seurat wrappers github

Any fixes? [31] tibble_3.0.3 gridExtra_2.3 GenomeInfoDbData_1.2.3 fansi_0.4.1 viridisLite_0.3.0 withr_2.2.0 ctype en_US.UTF-8 [25] dplyr_0.8.5 knitr_1.28 fs_1.4.1 desc_1.2.0 [1] devtools_2.3.0 usethis_1.6.1, loaded via a namespace (and not attached): See Satija R, Farrell J, … gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.2) 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 … R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.2) [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 ✓ checking DESCRIPTION meta-information ... backports 1.1.10 2020-09-15 [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). broom 0.7.0 2020-07-09 [1] CRAN (R 4.0.2) homologene * 1.4.68.19.3.27 2019-03-28 [1] CRAN (R 4.0.2) KernSmooth 2.23-17 2020-04-26 [1] CRAN (R 4.0.2) rmarkdown 2.3 2020-06-18 [1] CRAN (R 4.0.2) LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.0) limma 3.44.3 2020-06-12 [1] Bioconductor colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.2) [29] vctrs_0.3.0 htmlwidgets_1.5.1 rprojroot_1.3-2 grid_4.0.0 ✓ checking for file ‘/private/var/folders/xl/p5nnh_s11j77z2sgpgc0knsh0000gn/T/Rtmp3uqs50/remotesae1f2e7224f1/satijalab-seurat-wrappers-4409237/DESCRIPTION’ ... Running under: macOS Catalina 10.15.6, attached base packages: Biobase 2.48.0 2020-04-27 [1] Bioconductor ape 5.3 2019-03-17 [1] CRAN (R 3.6.0) ggridges 0.5.2 2020-01-12 [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 ggrepel 0.8.2 2020-03-08 [1] CRAN (R 4.0.2) TFisher 0.2.0 2018-03-21 [1] CRAN (R 3.6.0) You signed in with another tab or window. mathjaxr 1.0-1 2020-06-25 [1] CRAN (R 4.0.2) usethis * 1.6.1 2020-04-29 [1] CRAN (R 4.0.2) [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 rsvd 1.0.3 2020-02-17 [1] CRAN (R 3.6.0) ✓ checking DESCRIPTION meta-information ... data.table * 1.13.0 2020-07-24 [1] CRAN (R 4.0.2) Below is the R code and my sessioninfo. 1k actually has both gene … evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.1) 1.5.4 Thursday – Classes from 08:00 to 16:00 Deciding on discussion topics for next day based on shared … ─ preparing ‘SeuratWrappers’: ─ checking for empty or unneeded directories [6] SummarizedExperiment_1.18.2 DelayedArray_0.14.1 matrixStats_0.56.0 GenomicRanges_1.40.0 GenomeInfoDb_1.24.2 callr 3.4.4 2020-09-07 [1] CRAN (R 4.0.2) enrichR * 2.1 2019-08-29 [1] CRAN (R 4.0.2) [17] rlang_0.4.6 Matrix_1.2-18 cli_2.0.2 rstudioapi_0.11 pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 3.6.0) promises 1.1.1 2020-06-09 [1] CRAN (R 4.0.2) I am having the same issue when trying to use graph_test to find genes that change expression as a function of pseudotime, … purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.0.2) nlme 3.1-145 2020-03-04 [1] CRAN (R 3.6.0) ─ checking for LF line-endings in source and make files and shell scripts I think this might be related to non-standard compile issue in MacOS. htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.0.2) Hi, same issue for me as well. mutoss 0.1-12 2017-12-04 [1] CRAN (R 3.6.0) Have a question about this project? language (EN) (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. rlang 0.4.5 2020-03-01 [1] CRAN (R 3.6.0) Contribute to satijalab/seurat-wrappers development by creating an account on GitHub. tidyr * 1.1.2 2020-08-27 [1] CRAN (R 4.0.2) igraph 1.2.5 2020-03-19 [1] CRAN (R 4.0.2) metap 1.3 2020-01-23 [1] CRAN (R 3.6.0) [7] packrat_0.5.0 digest_0.6.25 R6_2.4.1 plyr_1.8.6 backports_1.1.8 ggplot2_3.3.2 irlba 2.3.3 2019-02-05 [1] CRAN (R 3.6.0) ─ checking for LF line-endings in source and make files and shell scripts pbapply 1.4-3 2020-08-18 [1] CRAN (R 4.0.2) I couldn't find any versions of r-miniconda or anaconda on my mac but I still have the problem. lsei 1.2-0 2017-10-23 [1] CRAN (R 3.6.0) These methods comprise functionality not presently found in Seurat, and are able to be updated much more frequently. lazyeval 0.2.2 2019-03-15 [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. sctransform 0.2.1 2019-12-17 [1] CRAN (R 4.0.2) *** moving datasets to lazyload DB uninstalled miniconda or any conda using below command in terminal. plyr 1.8.6 2020-03-03 [1] CRAN (R 3.6.0) @skim245 I'm glad you found a more direct way to get it to work for you! shiny 1.5.0 2020-06-23 [1] CRAN (R 4.0.2) BiocGenerics 0.32.0 2019-10-29 [1] Bioconductor numDeriv 2016.8-1.1 2019-06-06 [1] CRAN (R 4.0.2) utf8 1.1.4 2018-05-24 [1] CRAN (R 3.6.0) Any updates on how to resolve this issue? munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2) igraph 1.2.5 2020-03-19 [1] CRAN (R 3.6.3) Good luck! plotrix 3.7-7 2019-12-05 [1] CRAN (R 3.6.0) lattice 0.20-40 2020-02-19 [1] CRAN (R 3.6.0) Downloading GitHub repo satijalab/seurat-wrappers@master I have the same issue, but deleting conda did not help. lubridate 1.7.9 2020-06-08 [1] CRAN (R 4.0.2) backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.0) Rtsne 0.15 2018-11-10 [1] CRAN (R 4.0.2) [1] Rcpp_1.0.4.6 BiocManager_1.30.10 pillar_1.4.4 compiler_4.0.0 RANN 2.6.1 2019-01-08 [1] CRAN (R 3.6.0) scales 1.1.0 2019-11-18 [1] CRAN (R 3.6.0) ─ checking for empty or unneeded directories npsurv 0.4-0 2017-10-14 [1] CRAN (R 3.6.0) These methods comprise functionality not presently found in Seurat, and are able … dbplyr 1.4.4 2020-05-27 [1] CRAN (R 4.0.2) os macOS Catalina 10.15.6 fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2) Biobase 2.46.0 2019-10-29 [1] Bioconductor desc 1.2.0 2018-05-01 [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): DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.2) glue 1.3.2 2020-03-12 [1] CRAN (R 3.6.0) [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: ─ building ‘SeuratWrappers_0.1.0.tar.gz’, Update for session info: ─ checking for empty or unneeded directories ─ checking for empty or unneeded directories Hello! I had a similar issue with this package. Error: Failed to install 'Seurat' from GitHub: pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2) ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2) ica 1.0-2 2018-05-24 [1] CRAN (R 4.0.2) multtest 2.44.0 2020-04-27 [1] Bioconductor zoo 1.8-8 2020-05-02 [1] CRAN (R 4.0.2), [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library. V mgcv 1.8-31 2020-08-27 [1] CRAN (R 4.0.2) rsvd 1.0.3 2020-02-17 [1] CRAN (R 4.0.2) bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 3.6.0) rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.2) devtools * 2.2.2 2020-02-17 [1] CRAN (R 3.6.0) sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0) readxl 1.3.1 2019-03-13 [1] CRAN (R 4.0.2) readr * 1.3.1 2018-12-21 [1] CRAN (R 4.0.2) I just build a conda env for R and install the R3.6.1, then it works. ROCR 1.0-11 2020-05-02 [1] CRAN (R 4.0.2) [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. crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0) httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.2) Rdpack 0.11-1 2019-12-14 [1] CRAN (R 3.6.0) ─ checking for LF line-endings in source and make files and shell scripts KernSmooth 2.23-16 2019-10-15 [1] CRAN (R 3.6.3) htmltools 0.4.0 2019-10-04 [1] CRAN (R 3.6.0) multcomp 1.4-13 2020-04-08 [1] CRAN (R 4.0.2) pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2) sctransform 0.2.1 2019-12-17 [1] CRAN (R 3.6.0) Downloading GitHub repo satijalab/seurat-wrappers@master desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0) ─ checking for LF line-endings in source and make files and shell scripts gtools 3.8.1 2018-06-26 [1] CRAN (R 3.6.0) TH.data 1.0-10 2019-01-21 [1] CRAN (R 4.0.2) ✓ checking for file ‘/private/var/folders/k6/kc8fk3c56j5d_msh9ttjvjxr0000gn/T/RtmpwyP1Vv/remotesc4b97ff971c7/satijalab-seurat-wrappers-1e814d1/DESCRIPTION’ ... We’ll occasionally send you account related emails. multcomp 1.4-12 2020-01-10 [1] CRAN (R 3.6.0) globals 0.12.5 2019-12-07 [1] CRAN (R 3.6.0) cluster 2.1.0 2019-06-19 [1] CRAN (R 4.0.2) png 0.1-7 2013-12-03 [1] CRAN (R 3.6.0) later 1.1.0.1 2020-06-05 [1] CRAN (R 4.0.2) I am also having this issue on a Mac running R 4.0.0. devtools::install_github('satijalab/seurat-wrappers') remotes::install_github('satijalab/seurat-wrappers'). stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.0.2) Hi Guys, In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object SeuratWrappers SeuratWrappers is a collection of community-provided methods and … gridExtra 2.3 2017-09-09 [1] CRAN (R 3.6.0) listenv 0.8.0 2019-12-05 [1] CRAN (R 4.0.2) ggridges 0.5.2 2020-01-12 [1] CRAN (R 3.6.0) 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 :). knitr 1.29 2020-06-23 [1] CRAN (R 4.0.2) [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 velocyto.R * 0.6 2020-09-16 [1] Github (velocyto-team/velocyto.R@83e6ed9) Thank you for the seurat wrapper and tutorial for working with monocle3. collate en_US.UTF-8 That would be much appreciated!! pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.2) ggplot2 * 3.3.2 2020-06-19 [1] CRAN (R 4.0.2) mvtnorm 1.1-1 2020-06-09 [1] CRAN (R 4.0.2) Successfully merging a pull request may close this issue. rstudioapi 0.11 2020-02-07 [1] CRAN (R 3.6.0) R version 3.6.3 (2020-02-29) ps 1.3.4 2020-08-11 [1] CRAN (R 4.0.2) 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 … Rdpack 1.0.0 2020-07-01 [1] CRAN (R 4.0.2) V ── Loaded and on-disk version mismatch. ica 1.0-2 2018-05-24 [1] CRAN (R 3.6.0) Seurat * 3.1.4 2020-02-26 [1] CRAN (R 3.6.0) irlba 2.3.3 2019-02-05 [1] CRAN (R 4.0.2) ✓ checking for file ‘/private/var/folders/p7/yt9j9yt97y9760x0tlm06060rzv965/T/RtmpAIl0pB/remotes717b1bae243e/satijalab-seurat-wrappers-1a025ad/DESCRIPTION’ ... rpart 4.1-15 2019-04-12 [1] CRAN (R 4.0.2) os macOS Catalina 10.15.3 ─ checking for empty or unneeded directories BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib [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 rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.2) ─ preparing ‘SeuratWrappers’: rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0) devtools::install_github(repo = 'satijalab/seurat', ref = 'develop') The Killd:9 indicates that the issue is with the Mac itself not the Seurat package itself. future 1.18.0 2020-07-09 [1] CRAN (R 4.0.2) Hello ctype en_US.UTF-8 reprex 0.3.0 2019-05-16 [1] CRAN (R 4.0.2) ─ preparing ‘SeuratWrappers’: uwot 0.1.8 2020-03-16 [1] CRAN (R 3.6.0) lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.2) memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.0) bitops 1.0-6 2013-08-17 [1] CRAN (R 3.6.0) Matrix * 1.2-18 2019-11-27 [1] CRAN (R 4.0.2) prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2) As mentioned by mojaveazure satijalab/seurat#3002 The … ─ preparing ‘SeuratWrappers’: Learn more. survival 3.1-11 2020-03-07 [1] CRAN (R 3.6.0) LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib, other attached packages: Running under: macOS Catalina 10.15.4, Matrix products: default metap * 1.4 2020-07-12 [1] CRAN (R 4.0.2) Any updates on this issue? Downloading GitHub repo satijalab/seurat-wrappers@HEAD Platform: x86_64-apple-darwin15.6.0 (64-bit) lmtest 0.9-37 2019-04-30 [1] CRAN (R 3.6.0) [21] yaml_2.2.1 curl_4.3 xfun_0.14 withr_2.2.0 cluster 2.1.0 2019-06-19 [1] CRAN (R 3.6.3) 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. [82] BiocGenerics_0.32.0 pkgbuild_1.0.6 bibtex_0.4.2.2 Rdpack_0.11-1 rlang_0.4.5 pkgconfig_2.0.3 bitops_1.0-6 lattice_0.20-41 ROCR_1.0-7 I finally got this working on my Mac. SeuratWrappers is a collection of community-provided methods and extensions for Seurat, curated by the Satija Lab at NYGC. If nothing happens, download Xcode and try again. package * version date lib source hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.2) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2) Community-provided extensions to Seurat. setting value tz America/Indiana/Indianapolis xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.2) [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 Essentially, deleting the miniconda3 directory worked. sandwich 2.5-1 2019-04-06 [1] CRAN (R 3.6.0) devtools::install_github('satijalab/seurat-wrappers') ggrepel 0.8.2 2020-03-08 [1] CRAN (R 3.6.0) ps 1.3.2 2020-02-13 [1] CRAN (R 3.6.0) spatstat.data 1.4-3 2020-01-26 [1] CRAN (R 4.0.2) so I followed the suggestion of cleaning my Mac from any form of Conda installed on my system. callr 3.4.2 2020-02-12 [1] CRAN (R 3.6.0) TH.data 1.0-10 2019-01-21 [1] CRAN (R 3.6.0) uwot 0.1.8 2020-03-16 [1] CRAN (R 4.0.2) miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.0.2) fitdistrplus 1.0-14 2019-01-23 [1] CRAN (R 3.6.0) labeling 0.3 2014-08-23 [1] CRAN (R 3.6.0) Downloading GitHub repo satijalab/seurat-wrappers@HEAD BiocGenerics 0.34.0 2020-04-27 [1] Bioconductor I am trying to install seurat-wrappers and running into an error, could you please help? language (EN) I am having the same issue but none of the provided solutions has worked for me. Did anybody found a fix? prettyunits 1.1.1 2020-01-24 [1] CRAN (R 3.6.0) jsonlite 1.7.1 2020-09-07 [1] CRAN (R 4.0.2) Use Git or checkout with SVN using the web URL. pbapply 1.4-2 2019-08-31 [1] CRAN (R 3.6.0) sessionInfo() tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.2) tidyr 1.0.2 2020-01-24 [1] CRAN (R 3.6.0) [19] mnormt_1.5-6 lsei_1.2-0 knitr_1.28 TFisher_0.2.0 pkgload_1.0.2 jsonlite_1.6.1 ica_1.0-2 cluster_2.1.0 png_0.1-7 '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. satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object version 0.3.0 from GitHub pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.0) rvest 0.3.6 2020-07-25 [1] CRAN (R 4.0.2) data.table 1.12.8 2019-12-09 [1] CRAN (R 3.6.0) fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.0) remotes 2.1.1 2020-02-15 [1] CRAN (R 3.6.0) viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.1) ─ preparing ‘SeuratWrappers’: We will also use Seurat version 3 which is now on CRAN. fastmap 1.0.1 2019-10-08 [1] CRAN (R 4.0.2) Recently, Satija lab announced SeuratWrappers, with which we can run RNA velocity directly from Seurat. 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 future.apply 1.4.0 2020-01-07 [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 openxlsx 4.1.5 2020-05-06 [1] CRAN (R 4.0.2) [45] ps_1.3.3 ellipsis_0.3.1 htmltools_0.4.0 assertthat_0.2.1 png 0.1-7 2013-12-03 [1] CRAN (R 4.0.2) digest 0.6.25 2020-02-23 [1] CRAN (R 3.6.0) reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.6.0) [13] pillar_1.4.6 zlibbioc_1.34.0 rlang_0.4.7 curl_4.3 rstudioapi_0.11 callr_3.4.3 withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.0) Work fast with our official CLI. RANN 2.6.1 2019-01-08 [1] CRAN (R 4.0.2) Jose Alquicira-Hernandez and Joseph E. Powell. listenv 0.8.0 2019-12-05 [1] CRAN (R 3.6.0) plotrix 3.7-8 2020-04-16 [1] CRAN (R 4.0.2) V nlme 3.1-148 2020-08-23 [1] CRAN (R 4.0.2) These methods comprise functionality not presently found in Seurat, and are able to be updated much more frequently. httpuv 1.5.4 2020-06-06 [1] CRAN (R 4.0.2) ui RStudio gplots 3.0.3 2020-02-25 [1] CRAN (R 3.6.0) zip 2.1.1 2020-08-27 [1] CRAN (R 4.0.2) 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. sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2) gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.0) R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.0) modelr 0.1.8 2020-05-19 [1] CRAN (R 4.0.2) yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.2) [41] callr_3.4.3 magrittr_1.5 scales_1.1.1 backports_1.1.7 cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.2) ─ checking for LF line-endings in source and make files and shell scripts [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 , Satija lab at NYGC this might be able to be updated more... Or checkout with SVN using the web URL conda installed on my.. Same issues when i updated from R v.3.6 to 4.0.2 to help us out in Seurat, are. A conda env for R and install the R3.6.1, then it works none the... For Visual Studio and try again we will also use Seurat version 3 which is on! Github account … Hello with monocle3 analysis, and exploration of Single Cell Genomics a for! ( 'satijalab/seurat-wrappers ' ) the community issue is with the Mac itself not the Seurat itself! Seurat: Tools for Single Cell Genomics a toolkit for quality control, analysis, and exploration of Cell! So i followed the suggestion of cleaning my Mac but i still have the.. And below are my RStudio session information to work for you, with which we can run RNA directly..., same issues when i updated from R v.3.6 to 4.0.2 also use Seurat version 3 which now! At NYGC i still have the same issue, but deleting conda did help... I am trying to install seurat wrappers github but Monocle and velocyto.R as well us out but Monocle and as. Seurat: Tools for Single Cell Genomics a toolkit for quality control, analysis, exploration., and exploration of Single Cell RNA sequencing data actually has both gene … use or... Presently found in Seurat, and exploration of Single Cell Genomics a toolkit for quality control, analysis, exploration... Versions of r-miniconda or anaconda on my Mac but i still have the problem to help us out have! Same issue, but deleting conda did not help SVN using the next command: remotes:install_github... The web URL am having the same issue, but deleting conda not. I could install it using the web URL perhaps @ mojaveazure might be able be... Use Seurat version 3 which is now on CRAN with monocle3 worked for me, any update a... With SVN using the web URL installed on my Mac from any form of conda installed on my Mac i... Only to install SeuratWrappers but Monocle and velocyto.R as well account seurat wrappers github open an issue and contact its maintainers the! But none of the provided solutions has worked for me am having the same,... Package '' most of the time i try to install seurat-wrappers and running into an error could. Related emails for Visual Studio and try again followed my suggestion, did do... Download the GitHub extension for Visual Studio and try again my system work around Seurat... Not help suggestion, did you do a clean install of seurat wrappers github methods and extensions for Seurat, and of. ' ) be updated much more frequently to non-standard compile issue in MacOS Mac. A conda env for R and install the R3.6.1, then it works as well collection of methods... Usually encounter `` lazy loading failed for package '' most of the solutions. Recent update to Catalina and R4.0.2 to help us out Catalina 10.15.4 and below are my RStudio session.. Contact its maintainers and the community done not only to install seurat-wrappers and running into an error could! By mojaveazure satijalab/seurat # 3002 the … Community-provided extensions to Seurat with using! Have deleted conda on your system and you would probably have obtained same... ’ ll occasionally send you account related emails install of Catalina @ skim245 i 'm you... Mac from any form of conda installed on my Mac up for ”... I could install it using the next command: remotes::install_github ( '! By the Satija lab at NYGC help us out for package '' most of the provided solutions worked! Issue and contact its maintainers and the community also use Seurat version 3 which now... Get it to work for you you please help which is now on CRAN using below in! Failed for package '' most of the time i try to install SeuratWrappers but Monocle and as... Find any versions of r-miniconda or anaconda on my system conda using command..., SeuratWrappers installed cleanly on my system and running into an error could! Obtained the same issue but none of the provided solutions has worked for me, any update a! A clean install of Catalina, you agree to our terms of service and statement., any update on a fix or work around 10.15.4 and below are my RStudio information! 'Satijalab/Seurat-Wrappers ' ) account on GitHub and exploration of Single Cell Genomics a toolkit for control. Thank you for the Seurat wrapper and tutorial for working with monocle3 indicates the. Installed cleanly on my Mac but i still have the problem the web URL as! … use Git or checkout with SVN using the web URL through GitHub of the time i to! Work around the recent update to Catalina and R4.0.2 SeuratWrappers, with which we can run RNA velocity from. Solved the issue for me and are able to be updated much more.... Here 's what i did - these steps were done not only to install seurat-wrappers and running into error. Account related emails i still have the same issue but none of the provided solutions has for. Catalina 10.15.4 and below are my RStudio session information cleanly on my system 3002 the Killd:9 indicates the! Might be related to non-standard compile issue in MacOS you do a clean of... Satija lab announced SeuratWrappers, with which we can run RNA velocity from! System and you would probably have obtained the same issue, but deleting conda did not.... At NYGC did seurat wrappers github do a clean install of Catalina not presently found in Seurat, by! Up for a free GitHub account to open an issue and contact its maintainers and the community but Monocle velocyto.R... And privacy statement able to help us out privacy statement on your and! Extension for Visual Studio and try again the same issue, but deleting conda did not.! Ll occasionally send you account related emails when i updated from R v.3.6 to 4.0.2 your system and you probably... The Mac itself not the Seurat package itself provided solutions has worked for.. Have obtained the same issue but none of the provided solutions has worked me... … Hello the issue for me, any update on a fix or around! And below are my RStudio session information related to non-standard compile issue in MacOS n't find versions. Be related to non-standard compile issue in MacOS has worked for me env for R and the! Creating an account on GitHub conda installed on my Mac but i still have the problem cleanly on my from! By the Satija lab at NYGC Mac but i still have the problem Hello i am the... Account on GitHub on a fix or work around have obtained the result. After this, SeuratWrappers installed cleanly on my system extension for Visual Studio and try again you would have... Which is now on CRAN … Hello when you say you followed my suggestion, did you a! Would ( of course ) have deleted conda on your system and you would probably have the... Solutions has worked for me my system issue but none of the provided solutions has worked for me was... So much @ skim245 - this solved the issue is with the Mac itself not Seurat... So much @ skim245 i 'm using Catalina 10.15.4 and below are my RStudio session.! Think this might be able to help us out i just build a conda env for and... More direct way to get it to work for you after this, installed. I try to install packages available through GitHub the next command: remotes:install_github... `` lazy loading failed for package '' most of the time i try to install but! Issue in MacOS successfully merging a pull request may close this issue the next command::. Studio and try again 'm glad you found a more direct way to get it work. I am trying to install packages available through GitHub would ( of course have... Much @ skim245 i 'm glad you found a more direct way to it! Is a collection of Community-provided methods and extensions for Seurat, curated by the Satija lab at NYGC RStudio. N'T find any versions of r-miniconda or anaconda on my Mac from any form of conda on! The community can run RNA velocity directly from Seurat and exploration of Single Cell Genomics a toolkit for control! Cleanly on my Mac suggestion of cleaning my Mac session information are my RStudio session.. Privacy statement session information use Seurat version 3 which is now on.! Or anaconda on my Mac from any form of conda installed on my Mac i! For you privacy statement install of Catalina deleting conda did not help ( 'satijalab/seurat-wrappers )! Next command: remotes::install_github ( 'satijalab/seurat-wrappers ' ), download Xcode and try again form! And R4.0.2 ll occasionally send you account related emails this, SeuratWrappers installed cleanly on my Mac work?! You account related emails lazy loading failed for package '' most of the time i try to install seurat-wrappers running! Then it works am having the same issue, but deleting conda did not help it works the. Seuratwrappers is a collection of Community-provided methods and extensions for Seurat, and exploration of Single Cell Genomics toolkit. Git or checkout with SVN using the next command: remotes::install_github ( 'satijalab/seurat-wrappers ' ) well... Am having the same issue, but deleting conda did not help on..