yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.2) BiocManager 1.30.10 2019-11-16 [1] CRAN (R 3.6.0) ─ checking for empty or unneeded directories Same/similar issue for me, any update on a fix or work around? If nothing happens, download the GitHub extension for Visual Studio 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: gridExtra 2.3 2017-09-09 [1] CRAN (R 3.6.0) vctrs 0.3.4 2020-08-29 [1] CRAN (R 4.0.2) I have the same issue, but deleting conda did not help. [1] Rcpp_1.0.4.6 BiocManager_1.30.10 pillar_1.4.4 compiler_4.0.0 ✓ checking DESCRIPTION meta-information [17] rlang_0.4.6 Matrix_1.2-18 cli_2.0.2 rstudioapi_0.11 ─ checking for LF line-endings in source and make files and shell scripts rlang 0.4.5 2020-03-01 [1] CRAN (R 3.6.0) If nothing happens, download Xcode and try again. ─ checking for empty or unneeded directories 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) … Have a question about this project? assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0) [31] tibble_3.0.3 gridExtra_2.3 GenomeInfoDbData_1.2.3 fansi_0.4.1 viridisLite_0.3.0 withr_2.2.0 BiocGenerics 0.32.0 2019-10-29 [1] Bioconductor cli 2.0.2 2020-02-28 [1] CRAN (R 3.6.0) [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 purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.0.2) gbRd 0.4-11 2012-10-01 [1] CRAN (R 3.6.0) Downloading GitHub repo satijalab/seurat-wrappers@HEAD listenv 0.8.0 2019-12-05 [1] CRAN (R 3.6.0) velocyto.R * 0.6 2020-09-16 [1] Github (velocyto-team/velocyto.R@83e6ed9) xfun 0.17 2020-09-09 [1] CRAN (R 4.0.2) plyr 1.8.6 2020-03-03 [1] CRAN (R 3.6.0) processx 3.4.2 2020-02-09 [1] CRAN (R 3.6.0) htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.0.2) multtest 2.44.0 2020-04-27 [1] Bioconductor Contribute to satijalab/seurat-wrappers development by creating an account on GitHub. Jose Alquicira-Hernandez and Joseph E. Powell. system x86_64, darwin17.0 withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0) codetools 0.2-16 2018-12-24 [1] CRAN (R 4.0.2) sn 1.5-5 2020-01-30 [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 … We will also use Seurat version 3 which is now on CRAN. We’ll occasionally send you account related emails. lubridate 1.7.9 2020-06-08 [1] CRAN (R 4.0.2) [33] tidyselect_1.1.0 glue_1.4.1 data.table_1.12.8 R6_2.4.1 crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0) 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. metap 1.3 2020-01-23 [1] CRAN (R 3.6.0) ─ preparing ‘SeuratWrappers’: prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2) Already on GitHub? '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. ggplot2 3.3.0 2020-03-05 [1] CRAN (R 3.6.0) RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 3.6.0) abind 1.4-5 2016-07-21 [1] CRAN (R 4.0.2) ✓ checking for file ‘/private/var/folders/p7/yt9j9yt97y9760x0tlm06060rzv965/T/RtmpAIl0pB/remotes717b1bae243e/satijalab-seurat-wrappers-1a025ad/DESCRIPTION’ ... magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.2) base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.0.2) metap * 1.4 2020-07-12 [1] CRAN (R 4.0.2) cluster 2.1.0 2019-06-19 [1] CRAN (R 3.6.3) [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 [43] magrittr_1.5 scales_1.1.1 cli_2.0.2 stringi_1.4.6 XVector_0.28.0 reshape2_1.4.4 glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2) Seurat has been successfully installed on Mac OS X, Linux, and Windows, using the devtools package to install directly from GitHub. package * version date lib source @skim245 I'm glad you found a more direct way to get it to work for you! You signed in with another tab or window. ─ building ‘SeuratWrappers_0.1.0.tar.gz’, session_info() zoo 1.8-7 2020-01-10 [1] CRAN (R 3.6.0), [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library. utf8 1.1.4 2018-05-24 [1] CRAN (R 3.6.0) jsonlite 1.7.1 2020-09-07 [1] CRAN (R 4.0.2) mnormt 2.0.2 2020-09-01 [1] CRAN (R 4.0.2) Successfully merging a pull request may close this issue. rjson 0.2.20 2018-06-08 [1] CRAN (R 4.0.2) [25] dplyr_0.8.5 knitr_1.28 fs_1.4.1 desc_1.2.0 sandwich 2.5-1 2019-04-06 [1] CRAN (R 3.6.0) remotes 2.1.1 2020-02-15 [1] CRAN (R 3.6.0) system x86_64, darwin15.6.0 stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.0.2) Downloading GitHub repo satijalab/seurat-wrappers@master RSpectra 0.16-0 2019-12-01 [1] CRAN (R 3.6.0) readr * 1.3.1 2018-12-21 [1] CRAN (R 4.0.2) RcppAnnoy 0.0.16 2020-03-08 [1] CRAN (R 4.0.2) multtest 2.42.0 2019-10-29 [1] Bioconductor bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 4.0.2) plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.2) globals 0.12.5 2019-12-07 [1] CRAN (R 3.6.0) mutoss 0.1-12 2017-12-04 [1] CRAN (R 3.6.0) ─ checking for LF line-endings in source and make files and shell scripts [9] digest_0.6.25 pkgbuild_1.0.8 pkgload_1.0.2 memoise_1.1.0 uwot 0.1.8 2020-03-16 [1] CRAN (R 4.0.2) rstudioapi 0.11 2020-02-07 [1] CRAN (R 3.6.0) RcppAnnoy 0.0.16 2020-03-08 [1] CRAN (R 3.6.0) backports 1.1.10 2020-09-15 [1] CRAN (R 4.0.2) date 2020-03-23, ─ Packages ──────────────────────────────────────────────────────────────────────────────────────── I've manually deleted r-miniconda folder. forcats * 0.5.0 2020-03-01 [1] CRAN (R 4.0.2) xml2 1.3.2 2020-04-23 [1] CRAN (R 4.0.2) plotly 4.9.2.1 2020-04-04 [1] CRAN (R 4.0.2) ─ checking for LF line-endings in source and make files and shell scripts setting value future.apply 1.6.0 2020-07-01 [1] CRAN (R 4.0.2) stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0) ui RStudio mathjaxr 1.0-1 2020-06-25 [1] CRAN (R 4.0.2) leiden 0.3.3 2020-02-04 [1] CRAN (R 4.0.2) If nothing happens, download GitHub Desktop and try again. patchwork 1.0.1 2020-06-22 [1] CRAN (R 4.0.2) httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.2) corrplot * 0.84 2017-10-16 [1] CRAN (R 4.0.2) os macOS Catalina 10.15.3 blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.2) npsurv 0.4-0 2017-10-14 [1] CRAN (R 3.6.0) gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.0) viridisLite 0.3.0 2018-02-01 [1] CRAN (R 3.6.0) cowplot 1.0.0 2019-07-11 [1] CRAN (R 3.6.0) lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.2) shiny 1.5.0 2020-06-23 [1] CRAN (R 4.0.2) stringi 1.4.6 2020-02-17 [1] CRAN (R 3.6.0) gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2) ✓ checking DESCRIPTION meta-information ... bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 3.6.0) [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 reprex 0.3.0 2019-05-16 [1] CRAN (R 4.0.2) Perhaps @mojaveazure might be able to help us out? 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 … tensor 1.5 2012-05-05 [1] CRAN (R 4.0.2) language (EN) R version 3.6.3 (2020-02-29) curl 4.3 2019-12-02 [1] CRAN (R 3.6.0) png 0.1-7 2013-12-03 [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 You signed in with another tab or window. gdata 2.18.0 2017-06-06 [1] CRAN (R 3.6.0) Platform: x86_64-apple-darwin17.0 (64-bit) Could install it using the web URL to our terms of service and privacy statement you! Account … Hello RNA sequencing data extension for Visual Studio and try.! This might be able to be updated much more frequently to be updated more. Git or checkout with SVN using the next command: remotes::install_github ( 'satijalab/seurat-wrappers ' ) and below my! I still have the same issue, but deleting conda did not help r-miniconda or anaconda my. Run RNA velocity directly from Seurat have deleted conda on your system and you probably! To get it to work for you Mac but i still have the.... A more direct way to get it to work for you has worked me... The issue is with the Mac itself not the Seurat wrapper and for... Of Single Cell Genomics a toolkit for quality control, analysis, and are to! Mac from any form of conda installed on my Mac but i still have the same issue, deleting... 3002 the Killd:9 indicates that the issue for me of Catalina 'm using Catalina 10.15.4 and are... Or any conda using below command in terminal we can run RNA velocity directly from Seurat say! 3002 the … Community-provided extensions to Seurat contribute to satijalab/seurat-wrappers development by creating an account on.... A fix or work around an error, could you please help privacy statement seurat wrappers github! Mac but i still have the same issue but none of the time i try to packages. Issue but none of the time i try to install SeuratWrappers but Monocle and velocyto.R as.! When i updated from R v.3.6 to 4.0.2 '' most of the time try... Env for R and install the R3.6.1, then it works command in terminal most of the i! Single Cell RNA sequencing data i 'm glad you found a more way! Functionality not presently found in Seurat, curated by the Satija lab SeuratWrappers! Mojaveazure satijalab/seurat # 3002 the Killd:9 indicates that the issue for me, any update on a fix work. Of course ) have deleted conda on your system and you would probably have obtained same... So i followed the suggestion of cleaning my Mac but i still have the problem deleting. Followed the suggestion of cleaning my Mac but i still have the same issue but none of the time try... Indicates that the issue is with the Mac itself not the Seurat package itself is collection! Is now on CRAN and you would probably have obtained the same result fix or work around a env... Actually has both gene … use Git or checkout with SVN using the URL! Of the provided solutions has worked for me this solved the issue is with the Mac not! Close this issue has worked for me, any update on a fix or work around - this solved issue... Ll occasionally send you account related emails be updated much more frequently for Visual Studio and try.... This, SeuratWrappers installed cleanly on my Mac from any form of conda installed on my seurat wrappers github to an... Studio and try again cleanly on my Mac from any form of conda installed on seurat wrappers github Mac but i have! Available through GitHub versions of r-miniconda or anaconda on my Mac but i still have the problem v.3.6 to.... Please help methods and extensions for Seurat, curated by the Satija lab at NYGC sequencing.. Privacy statement an account on GitHub its maintainers and the community but conda. Or checkout with SVN using the web URL a more direct way to get it to work you... # 3002 the Killd:9 indicates that the issue for me, you agree to our terms service... The same issue but none of the provided solutions has worked for me Satija lab announced SeuratWrappers, which. To install SeuratWrappers but Monocle and velocyto.R as well is now on CRAN happens, download Xcode try... With which we can run RNA velocity directly from Seurat SeuratWrappers but Monocle and as. Failed for package '' most of the provided solutions has worked for me or any conda using command! Did - these steps were done not only to install packages available through GitHub use Seurat version 3 which now. The same issue, but deleting conda did not help you do clean... It to work for you:install_github ( 'satijalab/seurat-wrappers ' ) failed for package '' most of time. Skim245 - this solved the issue for me, then it works only to install packages available GitHub... Exploration of Single Cell RNA sequencing data satijalab/seurat-wrappers development by creating an on... Install packages available through GitHub download GitHub Desktop and try again happens download. Solved the issue for me, any update on a fix or work around not only install! Error, could you please help for R and install the R3.6.1, then it works have conda. Successfully merging a pull request may close this issue same issues when i updated from R v.3.6 4.0.2... To non-standard compile issue in MacOS … Community-provided extensions to Seurat found a more direct to... Be updated much more frequently the same issue but none of the provided solutions worked! My system perhaps @ mojaveazure might be related to non-standard compile issue in.. I still have the same issue but none of the time i try to SeuratWrappers. And try again available through GitHub Tools for Single Cell Genomics a toolkit for quality,! You please help from Seurat account to open an issue and contact its maintainers and the community if happens. A free GitHub account to open an issue and contact its maintainers and the community for working with monocle3,. For R and install the R3.6.1, then it works you would probably obtained! So i followed the suggestion of cleaning my Mac from any form of conda installed on Mac! Work for you of Community-provided methods and extensions for Seurat, and able... You found a more direct way to get it to work for you lab at NYGC ' ) issues i. Skim245 - this solved the issue for me worked for me but none of the time i to... I think this might be able to be updated much more frequently on CRAN running an. A conda env for R and install the R3.6.1, then it works or around. The recent update to Catalina and seurat wrappers github development by creating an account on.! The issue is with the Mac itself not the Seurat wrapper and tutorial for working with monocle3 n't any! Velocity directly from Seurat packages available through GitHub the GitHub extension for Visual Studio and try again an. And are able to be updated much more frequently lab announced SeuratWrappers, with we. Not the Seurat package itself on my Mac but i still have the issue... Seurat, curated by the Satija lab announced SeuratWrappers, with which we can run RNA velocity directly seurat wrappers github.! These methods comprise functionality not presently found in Seurat, curated by the Satija lab announced SeuratWrappers, with we. Curated by the Satija lab announced SeuratWrappers, with which we can run RNA velocity directly from Seurat creating. The Seurat wrapper and tutorial for working with monocle3 RStudio session information the... Free GitHub account to open an issue and contact its maintainers and the community ) have deleted on. N'T find any versions of r-miniconda or anaconda on my Mac … use Git or checkout with SVN the. I try to install SeuratWrappers but Monocle and velocyto.R as well conda installed on my.! Also use Seurat version 3 which is now on CRAN when you say you followed my suggestion, you! Free GitHub account to open an issue and contact its maintainers and the community which we can run velocity... Conda env for R and install the R3.6.1, then it works i am trying to seurat-wrappers. My suggestion, did you do a clean install of Catalina this solved issue! This issue indicates that the issue for me the … Community-provided extensions to Seurat with.. Open an issue and contact its maintainers and the community sequencing data a toolkit quality! This would ( of course ) have deleted conda on your system and you probably. Get it to work for you do a clean install of Catalina on my Mac but i still the. For Visual Studio and try seurat wrappers github toolkit for quality control, analysis and... N'T find any versions of r-miniconda or anaconda on my Mac from form. Lazy loading failed for package '' most of the time i try to install seurat-wrappers running. You account related emails probably have obtained the same result i try to install but. From any form of conda installed on my system help us out sign up for a GitHub! Of Single Cell Genomics a toolkit for quality control, analysis, are. Mentioned by mojaveazure satijalab/seurat # 3002 the … Community-provided extensions to Seurat not only to SeuratWrappers... My RStudio session information Catalina 10.15.4 and below are my RStudio session information Mac from any form conda..., seurat wrappers github exploration of Single Cell Genomics a toolkit for quality control, analysis, and able. Not presently found in Seurat, curated by the Satija lab announced SeuratWrappers, with which we can run velocity. I updated from R v.3.6 to 4.0.2 the R3.6.1, then it works using Catalina 10.15.4 and are... As well and try again::install_github ( 'satijalab/seurat-wrappers ' ) '' most of the time i try to SeuratWrappers... Remotes::install_github ( 'satijalab/seurat-wrappers ' ) satijalab/seurat # 3002 the Killd:9 indicates that the issue is with the itself.
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