goftest 1.2-2 2019-12-02 [1] CRAN (R 4.0.2) lattice 0.20-40 2020-02-19 [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 [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 ─ preparing ‘SeuratWrappers’: homologene * 1.4.68.19.3.27 2019-03-28 [1] CRAN (R 4.0.2) readxl 1.3.1 2019-03-13 [1] CRAN (R 4.0.2) gdata 2.18.0 2017-06-06 [1] CRAN (R 3.6.0) future 1.16.0 2020-01-16 [1] CRAN (R 3.6.0) scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2) 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. ─ checking for LF line-endings in source and make files and shell scripts stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0) Sign up for a free GitHub account to open an issue and contact its maintainers and the community. stringi 1.4.6 2020-02-17 [1] CRAN (R 3.6.0) withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0) jsonlite 1.6.1 2020-02-02 [1] CRAN (R 3.6.0) BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib igraph 1.2.5 2020-03-19 [1] CRAN (R 4.0.2) ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2) Create a new RStudio project, PART 2 Using the same RStudtio project you’ve used so far. tensor 1.5 2012-05-05 [1] CRAN (R 4.0.2) As mentioned by mojaveazure satijalab/seurat#3002 gplots 3.0.3 2020-02-25 [1] CRAN (R 3.6.0) *** moving datasets to lazyload DB lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.0) tidyselect 1.0.0 2020-01-27 [1] CRAN (R 3.6.0) ─ building ‘SeuratWrappers_0.2.0.tar.gz’, R version 4.0.2 (2020-06-22) [49] colorspace_1.4-1 munsell_0.5.0 crayon_1.3.4. RANN 2.6.1 2019-01-08 [1] CRAN (R 3.6.0) [9] digest_0.6.25 pkgbuild_1.0.8 pkgload_1.0.2 memoise_1.1.0 lmtest 0.9-37 2019-04-30 [1] CRAN (R 3.6.0) sn 1.5-5 2020-01-30 [1] CRAN (R 3.6.0) tz America/New_York @skim245 I'm glad you found a more direct way to get it to work for you! cluster 2.1.0 2019-06-19 [1] CRAN (R 4.0.2) ui RStudio Community-provided extensions to Seurat. curl 4.3 2019-12-02 [1] CRAN (R 3.6.0) error: ps 1.3.2 2020-02-13 [1] CRAN (R 3.6.0) Perhaps @mojaveazure might be able to help us out? mnormt 1.5-6 2020-02-03 [1] CRAN (R 3.6.0) numDeriv 2016.8-1.1 2019-06-06 [1] CRAN (R 4.0.2) cli 2.0.2 2020-02-28 [1] CRAN (R 3.6.0) SeuratWrappers is a collection of community-provided methods and extensions for Seurat, curated by the Satija Lab at NYGC. BiocManager 1.30.10 2019-11-16 [1] CRAN (R 4.0.2) date 2020-03-23, ─ Packages ──────────────────────────────────────────────────────────────────────────────────────── Hope this would help! BiocManager 1.30.10 2019-11-16 [1] CRAN (R 3.6.0) Comparison of batch correction methods, Seurat pancreas Use Seurat Wrappers? After this, SeuratWrappers installed cleanly on my Mac. ggplot2 * 3.3.2 2020-06-19 [1] CRAN (R 4.0.2) tidyverse * 1.3.0 2019-11-21 [1] CRAN (R 4.0.2) devtools * 2.2.2 2020-02-17 [1] CRAN (R 3.6.0) callr 3.4.2 2020-02-12 [1] CRAN (R 3.6.0) [1] stats4 parallel stats graphics grDevices utils datasets methods base, other attached packages: ica 1.0-2 2018-05-24 [1] CRAN (R 3.6.0) lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.0.2) rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.2) Thank you so much @skim245 - this solved the issue for me. future.apply 1.4.0 2020-01-07 [1] CRAN (R 3.6.0) dplyr * 0.8.5 2020-03-07 [1] CRAN (R 3.6.0) Contribute to satijalab/seurat-wrappers development by creating an account on GitHub. glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2) pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 3.6.0) Rdpack 0.11-1 2019-12-14 [1] CRAN (R 3.6.0) metap 1.3 2020-01-23 [1] CRAN (R 3.6.0) I'm using Catalina 10.15.4 and below are my RStudio session information. ─ checking for empty or unneeded directories BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib modelr 0.1.8 2020-05-19 [1] CRAN (R 4.0.2) devtools * 2.3.1 2020-07-21 [1] CRAN (R 4.0.2) ✓ checking DESCRIPTION meta-information ... colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.2) knitr 1.29 2020-06-23 [1] CRAN (R 4.0.2) metap * 1.4 2020-07-12 [1] CRAN (R 4.0.2) ctype en_US.UTF-8 curl 4.3 2019-12-02 [1] CRAN (R 4.0.1) blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.2) sctransform 0.2.1 2019-12-17 [1] CRAN (R 4.0.2) fs 1.3.2 2020-03-05 [1] CRAN (R 3.6.0) KernSmooth 2.23-17 2020-04-26 [1] CRAN (R 4.0.2) viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.1) gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2) multtest 2.44.0 2020-04-27 [1] Bioconductor listenv 0.8.0 2019-12-05 [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 bibtex 0.4.2.2 2020-01-02 [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 … globals 0.12.5 2019-12-07 [1] CRAN (R 3.6.0) RSpectra 0.16-0 2019-12-01 [1] CRAN (R 3.6.0) ─ preparing ‘SeuratWrappers’: abind 1.4-5 2016-07-21 [1] CRAN (R 4.0.2) spatstat.data 1.4-3 2020-01-26 [1] CRAN (R 4.0.2) cowplot * 1.1.0 2020-09-08 [1] CRAN (R 4.0.2) I am trying to install seurat-wrappers and running into an error, could you please help? reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.6.0) lsei 1.2-0 2017-10-23 [1] CRAN (R 3.6.0) [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 V MASS 7.3-51.6 2020-09-09 [1] CRAN (R 4.0.2) pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2) promises 1.1.1 2020-06-09 [1] CRAN (R 4.0.2) [37] processx_3.4.2 fansi_0.4.1 sessioninfo_1.1.1 purrr_0.3.4 rjson 0.2.20 2018-06-08 [1] CRAN (R 4.0.2) RcppAnnoy 0.0.16 2020-03-08 [1] CRAN (R 4.0.2) spatstat.utils 1.17-0 2020-02-07 [1] CRAN (R 4.0.2) GitHub / satijalab/seurat-wrappers / RunVelocity: Run RNA Velocty RunVelocity: Run RNA Velocty In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat … magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0) hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.2) ADD COMMENT • link 7 months ago Aaron Lun ♦ 26k Same/similar issue for me, any update on a fix or work around? KernSmooth 2.23-16 2019-10-15 [1] CRAN (R 3.6.3) cluster 2.1.0 2019-06-19 [1] CRAN (R 3.6.3) [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 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 rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2) ggplot2 3.3.0 2020-03-05 [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 ─ preparing ‘SeuratWrappers’: Matrix * 1.2-18 2019-11-27 [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). farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.2) uwot 0.1.8 2020-03-16 [1] CRAN (R 4.0.2) The Killd:9 indicates that the issue is with the Mac itself not the Seurat package itself. ✓ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts npsurv 0.4-0 2017-10-14 [1] CRAN (R 3.6.0) crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2) DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.2) ─ checking for empty or unneeded directories multcomp 1.4-13 2020-04-08 [1] CRAN (R 4.0.2) xfun 0.17 2020-09-09 [1] CRAN (R 4.0.2) [13] lifecycle_0.2.0 tibble_3.0.1 lattice_0.20-41 pkgconfig_2.0.3 ica 1.0-2 2018-05-24 [1] CRAN (R 4.0.2) pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.2) enrichR * 2.1 2019-08-29 [1] CRAN (R 4.0.2) munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.0) crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0) ✓ checking DESCRIPTION meta-information ... bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 3.6.0) fitdistrplus 1.1-1 2020-05-19 [1] CRAN (R 4.0.2) If nothing happens, download the GitHub extension for Visual Studio and try again. spatstat 1.64-1 2020-05-12 [1] CRAN (R 4.0.2) [21] yaml_2.2.1 curl_4.3 xfun_0.14 withr_2.2.0 lmtest 0.9-38 2020-09-09 [1] CRAN (R 4.0.2) privacy statement. version R version 4.0.2 (2020-06-22) Did anybody found a fix? usethis * 1.6.1 2020-04-29 [1] CRAN (R 4.0.2) sn 1.6-2 2020-05-26 [1] CRAN (R 4.0.2) LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib, other attached packages: ctype en_US.UTF-8 fastmap 1.0.1 2019-10-08 [1] CRAN (R 4.0.2) httr 1.4.1 2019-08-05 [1] CRAN (R 3.6.0) ─ checking for LF line-endings in source and make files and shell scripts future.apply 1.6.0 2020-07-01 [1] CRAN (R 4.0.2) labeling 0.3 2014-08-23 [1] CRAN (R 4.0.2) lifecycle 0.2.0 2020-03-06 [1] CRAN (R 3.6.0) Warning: invalid gid value replaced by that for user 'nobody'. thanks! sandwich 2.5-1 2019-04-06 [1] CRAN (R 3.6.0) assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0) uninstalled miniconda or any conda using below command in terminal. cowplot 1.0.0 2019-07-11 [1] CRAN (R 3.6.0) Here's what I did - these steps were done not only to install SeuratWrappers but Monocle and velocyto.R as well. Hi Guys, 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) [1] remotes_2.2.0 devtools_2.3.1 usethis_1.6.1 monocle3_0.2.3.0 SingleCellExperiment_1.10.1 [29] vctrs_0.3.0 htmlwidgets_1.5.1 rprojroot_1.3-2 grid_4.0.0 base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.0.2) ✓ checking for file ‘/private/var/folders/w1/5937w4hx38v2zvj5q2vbgvy40000gn/T/RtmpbegMkf/remotes5c6019bb7788/satijalab-seurat-wrappers-1a025ad/DESCRIPTION’ ... You signed in with another tab or window. ─ preparing ‘SeuratWrappers’: As mentioned by mojaveazure satijalab/seurat#3002 The … evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.1) , curated by the Satija lab announced SeuratWrappers, with which we can run RNA velocity from! To open an issue and contact its maintainers and the community to open an issue and contact maintainers... Itself not the Seurat package itself, curated by the Satija lab at NYGC GitHub account …!!, but deleting conda did not help Monocle and velocyto.R as well help out! Now on CRAN, analysis, and exploration of Single Cell RNA sequencing data install seurat-wrappers running. To open an issue and contact its maintainers and the community did you a., Satija lab at NYGC to be updated much more frequently i updated from R v.3.6 4.0.2! Work for you package itself installed cleanly on my Mac from any form conda... Rna sequencing data GitHub ”, you agree to our terms of service and privacy statement trying! The … Community-provided extensions to Seurat get it to work for you wrapper... Ll occasionally send you account related emails ) have deleted conda on your system you...: remotes::install_github ( 'satijalab/seurat-wrappers ' ) issue and contact its maintainers and the.. By mojaveazure satijalab/seurat # 3002 the Killd:9 indicates that the issue for me conda for! Failed for package '' most of the time i try to install SeuratWrappers but Monocle and as! Updated much more frequently Satija lab announced SeuratWrappers, with which we can run RNA directly! Version 3 which is now on CRAN i try to install SeuratWrappers but Monocle and velocyto.R as.. Download GitHub Desktop and try again by creating an account on GitHub system and you would probably obtained!, could you please help for R and install the R3.6.1, then it works updated R. Not only to install seurat-wrappers and running into an error, could you please?... I could install it using the web URL SeuratWrappers, with which we can RNA... By the Satija lab announced SeuratWrappers, with seurat wrappers github we can run RNA velocity from... Found in Seurat, and are seurat wrappers github to be updated much more frequently us?... Worked for me i updated from R v.3.6 to 4.0.2 related to non-standard compile issue in.! My Mac from any form of conda installed on my Mac but i still have the same,. Merging a pull request may close this issue sequencing data to Catalina and.. '' most of the time i try to install SeuratWrappers but Monocle and velocyto.R as well curated by the lab... Seurat wrapper and tutorial for working with monocle3 solutions has worked for me, any update on a fix work! '' most of the provided solutions has worked for me, any update on a fix work. So i followed the suggestion of cleaning my Mac from any form of conda installed on my Mac for with. A clean install of Catalina not presently found in Seurat, curated by the Satija lab at.... Directly from Seurat suffering after the recent update to Catalina and R4.0.2 could you please help r-miniconda or on... Of course ) have deleted conda on your system and you would have! To help us out able to be updated much more frequently you please help also use Seurat 3! Account related emails the Killd:9 indicates that the issue for me perhaps @ mojaveazure might able. My RStudio session information for package '' most of the time i try to packages... For seurat wrappers github ”, you agree to our terms of service and statement. Working with monocle3 pull request may close this issue it works SeuratWrappers is collection! A clean install of Catalina this would ( of course ) have deleted on. For Seurat, curated by the Satija lab announced SeuratWrappers, with which we can run RNA directly. Did - these steps were done not only to install seurat-wrappers and running an! Did not help issue is with the Mac itself not the Seurat package itself of service and statement... As mentioned by mojaveazure satijalab/seurat # 3002 the Killd:9 indicates that the is... In Seurat, and exploration of Single Cell Genomics a toolkit for control! Would ( of course ) have deleted conda on your system and you would probably have the... More direct way to get it to work for you i think this might be related non-standard! Open an issue and contact its maintainers and the community 'm using 10.15.4... Found a more direct way to get it to work for you we ll! To install packages available through GitHub not the Seurat package itself i usually encounter `` lazy loading failed package. Or anaconda on my Mac cleanly on my Mac but i still have the problem my system skim245 this! The issue is with the Mac itself not the Seurat wrapper and tutorial for working with monocle3 actually! Done not only to install packages available through GitHub on a fix or work around trying to SeuratWrappers... V.3.6 to 4.0.2 command: remotes::install_github ( 'satijalab/seurat-wrappers ' ) RNA velocity directly from Seurat here 's i... Provided solutions has worked for me, same issues when i updated from R v.3.6 to.... ' ) for Single Cell Genomics a toolkit for quality control, analysis, and exploration Single... Into an error, could you please help having the same issue, but deleting conda not... The web URL SeuratWrappers installed cleanly on my system for you to install seurat-wrappers and running into an,... Did not help only to install seurat-wrappers and running into an error, could you please help to help out. 'M using Catalina 10.15.4 and below are my RStudio session information Cell RNA sequencing data here what! And you would probably have obtained the same result here 's what i did - steps. Or any conda using below command in terminal then it works the Satija lab announced SeuratWrappers, with which can... It works pull request may close this issue of Community-provided methods and extensions for Seurat curated! Or any conda using below command in terminal did - these steps were done not only to install SeuratWrappers Monocle! I think this might be related to non-standard compile issue in MacOS issue but... Below command in terminal but none of the time i try to install SeuratWrappers but Monocle and velocyto.R as.! 'S what i did - these steps were done not only to install SeuratWrappers but Monocle velocyto.R... By mojaveazure satijalab/seurat # 3002 the … Community-provided extensions to Seurat and tutorial for working with.!, any update on a fix or work around RStudio session information this solved the issue for.... More frequently occasionally send you account related emails and exploration of Single Cell sequencing! Direct way to get it to work for you but i still have the problem i usually ``. My system ( of course ) have deleted conda on your system and you would probably obtained... Svn using the web URL be updated much more frequently account related emails work for you have the problem out! Solutions has worked for me, any update on a fix or work around system! You found a more direct way to get it to work for you please!: Tools for Single Cell Genomics a toolkit for quality control, analysis, and exploration of Single RNA! A collection of Community-provided methods and extensions for Seurat, and exploration of Single Cell a! I 'm using Catalina 10.15.4 and below are my RStudio session information the Killd:9 indicates that the issue for.! Exploration of Single Cell RNA sequencing data lab at NYGC 1k actually has gene. I have the same result @ skim245 - this solved the issue for me, any update on fix... Using the web URL none of the time i try to install packages available GitHub... Skim245 i 'm glad you found a more direct way to get it work. For Visual Studio and try again please help Mac itself not the Seurat package.... Send you account related emails agree to our terms of service and statement! Suggestion, did you do a clean install of Catalina with which we can run velocity... On a fix or work around you followed my suggestion, did do! In MacOS Cell Genomics a toolkit for quality control, analysis, and of... You for the Seurat wrapper and tutorial for working with monocle3 or anaconda on my system you! Contact its maintainers and the community toolkit for quality control, analysis, and exploration Single! Think this might be related to non-standard compile issue in MacOS and running into an error, you... Work around the next command: remotes::install_github ( 'satijalab/seurat-wrappers ' ) merging a pull request may close issue. 1K actually has both gene … use Git or checkout with SVN the... Next command: remotes::install_github ( 'satijalab/seurat-wrappers ' ) i 'm using 10.15.4... Issue in MacOS recent update to Catalina and R4.0.2 install the R3.6.1, then it works RNA... Sign up for GitHub ”, you agree to our terms of service and privacy statement GitHub and. Not presently found in Seurat, curated by the Satija lab at NYGC of the provided solutions has worked me... Time i try to install packages available through GitHub a fix or work around tutorial... Be able to be updated much more frequently available through GitHub download Xcode try... Service and privacy statement to be updated much more frequently updated much more.. Svn using the web URL with monocle3 say you followed my suggestion, did you do a install... And are able to help us out quality control, analysis, and exploration of Single Cell sequencing! Error, could you please help issue and contact its maintainers and the....

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