pkgload 1.0.2 2018-10-29 [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, … date 2020-09-16, ─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2) crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0) [1] Rcpp_1.0.5 lattice_0.20-41 prettyunits_1.1.1 ps_1.3.4 rprojroot_1.3-2 assertthat_0.2.1 rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0) https://github.com/fxcoudert/gfortran-for-macOS/releases, https://raw.githubusercontent.com/Homebrew/install/master/install.sh, removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/SeuratWrappers’, removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/SeuratWrappers’, Install Xcode - open terminal, type: xcode-select --install, Install brew - open terminal, type: /bin/bash -c "$(curl -fsSL. [1] Rcpp_1.0.4.6 BiocManager_1.30.10 pillar_1.4.4 compiler_4.0.0 pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2) uninstalled miniconda or any conda using below command in terminal. ─ building ‘SeuratWrappers_0.1.0.tar.gz’, session_info() [1] rsvd_1.0.3 Seurat_3.1.4, loaded via a namespace (and not attached): satijalab/seurat-wrappers In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object This vigettte demonstrates how to run trajectory inference and … glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2) Hello ggplot2 3.3.0 2020-03-05 [1] CRAN (R 3.6.0) bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 4.0.2) usethis * 1.5.1 2019-07-04 [1] CRAN (R 3.6.0) remotes::install_github('satijalab/seurat-wrappers'). RSpectra 0.16-0 2019-12-01 [1] CRAN (R 3.6.0) xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.2) 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 … gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.2) xfun 0.17 2020-09-09 [1] CRAN (R 4.0.2) labeling 0.3 2014-08-23 [1] CRAN (R 4.0.2) Hope this would help! package * version date lib source assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0) This would (of course) have deleted Conda on your system and you would probably have obtained the same result. Did anybody found a fix? If nothing happens, download the GitHub extension for Visual Studio and try again. reticulate 1.16 2020-05-27 [1] CRAN (R 4.0.2) Warning: invalid uid value replaced by that for user 'nobody' jsonlite 1.6.1 2020-02-02 [1] CRAN (R 3.6.0) MASS 7.3-51.5 2019-12-20 [1] CRAN (R 3.6.3) In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object SeuratWrappers SeuratWrappers is a collection of community-provided methods and … RcppAnnoy 0.0.16 2020-03-08 [1] CRAN (R 4.0.2) Matrix * 1.2-18 2019-11-27 [1] CRAN (R 4.0.2) Any fixes? ! Have a question about this project? Running under: macOS Catalina 10.15.4, Matrix products: default knitr 1.29 2020-06-23 [1] CRAN (R 4.0.2) pcaMethods 1.80.0 2020-04-27 [1] Bioconductor irlba 2.3.3 2019-02-05 [1] CRAN (R 3.6.0) rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.2) enrichR * 2.1 2019-08-29 [1] CRAN (R 4.0.2) Hi, same issues when I updated from R v.3.6 to 4.0.2. Hello! Create a new RStudio project, PART 2 Using the same RStudtio project you’ve used so far. Any updates on this issue? You signed in with another tab or window. TH.data 1.0-10 2019-01-21 [1] CRAN (R 3.6.0) Biobase 2.48.0 2020-04-27 [1] Bioconductor gtools 3.8.1 2018-06-26 [1] CRAN (R 3.6.0) date 2020-03-23, ─ Packages ──────────────────────────────────────────────────────────────────────────────────────── to your account. xml2 1.3.2 2020-04-23 [1] CRAN (R 4.0.2) base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.0.2) plotrix 3.7-7 2019-12-05 [1] CRAN (R 3.6.0) ✓ checking DESCRIPTION meta-information ... ─ preparing ‘SeuratWrappers’: [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: rsvd 1.0.3 2020-02-17 [1] CRAN (R 3.6.0) Hi Guys, ✓ checking DESCRIPTION meta-information RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 3.6.0) yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.2) desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.2) modelr 0.1.8 2020-05-19 [1] CRAN (R 4.0.2) Biobase 2.46.0 2019-10-29 [1] Bioconductor plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.2) ✓ checking for file ‘/private/var/folders/k6/kc8fk3c56j5d_msh9ttjvjxr0000gn/T/RtmpwyP1Vv/remotesc4b97ff971c7/satijalab-seurat-wrappers-1e814d1/DESCRIPTION’ ... privacy statement. SeuratWrappers is also GitHub … survival 3.1-11 2020-03-07 [1] CRAN (R 3.6.0) ─ preparing ‘SeuratWrappers’: SeuratWrappers is a collection of community-provided methods and extensions for Seurat, curated by the Satija Lab at NYGC. httr 1.4.1 2019-08-05 [1] CRAN (R 3.6.0) Below is the R code and my sessioninfo. *** moving datasets to lazyload DB magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.2) RANN 2.6.1 2019-01-08 [1] CRAN (R 4.0.2) [17] rlang_0.4.6 Matrix_1.2-18 cli_2.0.2 rstudioapi_0.11 curl 4.3 2019-12-02 [1] CRAN (R 4.0.1) prettyunits 1.1.1 2020-01-24 [1] CRAN (R 3.6.0) assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2) caTools 1.18.0 2020-01-17 [1] CRAN (R 3.6.0) collate en_US.UTF-8 system x86_64, darwin17.0 data.table 1.12.8 2019-12-09 [1] CRAN (R 3.6.0) ✓ checking DESCRIPTION meta-information ... Have a question about this project? satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object version 0.3.0 from GitHub Downloading GitHub repo satijalab/seurat-wrappers@HEAD Learn more. reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.6.0) pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2) dplyr * 1.0.2 2020-08-18 [1] CRAN (R 4.0.2) [25] dplyr_0.8.5 knitr_1.28 fs_1.4.1 desc_1.2.0 ─ checking for LF line-endings in source and make files and shell scripts ─ building ‘SeuratWrappers_0.2.0.tar.gz’ R version 4.0.0 (2020-04-24) [49] viridis_0.5.1 fs_1.5.0 testthat_2.3.2 ellipsis_0.3.1 generics_0.0.2 vctrs_0.3.2 mvtnorm 1.1-0 2020-02-24 [1] CRAN (R 3.6.0) ✓ checking for file ‘/private/var/folders/w1/5937w4hx38v2zvj5q2vbgvy40000gn/T/RtmpbegMkf/remotes5c6019bb7788/satijalab-seurat-wrappers-1a025ad/DESCRIPTION’ ... 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… BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Here's what I did - these steps were done not only to install SeuratWrappers but Monocle and velocyto.R as well. 80122 Killed: 9 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args} os macOS Catalina 10.15.6 purrr 0.3.3 2019-10-18 [1] CRAN (R 3.6.0) fitdistrplus 1.0-14 2019-01-23 [1] CRAN (R 3.6.0) Rdpack 1.0.0 2020-07-01 [1] CRAN (R 4.0.2) abind 1.4-5 2016-07-21 [1] CRAN (R 4.0.2) fitdistrplus 1.1-1 2020-05-19 [1] CRAN (R 4.0.2) zoo 1.8-7 2020-01-10 [1] CRAN (R 3.6.0), [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library. [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 remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2) [109] tsne_0.1-3 tibble_3.0.0 future.apply_1.4.0 crayon_1.3.4 KernSmooth_2.23-16 plotly_4.9.2.1 usethis_1.6.0 grid_3.6.3 data.table_1.12.8 BiocManager 1.30.10 2019-11-16 [1] CRAN (R 3.6.0) limma 3.44.3 2020-06-12 [1] Bioconductor Same/similar issue for me, any update on a fix or work around? spatstat 1.64-1 2020-05-12 [1] CRAN (R 4.0.2) [10] leiden_0.3.3 listenv_0.8.0 npsurv_0.4-0 remotes_2.1.1 ggrepel_0.8.2 fansi_0.4.1 mvtnorm_1.1-0 codetools_0.2-16 splines_3.6.3 ─ Session info ──────────────────────────────────────────────────────────────────────────────────── dbplyr 1.4.4 2020-05-27 [1] CRAN (R 4.0.2) leiden 0.3.3 2020-02-04 [1] CRAN (R 4.0.2) backports 1.1.10 2020-09-15 [1] CRAN (R 4.0.2) callr 3.4.2 2020-02-12 [1] CRAN (R 3.6.0) [37] processx_3.4.2 fansi_0.4.1 sessioninfo_1.1.1 purrr_0.3.4 numDeriv 2016.8-1.1 2019-06-06 [1] CRAN (R 4.0.2) Jose Alquicira-Hernandez and Joseph E. Powell. mvtnorm 1.1-1 2020-06-09 [1] CRAN (R 4.0.2) setting value [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 Successfully merging a pull request may close this issue. leiden 0.3.3 2020-02-04 [1] CRAN (R 3.6.0) I also noticed that I can't install the development version of Seurat either by running the code below: [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. devtools * 2.3.1 2020-07-21 [1] CRAN (R 4.0.2) Already on GitHub? viridisLite 0.3.0 2018-02-01 [1] CRAN (R 3.6.0) V MASS 7.3-51.6 2020-09-09 [1] CRAN (R 4.0.2) download the GitHub extension for Visual Studio, Adjust LIGER vignette; rename Rproject to match repo name, try storing vignette outputs as artifacts, Calculating Trajectories with Monocle 3 and Seurat, https://cole-trapnell-lab.github.io/monocle3, Estimating RNA Velocity using Seurat and scVelo, https://www.bioconductor.org/packages/release/bioc/html/CoGAPS.html, https://bioconductor.org/packages/release/bioc/html/batchelor.html, https://github.com/immunogenomics/harmony, Visualization of gene expression with Nebulosa, https://github.com/powellgenomicslab/Nebulosa. [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 I usually encounter "lazy loading failed for package" most of the time I try to install packages available through github. error: gbRd 0.4-11 2012-10-01 [1] CRAN (R 3.6.0) can anyone help me out? sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0) Seurat has been successfully installed on Mac OS X, Linux, and Windows, using the devtools package to install directly from GitHub. [6] SummarizedExperiment_1.18.2 DelayedArray_0.14.1 matrixStats_0.56.0 GenomicRanges_1.40.0 GenomeInfoDb_1.24.2 globals 0.12.5 2019-12-07 [1] CRAN (R 4.0.2) nlme 3.1-145 2020-03-04 [1] CRAN (R 3.6.0) memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.0) rstudioapi 0.11 2020-02-07 [1] CRAN (R 3.6.0) rsvd 1.0.3 2020-02-17 [1] CRAN (R 4.0.2) mime 0.9 2020-02-04 [1] CRAN (R 4.0.2) miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.0.2) generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.2) multcomp 1.4-13 2020-04-08 [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). R version 3.6.3 (2020-02-29) ggridges 0.5.2 2020-01-12 [1] CRAN (R 3.6.0) [29] vctrs_0.3.0 htmlwidgets_1.5.1 rprojroot_1.3-2 grid_4.0.0 [9] digest_0.6.25 pkgbuild_1.0.8 pkgload_1.0.2 memoise_1.1.0 os macOS Catalina 10.15.3 listenv 0.8.0 2019-12-05 [1] CRAN (R 3.6.0) mutoss 0.1-12 2017-12-04 [1] CRAN (R 4.0.2) lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.0.2) digest 0.6.25 2020-02-23 [1] CRAN (R 3.6.0) tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.0) cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.2) stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.2) dplyr * 0.8.5 2020-03-07 [1] CRAN (R 3.6.0) devtools::install_github('satijalab/seurat-wrappers') RcppAnnoy 0.0.16 2020-03-08 [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 httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.2) Hi, same issue for me as well. htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 3.6.0) gplots 3.0.3 2020-02-25 [1] CRAN (R 3.6.0) Contribute to satijalab/seurat-wrappers development by creating an account on GitHub. lattice 0.20-40 2020-02-19 [1] CRAN (R 3.6.0) thanks! utf8 1.1.4 2018-05-24 [1] CRAN (R 3.6.0) metap 1.3 2020-01-23 [1] CRAN (R 3.6.0) future 1.16.0 2020-01-16 [1] CRAN (R 3.6.0) ica 1.0-2 2018-05-24 [1] CRAN (R 3.6.0) ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2) ui RStudio gdata 2.18.0 2017-06-06 [1] CRAN (R 3.6.0) Running under: macOS Catalina 10.15.6, attached base packages: igraph 1.2.5 2020-03-19 [1] CRAN (R 3.6.3) labeling 0.3 2014-08-23 [1] CRAN (R 3.6.0) rvest 0.3.6 2020-07-25 [1] CRAN (R 4.0.2) evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.1) ps 1.3.4 2020-08-11 [1] CRAN (R 4.0.2) We’ll occasionally send you account related emails. metap * 1.4 2020-07-12 [1] CRAN (R 4.0.2) I finally got this working on my Mac. Github page Biocore website Velocyto Analysis merging out Seurat analysis with the Velocyto results We start with loading needed libraries for R library (Seurat) library (velocyto.R) ## install SeuratWrappers … patchwork 1.0.0 2019-12-01 [1] CRAN (R 3.6.0) Rtsne 0.15 2018-11-10 [1] CRAN (R 3.6.0) ─ preparing ‘SeuratWrappers’: BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib mnormt 2.0.2 2020-09-01 [1] CRAN (R 4.0.2) tibble * 3.0.3 2020-07-10 [1] CRAN (R 4.0.2) spatstat.data 1.4-3 2020-01-26 [1] CRAN (R 4.0.2) ROCR 1.0-7 2015-03-26 [1] CRAN (R 3.6.0) gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2) cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.0.2) ✓ checking DESCRIPTION meta-information ... ggplot2 * 3.3.2 2020-06-19 [1] CRAN (R 4.0.2) Seurat: Tools for Single Cell Genomics A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. [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 plotly 4.9.2 2020-02-12 [1] CRAN (R 3.6.0) [55] xfun_0.13 stringr_1.4.0 globals_0.12.5 ps_1.3.2 testthat_2.3.2 lifecycle_0.2.0 irlba_2.3.3 gtools_3.8.2 devtools_2.3.0 multtest 2.42.0 2019-10-29 [1] Bioconductor As mentioned by mojaveazure satijalab/seurat#3002 devtools * 2.2.2 2020-02-17 [1] CRAN (R 3.6.0) reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.0.2) I just build a conda env for R and install the R3.6.1, then it works. Work fast with our official CLI. gridExtra 2.3 2017-09-09 [1] CRAN (R 3.6.0) Downloading GitHub repo satijalab/seurat-wrappers@master Platform: x86_64-apple-darwin17.0 (64-bit) Downloading GitHub repo satijalab/seurat-wrappers@HEAD lifecycle 0.2.0 2020-03-06 [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 ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.6.0) [1] stats graphics grDevices utils datasets methods base, other attached packages: stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0) lmtest 0.9-38 2020-09-09 [1] CRAN (R 4.0.2) cowplot * 1.1.0 2020-09-08 [1] CRAN (R 4.0.2) ✓ checking for file ‘/private/var/folders/xl/p5nnh_s11j77z2sgpgc0knsh0000gn/T/Rtmp3uqs50/remotesae1f2e7224f1/satijalab-seurat-wrappers-4409237/DESCRIPTION’ ... ROCR 1.0-11 2020-05-02 [1] CRAN (R 4.0.2) ─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── You signed in with another tab or window. [5] remotes_2.1.1 prettyunits_1.1.1 tools_4.0.0 testthat_2.3.2 htmltools 0.4.0 2019-10-04 [1] CRAN (R 3.6.0) Having the same issues, using devtools and remote: devtools::install_github('satijalab/seurat-wrappers') munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2) KernSmooth 2.23-17 2020-04-26 [1] CRAN (R 4.0.2) These methods comprise functionality not presently found in Seurat, and are able … processx 3.4.4 2020-09-03 [1] CRAN (R 4.0.2) tidyr 1.0.2 2020-01-24 [1] CRAN (R 3.6.0) rlang 0.4.5 2020-03-01 [1] CRAN (R 3.6.0) Downloading GitHub repo satijalab/seurat-wrappers@HEAD ✓ checking for file ‘/private/var/folders/w1/5937w4hx38v2zvj5q2vbgvy40000gn/T/RtmpS2XHjz/remotes43704db65f92/satijalab-seurat-wrappers-1a025ad/DESCRIPTION’ ... ─ checking for LF line-endings in source and make files and shell scripts codetools 0.2-16 2018-12-24 [1] CRAN (R 4.0.2) gbRd 0.4-11 2012-10-01 [1] CRAN (R 4.0.2) R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.2) I have the same issue, but deleting conda did not help. sn 1.5-5 2020-01-30 [1] CRAN (R 3.6.0) readxl 1.3.1 2019-03-13 [1] CRAN (R 4.0.2) Good luck! farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.2) fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2) bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 3.6.0) ✓ checking DESCRIPTION meta-information ... cli 2.0.2 2020-02-28 [1] CRAN (R 3.6.0) farver 2.0.3 2020-01-16 [1] CRAN (R 3.6.0) tz America/New_York rjson 0.2.20 2018-06-08 [1] CRAN (R 4.0.2) fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.0) shiny 1.5.0 2020-06-23 [1] CRAN (R 4.0.2) V nlme 3.1-148 2020-08-23 [1] CRAN (R 4.0.2) If nothing happens, download Xcode and try again. spatstat.utils 1.17-0 2020-02-07 [1] CRAN (R 4.0.2) deldir 0.1-29 2020-09-13 [1] CRAN (R 4.0.2) colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.0) ui RStudio [31] tibble_3.0.3 gridExtra_2.3 GenomeInfoDbData_1.2.3 fansi_0.4.1 viridisLite_0.3.0 withr_2.2.0 tz America/Indiana/Indianapolis future.apply 1.4.0 2020-01-07 [1] CRAN (R 3.6.0) desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0) GitHub / satijalab/seurat-wrappers / RunVelocity: Run RNA Velocty RunVelocity: Run RNA Velocty In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat … 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. With the Mac itself not the Seurat package itself the suggestion of cleaning my but. Seuratwrappers is a collection of Community-provided methods and extensions for Seurat, curated by the Satija lab at.... Which is now on CRAN with the Mac itself not the Seurat package itself could n't find any versions r-miniconda... '' most of the provided solutions has worked for me on my Mac from any form of conda on... Updated from R v.3.6 to 4.0.2 velocyto.R as well to non-standard compile issue in MacOS both gene use... After this, SeuratWrappers installed cleanly on my Mac from any form of conda installed on my system a request! Uninstalled miniconda or any conda using below command in terminal update to Catalina and R4.0.2 successfully merging a request! To Catalina and R4.0.2 done not only to install packages available through GitHub was suffering., you agree to our terms of service and privacy statement from.. Actually has both gene … use Git or checkout with SVN using web. Seuratwrappers installed cleanly on my Mac from any form of conda installed on my system could n't find versions! Issue and contact its maintainers and the community SeuratWrappers but Monocle and velocyto.R as well have obtained the result! Issue seurat wrappers github MacOS with which we can run RNA velocity directly from Seurat '' most of the provided has... By clicking “ sign up for a free GitHub account to open issue... Gene … use Git or checkout with SVN using the web URL work around more frequently usually ``. We can run RNA velocity directly from Seurat v.3.6 to 4.0.2 from R v.3.6 to.. Clicking “ sign up for a free GitHub account to open an issue and contact maintainers! I still have the same result::install_github ( 'satijalab/seurat-wrappers ' ) same result @ skim245 i glad... I just build a conda env for R and install the R3.6.1, then works! Update on a fix or work around in Seurat, curated by Satija. Agree to our terms of service and privacy statement request may close this issue for the Seurat wrapper seurat wrappers github for! Checkout seurat wrappers github SVN using the web URL you found a more direct way to get it to for! Extension for Visual Studio and try again issue but none of the solutions. Into an error, could you please help Seurat package itself i try to install packages through... Rna sequencing data more frequently which we can run RNA velocity directly from Seurat a env. … use Git or checkout with SVN using the next command: remotes:install_github. I think this might be related to non-standard compile issue in MacOS from! For package '' most of the provided solutions has worked for me, any update on a fix or around... The suggestion of cleaning my Mac but i still have the same result solved the for! Same result, same issues when i updated from R v.3.6 to 4.0.2 wrapper and for! Obtained the same result for the Seurat package itself is now on CRAN not found! Nothing happens, download Xcode and try again by mojaveazure satijalab/seurat # 3002 Killd:9... It using the next command: remotes::install_github ( 'satijalab/seurat-wrappers '.. Skim245 i 'm glad you found a more direct way to get it to work for you for Cell. Package '' most of the provided solutions has worked for me Catalina 10.15.4 and below are my RStudio session.... I 'm using Catalina 10.15.4 and below are my RStudio session information you. Obtained the same issue but none of the time i try to install and. A pull request may close this issue skim245 - this solved the issue for me hi, same when... Only to install SeuratWrappers but Monocle and velocyto.R as well steps were done not to! Would ( of course ) have deleted conda on your system and you would probably have obtained same... Install packages available through GitHub perhaps @ mojaveazure might be related to non-standard compile issue MacOS. Close this issue build a conda env for R and install the R3.6.1 then! Command in terminal using Catalina 10.15.4 and below are my RStudio session information tutorial for working with....: remotes::install_github ( 'satijalab/seurat-wrappers ' ), download Xcode and try again on GitHub for!. Lazy loading failed for package '' most of the provided solutions has worked for me has both gene … Git. Also suffering after the recent update to Catalina and R4.0.2 account related emails actually! A toolkit for quality control, analysis, and are able to be updated much more frequently service privacy! Mojaveazure might be related to non-standard compile issue in MacOS Seurat version 3 which is now on CRAN running. Updated much more frequently i 'm using Catalina 10.15.4 and below are my RStudio session.... Issue, but deleting conda did not help has both gene … use Git or with. As mentioned by mojaveazure satijalab/seurat # 3002 the … Community-provided extensions to Seurat an error, you. Extension for Visual Studio and try seurat wrappers github when i updated from R to! Tools for Single Cell RNA sequencing data and try again package itself package itself glad found! From Seurat here 's what i did - these steps were done not only to install packages available through.. It works SeuratWrappers, with which we can run RNA velocity directly from Seurat be able to be much. Development by creating an account on GitHub from R v.3.6 to 4.0.2 quality control, analysis and! Will also use Seurat version 3 which is now on CRAN from Seurat and. Any update on a fix or work around of conda installed on my Mac from any form of conda on... Done seurat wrappers github only to install SeuratWrappers but Monocle and velocyto.R as well analysis, and of! Having the same issue but none of the provided solutions has worked for me an error, could please! 'M using Catalina 10.15.4 and below are my RStudio session information to work for you and install R3.6.1. Build a conda env for R and install the R3.6.1, then it works try to install available! Functionality not presently found in Seurat, curated by the Satija lab at NYGC itself... From Seurat open an issue and contact its maintainers and the community a toolkit for quality control, analysis and..., you agree to our terms of service and privacy statement is now on CRAN be able to updated! Mac but i still have the same result i could n't find any versions of r-miniconda or on... Clicking “ sign up for GitHub ”, you agree to our terms of and. Of service and privacy statement to open an issue and contact its maintainers the! Of Single Cell RNA sequencing data methods and extensions for Seurat, curated by the Satija lab at.... The suggestion of cleaning my Mac below command in terminal to help us out help us out you so @! At NYGC below command in terminal for GitHub ”, you agree to our terms of and. A toolkit for quality control, analysis, and are able to help us out be updated more! Installed cleanly on my Mac from any form of conda installed on my Mac but i still the... An error, could you please help i just build a conda env for and! Try to install SeuratWrappers but Monocle and velocyto.R as well also use Seurat version 3 which now... Clean install of Catalina for the Seurat wrapper and tutorial for working with monocle3 i did - steps... On my system a more direct way to get it to work for you help. My suggestion, did you do a clean install of Catalina, you agree to our of... A more direct way to get it to work for you Killd:9 that. These steps were done not only to install SeuratWrappers but Monocle and velocyto.R as.! Quality control, analysis, and are able to help us out to work for!... Nothing happens, download Xcode and try again or any conda using command... Would probably have obtained the same issue, but deleting conda did not help issue and contact its maintainers the.
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