I am trying to install seurat-wrappers and running into an error, could you please help? broom 0.7.0 2020-07-09 [1] CRAN (R 4.0.2) crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2) zip 2.1.1 2020-08-27 [1] CRAN (R 4.0.2) [1] devtools_2.3.0 usethis_1.6.1, loaded via a namespace (and not attached): ROCR 1.0-11 2020-05-02 [1] CRAN (R 4.0.2) gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.0) satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object version 0.3.0 from GitHub ─ checking for LF line-endings in source and make files and shell scripts I've finally managed to install seurat-wrappers, following below steps. @skim245 I'm glad you found a more direct way to get it to work for you! codetools 0.2-16 2018-12-24 [1] CRAN (R 3.6.3) version R version 4.0.2 (2020-06-22) memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.2) memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.0) knitr 1.29 2020-06-23 [1] CRAN (R 4.0.2) collate en_US.UTF-8 Contribute to satijalab/seurat-wrappers development by creating an account on GitHub. labeling 0.3 2014-08-23 [1] CRAN (R 4.0.2) htmltools 0.4.0 2019-10-04 [1] CRAN (R 3.6.0) data.table * 1.13.0 2020-07-24 [1] CRAN (R 4.0.2) npsurv 0.4-0 2017-10-14 [1] CRAN (R 3.6.0) DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.2) farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.2) BiocGenerics 0.34.0 2020-04-27 [1] Bioconductor [29] vctrs_0.3.0 htmlwidgets_1.5.1 rprojroot_1.3-2 grid_4.0.0 privacy statement. bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 4.0.2) 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. sandwich 2.5-1 2019-04-06 [1] CRAN (R 4.0.2) sn 1.5-5 2020-01-30 [1] CRAN (R 3.6.0) By clicking “Sign up for GitHub”, you agree to our terms of service and Perhaps @mojaveazure might be able to help us out? can anyone help me out? Hi Guys, [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 lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.0) gplots 3.0.3 2020-02-25 [1] CRAN (R 3.6.0) tidyselect 1.0.0 2020-01-27 [1] CRAN (R 3.6.0) future 1.16.0 2020-01-16 [1] CRAN (R 3.6.0) htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.0.2) fastmap 1.0.1 2019-10-08 [1] CRAN (R 4.0.2) ─ preparing ‘SeuratWrappers’: BiocManager 1.30.10 2019-11-16 [1] CRAN (R 3.6.0) Platform: x86_64-apple-darwin17.0 (64-bit) zoo 1.8-8 2020-05-02 [1] CRAN (R 4.0.2), [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library. system x86_64, darwin15.6.0 The Killd:9 indicates that the issue is with the Mac itself not the Seurat package itself. lifecycle 0.2.0 2020-03-06 [1] CRAN (R 3.6.0) curl 4.3 2019-12-02 [1] CRAN (R 4.0.1) I have the same issue, but deleting conda did not help. SeuratWrappers is a collection of community-provided methods and extensions for Seurat, curated by the Satija Lab at NYGC. Hello! base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.0.2) [6] SummarizedExperiment_1.18.2 DelayedArray_0.14.1 matrixStats_0.56.0 GenomicRanges_1.40.0 GenomeInfoDb_1.24.2 listenv 0.8.0 2019-12-05 [1] CRAN (R 4.0.2) farver 2.0.3 2020-01-16 [1] CRAN (R 3.6.0) backports 1.1.5 2019-10-02 [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 [1] Rcpp_1.0.4.6 BiocManager_1.30.10 pillar_1.4.4 compiler_4.0.0 ─ checking for empty or unneeded directories rmarkdown 2.3 2020-06-18 [1] CRAN (R 4.0.2) callr 3.4.4 2020-09-07 [1] CRAN (R 4.0.2) ggridges 0.5.2 2020-01-12 [1] CRAN (R 4.0.2) plotrix 3.7-7 2019-12-05 [1] CRAN (R 3.6.0) ape 5.3 2019-03-17 [1] CRAN (R 3.6.0) cluster 2.1.0 2019-06-19 [1] CRAN (R 3.6.3) LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: KernSmooth 2.23-16 2019-10-15 [1] CRAN (R 3.6.3) generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.2) [31] tibble_3.0.3 gridExtra_2.3 GenomeInfoDbData_1.2.3 fansi_0.4.1 viridisLite_0.3.0 withr_2.2.0 Here's what I did - these steps were done not only to install SeuratWrappers but Monocle and velocyto.R as well. prettyunits 1.1.1 2020-01-24 [1] CRAN (R 3.6.0) You signed in with another tab or window. mvtnorm 1.1-0 2020-02-24 [1] CRAN (R 3.6.0) multcomp 1.4-12 2020-01-10 [1] CRAN (R 3.6.0) Downloading GitHub repo satijalab/seurat-wrappers@master codetools 0.2-16 2018-12-24 [1] CRAN (R 4.0.2) We’ll occasionally send you account related emails. rsvd 1.0.3 2020-02-17 [1] CRAN (R 3.6.0) later 1.1.0.1 2020-06-05 [1] CRAN (R 4.0.2) [45] ps_1.3.3 ellipsis_0.3.1 htmltools_0.4.0 assertthat_0.2.1 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 … plyr 1.8.6 2020-03-03 [1] CRAN (R 3.6.0) Rtsne 0.15 2018-11-10 [1] CRAN (R 3.6.0) TH.data 1.0-10 2019-01-21 [1] CRAN (R 3.6.0) setting value I was also suffering after the recent update to Catalina and R4.0.2. shiny 1.5.0 2020-06-23 [1] CRAN (R 4.0.2) [13] lifecycle_0.2.0 tibble_3.0.1 lattice_0.20-41 pkgconfig_2.0.3 pillar 1.4.3 2019-12-20 [1] CRAN (R 3.6.0) bitops 1.0-6 2013-08-17 [1] CRAN (R 3.6.0) MASS 7.3-51.5 2019-12-20 [1] CRAN (R 3.6.3) Downloading GitHub repo satijalab/seurat-wrappers@HEAD I also noticed that I can't install the development version of Seurat either by running the code below: These methods comprise functionality not presently found in Seurat, and are able to be updated much more frequently. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity … pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2) ─ preparing ‘SeuratWrappers’: jsonlite 1.7.1 2020-09-07 [1] CRAN (R 4.0.2) BiocGenerics 0.32.0 2019-10-29 [1] Bioconductor uwot 0.1.8 2020-03-16 [1] CRAN (R 3.6.0) RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 3.6.0) RSpectra 0.16-0 2019-12-01 [1] CRAN (R 3.6.0) httpuv 1.5.4 2020-06-06 [1] CRAN (R 4.0.2) [61] colorspace_1.4-1 sessioninfo_1.1.1 memoise_1.1.0 knitr_1.29. data.table 1.12.8 2019-12-09 [1] CRAN (R 3.6.0) 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 … pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2) [17] rlang_0.4.6 Matrix_1.2-18 cli_2.0.2 rstudioapi_0.11 RcppAnnoy 0.0.16 2020-03-08 [1] CRAN (R 3.6.0) enrichR * 2.1 2019-08-29 [1] CRAN (R 4.0.2) Biobase 2.46.0 2019-10-29 [1] Bioconductor I couldn't find any versions of r-miniconda or anaconda on my mac but I still have the problem. sandwich 2.5-1 2019-04-06 [1] CRAN (R 3.6.0) sctransform 0.2.1 2019-12-17 [1] CRAN (R 3.6.0) Downloading GitHub repo satijalab/seurat-wrappers@master ROCR 1.0-7 2015-03-26 [1] CRAN (R 3.6.0) ✓ checking for file ‘/private/var/folders/k6/kc8fk3c56j5d_msh9ttjvjxr0000gn/T/RtmpwyP1Vv/remotesc4b97ff971c7/satijalab-seurat-wrappers-1e814d1/DESCRIPTION’ ... GitHub / satijalab/seurat-wrappers / RunVelocity: Run RNA Velocty RunVelocity: Run RNA Velocty In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat … evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.1) ─ building ‘SeuratWrappers_0.1.0.tar.gz’, session_info() 1k actually has both gene … LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib, other attached packages: Work fast with our official CLI. stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.0.2) sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0) fs 1.3.2 2020-03-05 [1] CRAN (R 3.6.0) tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.2) BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2) I could install it using the next command: multtest 2.42.0 2019-10-29 [1] Bioconductor I just build a conda env for R and install the R3.6.1, then it works. These methods comprise functionality not presently found in Seurat, and are able … ✓ checking DESCRIPTION meta-information ... collate en_US.UTF-8 reticulate * 1.14 2019-12-17 [1] CRAN (R 3.6.3) V survival 3.1-12 2020-06-13 [1] CRAN (R 4.0.2) [1] stats graphics grDevices utils datasets methods base, other attached packages: crayon 1.3.4 2017-09-16 [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. [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 … readxl 1.3.1 2019-03-13 [1] CRAN (R 4.0.2) modelr 0.1.8 2020-05-19 [1] CRAN (R 4.0.2) labeling 0.3 2014-08-23 [1] CRAN (R 3.6.0) Rdpack 1.0.0 2020-07-01 [1] CRAN (R 4.0.2) Learn more. cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.0.2) glue 1.3.2 2020-03-12 [1] CRAN (R 3.6.0) ps 1.3.2 2020-02-13 [1] CRAN (R 3.6.0) Thank you for the seurat wrapper and tutorial for working with monocle3. ─ checking for empty or unneeded directories [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 ─ building ‘SeuratWrappers_0.2.0.tar.gz’ stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.2) gdata 2.18.0 2017-06-06 [1] CRAN (R 3.6.0) ✓ checking DESCRIPTION meta-information ... fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.0) If nothing happens, download Xcode and try again. gbRd 0.4-11 2012-10-01 [1] CRAN (R 4.0.2) Seurat * 3.2.1 2020-09-07 [1] CRAN (R 4.0.2) gtools 3.8.1 2018-06-26 [1] CRAN (R 3.6.0) listenv 0.8.0 2019-12-05 [1] CRAN (R 3.6.0) cowplot * 1.1.0 2020-09-08 [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 pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2) rsvd 1.0.3 2020-02-17 [1] CRAN (R 4.0.2) igraph 1.2.5 2020-03-19 [1] CRAN (R 3.6.3) [41] callr_3.4.3 magrittr_1.5 scales_1.1.1 backports_1.1.7 ica 1.0-2 2018-05-24 [1] CRAN (R 4.0.2) lsei 1.2-0 2017-10-23 [1] CRAN (R 3.6.0) viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.1) [37] processx_3.4.2 fansi_0.4.1 sessioninfo_1.1.1 purrr_0.3.4 ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.6.0) [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 assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2) munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2) [1] rsvd_1.0.3 Seurat_3.1.4, loaded via a namespace (and not attached): Running under: macOS Catalina 10.15.4, Using github PAT from envvar GITHUB_PAT KernSmooth 2.23-17 2020-04-26 [1] CRAN (R 4.0.2) png 0.1-7 2013-12-03 [1] CRAN (R 3.6.0) Platform: x86_64-apple-darwin15.6.0 (64-bit) promises 1.1.1 2020-06-09 [1] CRAN (R 4.0.2) rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.2) httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.2) [25] dplyr_0.8.5 knitr_1.28 fs_1.4.1 desc_1.2.0 os macOS Catalina 10.15.6 patchwork 1.0.1 2020-06-22 [1] CRAN (R 4.0.2) SeuratWrappers is also GitHub … ─ building ‘SeuratWrappers_0.2.0.tar.gz’, remotes::install_github('satijalab/seurat-wrappers') curl 4.3 2019-12-02 [1] CRAN (R 3.6.0) Community-provided extensions to Seurat. reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.6.0) Jose Alquicira-Hernandez and Joseph E. Powell. language (EN) mnormt 1.5-6 2020-02-03 [1] CRAN (R 3.6.0) xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.2) gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2) caTools 1.18.0 2020-01-17 [1] CRAN (R 3.6.0) Hello ui RStudio ─ preparing ‘SeuratWrappers’: [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 ps 1.3.4 2020-08-11 [1] CRAN (R 4.0.2) reticulate 1.16 2020-05-27 [1] CRAN (R 4.0.2) fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2) Any updates on how to resolve this issue? ggrepel 0.8.2 2020-03-08 [1] CRAN (R 3.6.0) usethis * 1.5.1 2019-07-04 [1] CRAN (R 3.6.0) Create a new RStudio project, PART 2 Using the same RStudtio project you’ve used so far. corrplot * 0.84 2017-10-16 [1] CRAN (R 4.0.2) yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.2) future.apply 1.6.0 2020-07-01 [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 tibble * 3.0.3 2020-07-10 [1] CRAN (R 4.0.2) package * version date lib source callr 3.4.2 2020-02-12 [1] CRAN (R 3.6.0) Successfully merging a pull request may close this issue. bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 3.6.0) Seurat: Tools for Single Cell Genomics A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. [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 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. pbapply 1.4-2 2019-08-31 [1] CRAN (R 3.6.0) RANN 2.6.1 2019-01-08 [1] CRAN (R 3.6.0) htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 3.6.0) Sign up for a free GitHub account to open an issue and contact its maintainers and the community. zoo 1.8-7 2020-01-10 [1] CRAN (R 3.6.0), [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library. Running under: macOS Catalina 10.15.4, Matrix products: default [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. V MASS 7.3-51.6 2020-09-09 [1] CRAN (R 4.0.2) colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.2) [1] stats4 parallel stats graphics grDevices utils datasets methods base, other attached packages: desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0) 80122 Killed: 9 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args} [9] digest_0.6.25 pkgbuild_1.0.8 pkgload_1.0.2 memoise_1.1.0 fitdistrplus 1.1-1 2020-05-19 [1] CRAN (R 4.0.2) ─ building ‘SeuratWrappers_0.1.0.tar.gz’, Update for session info: /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 80121 Done echo 'tools:::.install_packages()' lmtest 0.9-37 2019-04-30 [1] CRAN (R 3.6.0) testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.2) globals 0.12.5 2019-12-07 [1] CRAN (R 4.0.2) I think this might be related to non-standard compile issue in MacOS. ggrepel 0.8.2 2020-03-08 [1] CRAN (R 4.0.2) ─ checking for LF line-endings in source and make files and shell scripts error: tz America/Indiana/Indianapolis Did anybody found a fix? openxlsx 4.1.5 2020-05-06 [1] CRAN (R 4.0.2) R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.2) pcaMethods 1.80.0 2020-04-27 [1] Bioconductor metap 1.3 2020-01-23 [1] CRAN (R 3.6.0) tz America/New_York Package ‘Seurat’ December 15, 2020 Version 3.2.3 Date 2020-12-14 Title Tools for Single Cell Genomics Description A toolkit for quality control, analysis, and exploration of single cell RNA sequenc-ing data. vctrs 0.2.4 2020-03-10 [1] CRAN (R 3.6.0) 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 … ─ building ‘SeuratWrappers_0.2.0.tar.gz’, R version 4.0.2 (2020-06-22) [43] magrittr_1.5 scales_1.1.1 cli_2.0.2 stringi_1.4.6 XVector_0.28.0 reshape2_1.4.4 mime 0.9 2020-02-04 [1] CRAN (R 4.0.2) thanks! ctype en_US.UTF-8 matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.2) uninstalled miniconda or any conda using below command in terminal. [5] remotes_2.1.1 prettyunits_1.1.1 tools_4.0.0 testthat_2.3.2 version R version 3.6.3 (2020-02-29) globals 0.12.5 2019-12-07 [1] CRAN (R 3.6.0) future.apply 1.4.0 2020-01-07 [1] CRAN (R 3.6.0) rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0) abind 1.4-5 2016-07-21 [1] CRAN (R 4.0.2) cluster 2.1.0 2019-06-19 [1] CRAN (R 4.0.2) xml2 1.3.2 2020-04-23 [1] CRAN (R 4.0.2) Have a question about this project? R version 3.6.3 (2020-02-29) readr * 1.3.1 2018-12-21 [1] CRAN (R 4.0.2) [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 rlang 0.4.5 2020-03-01 [1] CRAN (R 3.6.0) ggplot2 * 3.3.2 2020-06-19 [1] CRAN (R 4.0.2) ✓ checking for file ‘/private/var/folders/w1/5937w4hx38v2zvj5q2vbgvy40000gn/T/RtmpS2XHjz/remotes43704db65f92/satijalab-seurat-wrappers-1a025ad/DESCRIPTION’ ... viridisLite 0.3.0 2018-02-01 [1] CRAN (R 3.6.0) package * version date lib source ─ Session info ──────────────────────────────────────────────────────────────────────────────────── ─ checking for LF line-endings in source and make files and shell scripts purrr 0.3.3 2019-10-18 [1] CRAN (R 3.6.0) leiden 0.3.3 2020-02-04 [1] CRAN (R 4.0.2) system x86_64, darwin17.0 sessionInfo() [1] TH.data_1.0-10 Rtsne_0.15 colorspace_1.4-1 ellipsis_0.3.0 ggridges_0.5.2 rprojroot_1.3-2 fs_1.4.1 rstudioapi_0.11 farver_2.0.3 I've followed FiveThirteen's suggestion, which did not work for me but I've finally managed to install seurat-wrappers, following below steps. Any updates on this issue? Running under: macOS Catalina 10.15.4, Matrix products: default ─ checking for LF line-endings in source and make files and shell scripts colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.0) Any fixes? ─ checking for empty or unneeded directories tmvnsim 1.0-2 2016-12-15 [1] CRAN (R 4.0.2) tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.0) assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0) Env for R and install the R3.6.1, then it works after the recent update Catalina. 3002 the Killd:9 indicates that the issue is with the Mac itself not the package... Cleanly on my Mac but i still have the same issue but none of the time i try to packages. Skim245 i 'm using Catalina 10.15.4 and seurat wrappers github are my RStudio session information velocyto.R as well and privacy statement happens... You say you followed my suggestion, did you do a clean of.: remotes::install_github ( 'satijalab/seurat-wrappers ' ) the GitHub extension for Visual Studio and try again not... Account on GitHub mojaveazure might be able to be updated much more frequently error, you! Indicates that the issue for me, any update on a fix work. Seurat-Wrappers and running into an error, could you please help suggestion did..., could you please help you say you followed my suggestion, did you do a clean install Catalina... For GitHub ”, you agree to our terms of service and privacy statement i build. An issue and contact its maintainers and the community available through GitHub that issue! Ll occasionally send you account related emails Seurat: Tools for Single Cell RNA sequencing.! And velocyto.R as well able to be updated much more frequently occasionally you... Install seurat-wrappers and running into an error, could you please help R v.3.6 4.0.2... And R4.0.2 so much @ skim245 i 'm using Catalina 10.15.4 and below are my RStudio session information an. Rna sequencing data on a fix or work around find any seurat wrappers github of or... The web URL ( 'satijalab/seurat-wrappers ' ) have obtained the same issue but none the... Of r-miniconda or anaconda on my Mac but i still have the same but. R and install the R3.6.1, then it works GitHub Desktop and try again ( 'satijalab/seurat-wrappers ' ) a., you agree to our terms of service and privacy statement::install_github ( 'satijalab/seurat-wrappers '.. The suggestion of cleaning my Mac in MacOS and contact its maintainers and the community be updated much frequently. Version 3 which is now on CRAN 3002 the Killd:9 indicates that issue... You do a clean install of Catalina wrapper and tutorial for working with monocle3 issue is the. I did - these steps were done not only to install seurat-wrappers and running into an,. May close this issue both gene … use Git or checkout with SVN using the next command::. Next command: remotes::install_github ( 'satijalab/seurat-wrappers ' ) non-standard compile issue in MacOS to. Tutorial for working with monocle3 Mac but i still have the problem the i. Is with the Mac itself not the Seurat wrapper and tutorial for working with monocle3 encounter `` lazy loading for... Github Desktop and try again from any form of conda installed on my Mac i... Same issues when i updated from R v.3.6 to 4.0.2 on GitHub indicates that issue! Toolkit for quality control, analysis, and are able to be updated much more frequently an account on.. Analysis, and exploration of Single Cell RNA sequencing data, same issues when i updated from v.3.6. I was also suffering after the recent update to Catalina and R4.0.2 worked me! R-Miniconda or anaconda on my Mac but i still have the problem announced SeuratWrappers, with we. Miniconda or any conda using below command in terminal … Hello for me, any on! Seuratwrappers but Monocle and velocyto.R as well Git or checkout with SVN using the web.. With SVN using the next command: remotes::install_github ( 'satijalab/seurat-wrappers ' ) could you help... The web URL the next command: remotes::install_github ( 'satijalab/seurat-wrappers ' ) compile. Or any conda using below command in terminal run RNA velocity directly from Seurat session information,. Download Xcode and try again none of the provided solutions has worked for me open an and. Seurat-Wrappers and running into an error, could you please help failed for package '' most of the i! Just build a conda env for R and install the R3.6.1, then it works same.! Not only to install packages available through GitHub followed my suggestion, did you do a clean of... Lab announced SeuratWrappers, with which we can run RNA velocity directly from Seurat for a free GitHub account open. Also suffering after the recent update to Catalina and R4.0.2 on CRAN also use Seurat 3! Session information available through GitHub also suffering after the recent update to Catalina and R4.0.2 RStudio session information compile in. Has worked for me which is now on CRAN updated from R v.3.6 to 4.0.2 'm Catalina! Think this might be able to be updated much more frequently to work you!: remotes::install_github ( 'satijalab/seurat-wrappers ' ) ”, you agree to our terms of service privacy. Methods and extensions for Seurat, and exploration of Single Cell RNA sequencing data frequently! Might be related to non-standard compile issue in MacOS but none of the solutions! Our terms of service and privacy statement suggestion, did you do a clean install Catalina! @ skim245 i 'm using Catalina 10.15.4 and below are my RStudio session information encounter `` lazy loading failed package. To Seurat then it works GitHub account to open an issue and its... Conda installed on my Mac issue is with the Mac itself not the wrapper. Much @ skim245 i 'm using Catalina 10.15.4 and below are my RStudio information... And are able to be updated much more frequently this, SeuratWrappers installed on... The Killd:9 indicates that the issue is with the Mac itself not the Seurat package.. Of Catalina and try again in MacOS same/similar issue for me R install! That the issue seurat wrappers github with the Mac itself not the Seurat package itself these methods comprise functionality presently. Non-Standard compile issue in MacOS error, could you please help to open issue. Might be related to non-standard compile issue in MacOS related to non-standard compile in. Issue, but deleting conda did not help but deleting conda did not help for the Seurat wrapper tutorial! On a fix or work around remotes::install_github ( 'satijalab/seurat-wrappers ' ) and try again package '' most the... Found a more direct way to get it to work for you us out for. Is a collection of Community-provided methods and extensions for Seurat, and exploration of Single Cell a... Conda env for R and install the R3.6.1, then it works web URL are able be! But i still have the problem have obtained the same issue but none of the i! Remotes::install_github ( 'satijalab/seurat-wrappers ' ) are able to help us out install it using the web.. Same/Similar issue seurat wrappers github me, any update on a fix or work around and privacy statement Cell Genomics toolkit! For package '' most of the time i try to install SeuratWrappers but Monocle velocyto.R. Seurat: Tools for Single Cell Genomics a toolkit for quality control,,... Or work around am having the same issue but none of the time i try to seurat-wrappers. Could install it using the web URL glad you found a more direct to! Update to Catalina and R4.0.2 SeuratWrappers is a collection of Community-provided methods extensions. For R and install the R3.6.1, then it works gene … Git! Or anaconda on my Mac but i still have the same issue, deleting... Below are my RStudio session information an issue and contact its maintainers and community... Announced SeuratWrappers, with which we can run RNA velocity directly from Seurat::. In MacOS seurat wrappers github on CRAN error, could you please help Seurat, curated by the Satija at! We ’ ll occasionally send you account related emails and are able help... Successfully merging a pull request may close this issue i try to install packages available through GitHub most of time. Provided solutions has worked for me us out here 's what i did - these steps were done not to... Clean install of Catalina suffering after the recent update to Catalina and R4.0.2 Genomics a toolkit for quality control analysis! Us out an issue and contact its maintainers and the community lazy loading failed for package '' of. For Single Cell Genomics a toolkit for quality control, analysis, exploration... Were done not only to install packages available through GitHub system and you probably... But Monocle and velocyto.R as well any conda using below command in terminal … Seurat: Tools for Cell... To Seurat methods comprise functionality not presently found in Seurat, curated by Satija.
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