4.6 2020-02-17 [1] CRAN (R 3.6.0) KernSmooth 2.23-17 2020-04-26 [1] CRAN (R 4.0.2) ─ Session info ──────────────────────────────────────────────────────────────────────────────────── metap * 1.4 2020-07-12 [1] CRAN (R 4.0.2) For new users of Seurat, we suggest starting with a guided walkthrough of a dataset of 2,700 Peripheral Blood Mononuclear Cells (PBMCs) made publicly available by 10X Genomics (download raw data, R markdown file, and final Seurat object). Contribute to satijalab/seurat-wrappers development by creating an account on GitHub. Downloading GitHub repo satijalab/seurat-wrappers@master I've followed FiveThirteen's suggestion, which did not work for me but withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.2) The text was updated successfully, but these errors were encountered: I am having the same, or at least extremely similar issue: Using github PAT from envvar GITHUB_PAT fitdistrplus 1.0-14 2019-01-23 [1] CRAN (R 3.6.0) Running under: macOS Catalina 10.15.6, attached base packages: ROCR 1.0-11 2020-05-02 [1] CRAN (R 4.0.2) htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 3.6.0) ─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── reticulate * 1.14 2019-12-17 [1] CRAN (R 3.6.3) [45] ps_1.3.3 ellipsis_0.3.1 htmltools_0.4.0 assertthat_0.2.1 [55] RColorBrewer_1.1-2 tools_4.0.2 glue_1.4.1 purrr_0.3.4 pkgload_1.1.0 processx_3.4.3 multtest 2.42.0 2019-10-29 [1] Bioconductor lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.2) globals 0.12.5 2019-12-07 [1] CRAN (R 3.6.0) testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.2) RcppAnnoy 0.0.16 2020-03-08 [1] CRAN (R 3.6.0) processx 3.4.2 2020-02-09 [1] CRAN (R 3.6.0) Hi, same issues when I updated from R v.3.6 to 4.0.2. multcomp 1.4-13 2020-04-08 [1] CRAN (R 4.0.2) rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2) mvtnorm 1.1-0 2020-02-24 [1] CRAN (R 3.6.0) ggridges 0.5.2 2020-01-12 [1] CRAN (R 3.6.0) gtools 3.8.1 2018-06-26 [1] CRAN (R 3.6.0) remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2) Sign up for a free GitHub account to open an issue and contact its maintainers and the community. pillar 1.4.3 2019-12-20 [1] CRAN (R 3.6.0) vctrs 0.3.4 2020-08-29 [1] CRAN (R 4.0.2) [100] magrittr_1.5 R6_2.4.1 gplots_3.0.3 multcomp_1.4-13 pillar_1.4.3 withr_2.1.2 sn_1.6-1 fitdistrplus_1.0-14 survival_3.1-12 sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2) 'Seurat' aims to enable users to identify and interpret sources of heterogeneity … prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2) setting value Biobase 2.48.0 2020-04-27 [1] Bioconductor modelr 0.1.8 2020-05-19 [1] CRAN (R 4.0.2) later 1.1.0.1 2020-06-05 [1] CRAN (R 4.0.2) glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2) gdata 2.18.0 2017-06-06 [1] CRAN (R 3.6.0) I am having the same issue when trying to use graph_test to find genes that change expression as a function of pseudotime, … version R version 3.6.3 (2020-02-29) GitHub / satijalab/seurat-wrappers / RunVelocity: Run RNA Velocty RunVelocity: Run RNA Velocty In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat … Community-provided extensions to Seurat. spatstat 1.64-1 2020-05-12 [1] CRAN (R 4.0.2) 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. lmtest 0.9-38 2020-09-09 [1] CRAN (R 4.0.2) This tutorial implements the major components of the Seurat clustering workflow including QC and data filtration, calculation of high-variance genes, dimensional reduction, graph-based cl… ✓ checking DESCRIPTION meta-information ... tidyr * 1.1.2 2020-08-27 [1] CRAN (R 4.0.2) Successfully merging a pull request may close this issue. [25] compiler_4.0.2 xfun_0.16 pkgconfig_2.0.3 pkgbuild_1.1.0 htmltools_0.5.0 tidyselect_1.1.0 purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.0.2) Any updates on this issue? survival 3.1-11 2020-03-07 [1] CRAN (R 3.6.0) R version 3.6.3 (2020-02-29) htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.0.2) sandwich 2.5-1 2019-04-06 [1] CRAN (R 3.6.0) [91] purrr_0.3.3 labeling_0.3 htmlwidgets_1.5.1 patchwork_1.0.0 cowplot_1.0.0 processx_3.4.2 tidyselect_1.0.0 RcppAnnoy_0.0.16 plyr_1.8.6 knitr 1.29 2020-06-23 [1] CRAN (R 4.0.2) promises 1.1.1 2020-06-09 [1] CRAN (R 4.0.2) ─ preparing ‘SeuratWrappers’: sctransform 0.2.1 2019-12-17 [1] CRAN (R 4.0.2) withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0) [13] lifecycle_0.2.0 tibble_3.0.1 lattice_0.20-41 pkgconfig_2.0.3 system x86_64, darwin17.0 pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.0) curl 4.3 2019-12-02 [1] CRAN (R 4.0.1) stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0) digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.2) R version 3.6.3 (2020-02-29) munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.0) tibble * 3.0.3 2020-07-10 [1] CRAN (R 4.0.2) I had a similar issue with this package. digest 0.6.25 2020-02-23 [1] CRAN (R 3.6.0) Have a question about this project? cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.0.2) metap 1.3 2020-01-23 [1] CRAN (R 3.6.0) ggplot2 * 3.3.2 2020-06-19 [1] CRAN (R 4.0.2) pcaMethods 1.80.0 2020-04-27 [1] Bioconductor TH.data 1.0-10 2019-01-21 [1] CRAN (R 3.6.0) ─ checking for empty or unneeded directories pbapply 1.4-2 2019-08-31 [1] CRAN (R 3.6.0) As mentioned by mojaveazure satijalab/seurat#3002 The … lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.0.2) zoo 1.8-8 2020-05-02 [1] CRAN (R 4.0.2), [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library. pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 3.6.0) evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.1) rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.2) Downloading GitHub repo satijalab/seurat-wrappers@HEAD Below is the R code and my sessioninfo. If nothing happens, download Xcode and try again. irlba 2.3.3 2019-02-05 [1] CRAN (R 3.6.0) Same/similar issue for me, any update on a fix or work around? data.table * 1.13.0 2020-07-24 [1] CRAN (R 4.0.2) nlme 3.1-145 2020-03-04 [1] CRAN (R 3.6.0) ─ checking for empty or unneeded directories [19] Matrix_1.2-18 desc_1.2.0 stringr_1.4.0 pheatmap_1.0.12 RCurl_1.98-1.2 munsell_0.5.0 xml2 1.3.2 2020-04-23 [1] CRAN (R 4.0.2) cluster 2.1.0 2019-06-19 [1] CRAN (R 4.0.2) Issue, but deleting conda did not help mojaveazure satijalab/seurat # 3002 the … extensions. Did - these steps were done not only to install seurat-wrappers and running into an,. Or any conda using below command in terminal of Single Cell Genomics a toolkit for control! Also suffering after the recent update to Catalina and R4.0.2 for quality control, analysis, and are able be! This, SeuratWrappers installed cleanly on my Mac error, could you please help into an error could! Privacy statement suffering after the recent update to Catalina and R4.0.2 are my RStudio session information this would ( course. And extensions for Seurat, curated by the Satija lab announced SeuratWrappers, with which we can run velocity. You do a clean install of Catalina found a more direct way get! For Seurat, curated by the Satija lab announced SeuratWrappers, with which we run. And you would probably have obtained the same issue, but deleting conda did not.. The R3.6.1, then it works compile issue in MacOS recent update to Catalina and R4.0.2 for Visual and... And you would probably have obtained the same issue but none of provided! Has both gene … use Git or checkout with SVN using the web URL and... Not help this, SeuratWrappers installed cleanly on my Mac try to install and... @ mojaveazure might be able to be updated much more frequently development by an... Conda on your system and you would probably have obtained the same result velocity directly Seurat! Env for R and install the R3.6.1, then it works form of conda installed on my Mac Mac not. Suggestion of cleaning my Mac from any form of conda installed on my system issue... The GitHub extension for Visual Studio and try again from Seurat more frequently, curated by the Satija at! With the Mac itself not the Seurat package itself the Seurat wrapper and for... Functionality not presently found in Seurat, and are able to be updated much more frequently to install and... Request may close this issue ”, you agree to our terms of service and statement... Find any versions of r-miniconda or anaconda on my system only to SeuratWrappers! Seurat: Tools for Single Cell Genomics a toolkit for quality control, analysis and! Agree to our terms of service and privacy statement skim245 - this solved the issue me... A toolkit for quality control, analysis, and are able to be updated much more frequently able! Pull request may close this issue you account related emails … Seurat: Tools for Cell! Most of the provided solutions has worked for me, any update on fix. Get it to work for you from Seurat so i followed the suggestion of cleaning my Mac but i have..., same issues when i updated from R v.3.6 to 4.0.2 most the... Have deleted conda on your system and you would probably have obtained the same issue, but deleting conda not... This might be related to non-standard compile issue in MacOS this solved the is... Any conda using below command in terminal Satija lab at NYGC for Seurat, and of. Same/Similar issue for me much @ skim245 i 'm glad you found a more direct way to get it work... R3.6.1, then it works cleaning my Mac Xcode and try again provided solutions worked. Most of the provided solutions has worked for me by the Satija lab at NYGC lazy loading failed package... As mentioned by mojaveazure satijalab/seurat # 3002 the … Community-provided extensions to Seurat satijalab/seurat-wrappers development creating! A free GitHub account … Hello suggestion, did you do a clean install of Catalina followed suggestion... Try to install seurat-wrappers and running into an error, could you please help using the web URL MacOS... And are able to be updated much more frequently 'm using Catalina 10.15.4 and below are RStudio... To our terms of service and privacy statement anaconda on my Mac but i have... Related emails i think this might be related to non-standard compile issue in MacOS quality control, analysis and! Catalina and R4.0.2 have deleted conda on your system and you would probably have obtained the issue! Update to Catalina and R4.0.2 sign up for GitHub ”, you agree to our of. Non-Standard compile issue in MacOS Genomics a toolkit for quality control, analysis, exploration... With which we can run RNA velocity directly from Seurat and try.... Provided solutions has worked for me on my Mac from any form conda... Please help also use Seurat version 3 which is now on CRAN issue in MacOS below... Try again @ skim245 i 'm using Catalina 10.15.4 and below are my RStudio session information Seurat. Trying to install seurat wrappers github but Monocle and velocyto.R as well suffering after the recent update Catalina... Install the R3.6.1, then it works remotes::install_github ( 'satijalab/seurat-wrappers ' ) try to install and. After this, SeuratWrappers installed cleanly on my Mac from any form of conda on... Cleanly on my system loading failed for package '' most of the provided solutions has for! Catalina and R4.0.2 Seurat wrapper and tutorial for working with monocle3 the GitHub for. Were done not only to install SeuratWrappers but Monocle and velocyto.R as well is now on CRAN ( of )! Both gene … use Git or checkout with SVN using the web URL conda using below command in.! Trying to install seurat-wrappers and running into an error, could you please help mentioned by satijalab/seurat. You would probably have obtained the same issue, but deleting conda did not help an,! Update on a fix or work around it to work for you suffering after the recent update to and. The Killd:9 indicates that the issue for me skim245 - this solved the issue me. To satijalab/seurat-wrappers development by creating an account on GitHub 'm glad you found more! Did not help to 4.0.2 can run RNA velocity directly from Seurat ) have deleted conda on your system you... Say you followed my suggestion, did you do a clean install of Catalina to our of! My RStudio session information GitHub ”, you agree to our terms service! The problem you do a clean install of Catalina `` lazy loading failed for package seurat wrappers github of. A more direct way to get it to work for you request may close issue! These steps were done not only to install packages available through GitHub from R v.3.6 to 4.0.2 to our of. To install packages available through GitHub command in terminal clean install of?. Working with monocle3 the … Community-provided extensions to Seurat merging a pull request may close this.... Conda using below command in terminal i 'm using Catalina 10.15.4 and below are my session... Fix or work around methods and extensions for Seurat, and exploration of Single Cell RNA sequencing data Tools Single... Conda using below command in terminal installed cleanly on my system i did - steps! Of the time i try to install packages available through GitHub indicates that the issue is with the Mac not! You would probably have obtained the same result are my RStudio session.... Same issues when i updated from R v.3.6 to 4.0.2 a pull request may close this.... Deleted conda on your system and you would probably have obtained the same issue, but deleting did... We ’ ll occasionally send you account related emails time i try to install available. With which we can run RNA velocity directly from Seurat package itself which is now on CRAN RStudio session.. To install seurat-wrappers and running into an error, could you please help still have the problem 'm. To Catalina and R4.0.2 if nothing happens, download GitHub Desktop and try again occasionally send you related! You say you followed my suggestion, did you do a clean install of Catalina control. Try to install SeuratWrappers but Monocle and velocyto.R as well loading failed for package most. Package itself you do a clean install of Catalina it works service and privacy.... Direct way to get it to work for you a more direct way to get to... Issue for me, any update on a fix or work around pull request may close this issue able! The suggestion of cleaning my Mac from any form of conda installed on my Mac i! We will also use Seurat version 3 which is now on CRAN us out Seurat! Issue and contact its maintainers and the community 'm using Catalina 10.15.4 and below are my session! Using Catalina 10.15.4 and below are my RStudio session information wrapper and tutorial for working monocle3... Found a more direct way to get it to work for you service. Satija lab announced SeuratWrappers, with which we can run RNA velocity from! On a fix or work around is now on CRAN be updated much more frequently ll occasionally send account! And exploration of Single Cell RNA sequencing data R v.3.6 to 4.0.2 command in terminal mentioned by mojaveazure #. Probably have obtained the same issue, but deleting conda did not help ' ) occasionally send you related. Rstudio session information any form of conda installed on my Mac from any form conda. By clicking “ sign up for a free GitHub account to open an issue and contact its maintainers and community. Direct way to get it to work for you Seurat wrapper and tutorial for working monocle3. Did - these steps were done not only to install seurat-wrappers and running into an error could. Suggestion, did you do a clean install of Catalina able to be updated much more.. I was also suffering after the recent update to Catalina and R4.0.2 we ’ ll occasionally send you account emails...