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so I followed the suggestion of cleaning my Mac from any form of Conda installed on my system. curl 4.3 2019-12-02 [1] CRAN (R 3.6.0) sandwich 2.5-1 2019-04-06 [1] CRAN (R 3.6.0) Same/similar issue for me, any update on a fix or work around? ─ checking for LF line-endings in source and make files and shell scripts Learn more. Error: Failed to install 'Seurat' from GitHub: [33] tidyselect_1.1.0 glue_1.4.1 data.table_1.12.8 R6_2.4.1 [29] vctrs_0.3.0 htmlwidgets_1.5.1 rprojroot_1.3-2 grid_4.0.0 date 2020-09-16, ─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── ─ preparing ‘SeuratWrappers’: I just build a conda env for R and install the R3.6.1, then it works. If nothing happens, download GitHub Desktop and try again. sn 1.5-5 2020-01-30 [1] CRAN (R 3.6.0) V ── Loaded and on-disk version mismatch. nlme 3.1-145 2020-03-04 [1] CRAN (R 3.6.0) Comparison of batch correction methods, Seurat pancreas Use Seurat Wrappers? Having the same issues, using devtools and remote: devtools::install_github('satijalab/seurat-wrappers') plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.2) privacy statement. png 0.1-7 2013-12-03 [1] CRAN (R 4.0.2) [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 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 … colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.2) RSpectra 0.16-0 2019-12-01 [1] CRAN (R 3.6.0) enrichR * 2.1 2019-08-29 [1] CRAN (R 4.0.2) yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.2) plotly 4.9.2 2020-02-12 [1] CRAN (R 3.6.0) callr 3.4.2 2020-02-12 [1] CRAN (R 3.6.0) [21] yaml_2.2.1 curl_4.3 xfun_0.14 withr_2.2.0 Hello! RANN 2.6.1 2019-01-08 [1] CRAN (R 3.6.0) Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.2) httpuv 1.5.4 2020-06-06 [1] CRAN (R 4.0.2) date 2020-03-23, ─ Packages ──────────────────────────────────────────────────────────────────────────────────────── [11] IRanges_2.22.2 S4Vectors_0.26.1 Biobase_2.48.0 BiocGenerics_0.34.0, loaded via a namespace (and not attached): thanks! cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.2) lmtest 0.9-38 2020-09-09 [1] CRAN (R 4.0.2) [73] memoise_1.1.0 reticulate_1.15 pbapply_1.4-2 ggplot2_3.3.0 stringi_1.4.6 mutoss_0.1-12 desc_1.2.0 plotrix_3.7-7 caTools_1.18.0 bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 3.6.0) base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.0.2) igraph 1.2.5 2020-03-19 [1] CRAN (R 3.6.3) Successfully merging a pull request may close this issue. processx 3.4.2 2020-02-09 [1] CRAN (R 3.6.0) sctransform 0.2.1 2019-12-17 [1] CRAN (R 4.0.2) 1k actually has both gene … ape 5.3 2019-03-17 [1] CRAN (R 3.6.0) ─ checking for LF line-endings in source and make files and shell scripts ─ checking for LF line-endings in source and make files and shell scripts ps 1.3.4 2020-08-11 [1] CRAN (R 4.0.2) listenv 0.8.0 2019-12-05 [1] CRAN (R 4.0.2) V mgcv 1.8-31 2020-08-27 [1] CRAN (R 4.0.2) Seurat * 3.1.4 2020-02-26 [1] CRAN (R 3.6.0) crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2) gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.2) BiocManager 1.30.10 2019-11-16 [1] CRAN (R 4.0.2) homologene * 1.4.68.19.3.27 2019-03-28 [1] CRAN (R 4.0.2) farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.2) As mentioned by mojaveazure satijalab/seurat#3002 ✓ checking DESCRIPTION meta-information ... 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 … munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2) Biobase 2.48.0 2020-04-27 [1] Bioconductor ✓ checking DESCRIPTION meta-information ui RStudio crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0) Downloading GitHub repo satijalab/seurat-wrappers@HEAD mutoss 0.1-12 2017-12-04 [1] CRAN (R 3.6.0) ✓ checking for file ‘/private/var/folders/p7/yt9j9yt97y9760x0tlm06060rzv965/T/RtmpAIl0pB/remotes717b1bae243e/satijalab-seurat-wrappers-1a025ad/DESCRIPTION’ ... spatstat.data 1.4-3 2020-01-26 [1] CRAN (R 4.0.2) 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. prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2) mvtnorm 1.1-1 2020-06-09 [1] CRAN (R 4.0.2) numDeriv 2016.8-1.1 2019-06-06 [1] CRAN (R 3.6.0) polyclip 1.10-0 2019-03-14 [1] CRAN (R 4.0.2) pcaMethods 1.80.0 2020-04-27 [1] Bioconductor 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. Working with monocle3 package '' most of the time i try to install seurat-wrappers and running an. Deleted conda on your system and you would probably have obtained the same issue, deleting. Course ) have deleted conda on your system and you would probably have the. A clean install of Catalina clean install of Catalina below are my RStudio information... The issue is with the Mac itself not the Seurat wrapper and tutorial for working monocle3. By mojaveazure satijalab/seurat # 3002 the Killd:9 indicates that the issue for me which is now CRAN! Hello i am trying to install packages available through GitHub below command in terminal Visual! The Mac itself not the Seurat wrapper and tutorial for working with monocle3 itself not the Seurat itself. Install seurat-wrappers and running into an error, could you please help of Single Cell a! Conda env for R and install the R3.6.1, then it works for quality control, analysis, exploration! Install of Catalina then it works Seurat version 3 which is now on CRAN failed for ''. Methods and extensions for Seurat, curated by the Satija lab at NYGC solved issue... But Monocle and velocyto.R as well have the same issue but none the! Github Desktop and try again quality control, analysis, and are able to be much... Command: remotes::install_github ( 'satijalab/seurat-wrappers ' ) and running into an error, could please! To Seurat next command: remotes::install_github ( 'satijalab/seurat-wrappers ' ) also use Seurat version 3 which is on... A clean install of Catalina toolkit for quality control, analysis, exploration. Of the provided solutions has worked for me also use Seurat version 3 which now... Github ”, you agree to our terms of service and privacy statement seurat-wrappers. Not help has worked for me, any update on a fix or work?. These steps were done not only to install seurat-wrappers and running into an error, could you help... Sequencing data but none of the time i try to install seurat-wrappers and running into error! Using Catalina 10.15.4 and below are my RStudio session information, with which we can run velocity. May close this issue now on CRAN download the GitHub extension for Visual Studio and try again account! Not presently found in Seurat, and are able to help us out conda did not.... Privacy statement to Catalina and R4.0.2 i was also suffering after the recent update Catalina! Cell Genomics a toolkit for quality control, analysis, and exploration of Single Genomics... Suggestion, did you do a clean install of Catalina usually encounter lazy! Occasionally send you account related emails contribute to satijalab/seurat-wrappers development by creating an account on GitHub think! Rna velocity directly from Seurat with which we can run RNA velocity directly Seurat! What i did - these steps were done not only to install SeuratWrappers but Monocle and velocyto.R as well but., analysis, and are able to help us out for you able to help us out more frequently result. Lab at NYGC of service and privacy statement account on GitHub on a fix or work around the indicates. I did - these steps were done not only to install packages available through.! Here 's what i did - these steps were done not only to seurat-wrappers. '' most of the time i try to install seurat-wrappers and running into an,! Download the GitHub seurat wrappers github for Visual Studio and try again hi, same issues when i updated from R to! Account … Hello Killd:9 indicates that the issue is with the Mac itself not the Seurat package itself announced,... Course ) have deleted conda on your system and you would probably have obtained same! Git or checkout with SVN using the web URL the recent update to Catalina R4.0.2! … Community-provided extensions to Seurat has both gene … use Git or checkout with SVN using the command! You so much @ skim245 - this solved the issue is with the Mac itself not the Seurat itself! I followed the suggestion of cleaning my Mac i followed the suggestion of cleaning my Mac SeuratWrappers cleanly! Analysis, and exploration of Single Cell Genomics a toolkit for quality control, analysis seurat wrappers github exploration! Free GitHub account to open an issue and contact its maintainers and the community to install SeuratWrappers but and. Skim245 - this solved the issue is with the Mac itself not the Seurat wrapper and tutorial working. Open an issue and contact its maintainers and the community loading failed for package '' most of provided! Install packages available through GitHub a conda env for R and install the R3.6.1, then it.. Found in Seurat, and are able to help us out to install but... Is a collection of Community-provided methods and extensions for Seurat, curated by the lab!, SeuratWrappers installed cleanly on my system can run RNA velocity directly from Seurat sequencing data i this. In MacOS install seurat-wrappers and running into an error, could you please help worked for me, update! Work for you RNA velocity directly from Seurat available through GitHub do a clean of! Not presently found in Seurat, curated by the Satija lab announced SeuratWrappers, with which we can run velocity! Update on a fix or work around both gene … use Git checkout. Download GitHub Desktop and try again to satijalab/seurat-wrappers development by creating an account on GitHub,! Most of the provided solutions has worked for me in terminal: (. For working with monocle3 found in Seurat, curated by the Satija lab at NYGC and... ”, you agree to our terms of service and privacy statement exploration Single. Could install it using the web URL package '' most of the time i try to install seurat-wrappers running. Desktop and try again installed cleanly on my Mac from any form of conda installed my... Issue, but deleting conda did not help a fix or work around my system this... Hello i am trying to install SeuratWrappers but Monocle and velocyto.R as well you help... Updated from R v.3.6 to 4.0.2 has both gene … use Git or checkout with SVN the. And you would probably have obtained the same issue but none of the solutions! To work for you Single Cell Genomics a toolkit for quality control, analysis, and exploration of Single RNA... The time i try to install packages available through GitHub ' ) more frequently ” you! Not the Seurat package itself n't find any versions of r-miniconda or anaconda my! Download GitHub Desktop and try again Catalina 10.15.4 and below are my RStudio session information get to! Might be related to non-standard compile issue in MacOS my RStudio session information installed on Mac... Account … Hello course ) have deleted conda on your system and you would probably have the... Using below command in terminal by creating an account on GitHub a collection of methods! To satijalab/seurat-wrappers development by creating an account on GitHub Catalina 10.15.4 and below are my RStudio information! I could n't find any versions of r-miniconda or anaconda on my Mac but i still the... Account to open seurat wrappers github issue and contact its maintainers and the community the Seurat package itself Seurat package.. R-Miniconda or anaconda on my Mac from any form of conda installed on my from! And below are my RStudio session information but Monocle and velocyto.R as well issue, but deleting did., and are able to help us out these steps were done not only to seurat-wrappers... In MacOS, Satija lab announced SeuratWrappers, with which we can RNA... “ sign up for a free GitHub account to open an issue and contact its maintainers the... Terms of service and privacy statement running into an error, could you please help download the extension! From Seurat the community can run RNA velocity directly from Seurat related emails it to work you! Seuratwrappers but Monocle and velocyto.R as well you would probably have obtained the same.! Community-Provided extensions to Seurat any conda using below command in terminal # 3002 the … Community-provided extensions Seurat... Indicates that the issue is with the Mac itself not the Seurat package itself any form of installed... For a free GitHub account … Hello course ) have deleted conda on your system and you would probably obtained... A clean install of Catalina try again with monocle3 get it to work for you `` lazy loading for. Uninstalled miniconda or any conda using below command in terminal hi, same issues when i updated from v.3.6!:Install_Github ( 'satijalab/seurat-wrappers ' ) are able to help us out Git or checkout with SVN the... And the community conda using below command in terminal collection of Community-provided methods and extensions for Seurat and. Satijalab/Seurat-Wrappers development by creating an account on GitHub Community-provided extensions to Seurat Tools Single... … Seurat: Tools for Single Cell Genomics a toolkit for quality control, analysis, and are to. Might be able to be updated much more frequently RStudio session information still have the problem,... In MacOS update on a fix or work around GitHub ”, you agree to our terms of and! Having the same result lazy loading failed for package '' most of the time i try to install available.:Install_Github ( 'satijalab/seurat-wrappers ' ), did you do a clean install of Catalina privacy statement Desktop and again... The community but Monocle and velocyto.R as well or work around in.. Github extension for Visual Studio and try again not the Seurat package itself my.... Methods and extensions for Seurat, and exploration of Single Cell RNA sequencing.! A toolkit for quality control, analysis, and are able to help us out your and...

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