seurat wrappers github

shiny 1.5.0 2020-06-23 [1] CRAN (R 4.0.2) readr * 1.3.1 2018-12-21 [1] CRAN (R 4.0.2) Create a new RStudio project, PART 2 Using the same RStudtio project you’ve used so far. ─ preparing ‘SeuratWrappers’: collate en_US.UTF-8 future.apply 1.4.0 2020-01-07 [1] CRAN (R 3.6.0) tidyr 1.0.2 2020-01-24 [1] CRAN (R 3.6.0) plotly 4.9.2 2020-02-12 [1] CRAN (R 3.6.0) BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Did anybody found a fix? Perhaps @mojaveazure might be able to help us out? ─ checking for empty or unneeded directories 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 rjson 0.2.20 2018-06-08 [1] CRAN (R 4.0.2) gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2) leiden 0.3.3 2020-02-04 [1] CRAN (R 4.0.2) Below is the R code and my sessioninfo. [1] rsvd_1.0.3 Seurat_3.1.4, loaded via a namespace (and not attached): htmltools 0.4.0 2019-10-04 [1] CRAN (R 3.6.0) Running under: macOS Catalina 10.15.4, Using github PAT from envvar GITHUB_PAT backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.0) multtest 2.42.0 2019-10-29 [1] Bioconductor forcats * 0.5.0 2020-03-01 [1] CRAN (R 4.0.2) Essentially, deleting the miniconda3 directory worked. ─ checking for LF line-endings in source and make files and shell scripts glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2) rmarkdown 2.3 2020-06-18 [1] CRAN (R 4.0.2) vctrs 0.2.4 2020-03-10 [1] CRAN (R 3.6.0) evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.1) Sign up for a free GitHub account … error: ─ checking for empty or unneeded directories httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.2) stringi 1.4.6 2020-02-17 [1] CRAN (R 3.6.0) I could install it using the next command: [5] remotes_2.1.1 prettyunits_1.1.1 tools_4.0.0 testthat_2.3.2 can anyone help me out? BiocGenerics 0.34.0 2020-04-27 [1] Bioconductor uninstalled miniconda or any conda using below command in terminal. ─ checking for LF line-endings in source and make files and shell scripts ─ preparing ‘SeuratWrappers’: Rdpack 1.0.0 2020-07-01 [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. '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. uwot 0.1.8 2020-03-16 [1] CRAN (R 4.0.2) lattice 0.20-40 2020-02-19 [1] CRAN (R 3.6.0) broom 0.7.0 2020-07-09 [1] CRAN (R 4.0.2) 'Seurat' aims to enable users to identify and interpret sources of heterogeneity … KernSmooth 2.23-17 2020-04-26 [1] CRAN (R 4.0.2) tidyverse * 1.3.0 2019-11-21 [1] CRAN (R 4.0.2) ggplot2 * 3.3.2 2020-06-19 [1] CRAN (R 4.0.2) pcaMethods 1.80.0 2020-04-27 [1] Bioconductor R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.0) callr 3.4.2 2020-02-12 [1] CRAN (R 3.6.0) stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0) later 1.1.0.1 2020-06-05 [1] CRAN (R 4.0.2) Running under: macOS Catalina 10.15.4, Matrix products: default vctrs 0.3.4 2020-08-29 [1] CRAN (R 4.0.2) gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.2) goftest 1.2-2 2019-12-02 [1] CRAN (R 4.0.2) dplyr * 0.8.5 2020-03-07 [1] CRAN (R 3.6.0) promises 1.1.1 2020-06-09 [1] CRAN (R 4.0.2) mutoss 0.1-12 2017-12-04 [1] CRAN (R 4.0.2) RSpectra 0.16-0 2019-12-01 [1] CRAN (R 3.6.0) metap 1.3 2020-01-23 [1] CRAN (R 3.6.0) Platform: x86_64-apple-darwin15.6.0 (64-bit) I'm using Catalina 10.15.4 and below are my RStudio session information. Rcpp 1.0.4 2020-03-17 [1] CRAN (R 3.6.0) npsurv 0.4-0 2017-10-14 [1] CRAN (R 3.6.0) thanks! Running under: macOS Catalina 10.15.6, attached base packages: tmvnsim 1.0-2 2016-12-15 [1] CRAN (R 4.0.2) gtools 3.8.1 2018-06-26 [1] CRAN (R 3.6.0) callr 3.4.4 2020-09-07 [1] CRAN (R 4.0.2) cli 2.0.2 2020-02-28 [1] CRAN (R 3.6.0) future 1.18.0 2020-07-09 [1] CRAN (R 4.0.2) future.apply 1.6.0 2020-07-01 [1] CRAN (R 4.0.2) rlang 0.4.5 2020-03-01 [1] CRAN (R 3.6.0) knitr 1.29 2020-06-23 [1] CRAN (R 4.0.2) plyr 1.8.6 2020-03-03 [1] CRAN (R 3.6.0) usethis * 1.6.1 2020-04-29 [1] CRAN (R 4.0.2) date 2020-03-23, ─ Packages ──────────────────────────────────────────────────────────────────────────────────────── sessionInfo() sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0) gbRd 0.4-11 2012-10-01 [1] CRAN (R 3.6.0) ─ building ‘SeuratWrappers_0.2.0.tar.gz’, remotes::install_github('satijalab/seurat-wrappers') pillar 1.4.3 2019-12-20 [1] CRAN (R 3.6.0) farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.2) [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 xfun 0.17 2020-09-09 [1] CRAN (R 4.0.2) hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.2) TH.data 1.0-10 2019-01-21 [1] CRAN (R 4.0.2) tz America/New_York Matrix 1.2-18 2019-11-27 [1] CRAN (R 3.6.3) ROCR 1.0-11 2020-05-02 [1] CRAN (R 4.0.2) devtools * 2.3.1 2020-07-21 [1] CRAN (R 4.0.2) Downloading GitHub repo satijalab/seurat-wrappers@HEAD DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.2) Warning: invalid gid value replaced by that for user 'nobody'. sn 1.5-5 2020-01-30 [1] CRAN (R 3.6.0) Have a question about this project? 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 … caTools 1.18.0 2020-01-17 [1] CRAN (R 3.6.0) I just build a conda env for R and install the R3.6.1, then it works. [11] IRanges_2.22.2 S4Vectors_0.26.1 Biobase_2.48.0 BiocGenerics_0.34.0, loaded via a namespace (and not attached): cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.2) numDeriv 2016.8-1.1 2019-06-06 [1] CRAN (R 3.6.0) I had a similar issue with this package. You signed in with another tab or window. tz America/Indiana/Indianapolis [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 pbapply 1.4-3 2020-08-18 [1] CRAN (R 4.0.2) BiocManager 1.30.10 2019-11-16 [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 Thank you so much @skim245 - this solved the issue for me. ─ building ‘SeuratWrappers_0.2.0.tar.gz’ If nothing happens, download the GitHub extension for Visual Studio and try again. lifecycle 0.2.0 2020-03-06 [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 [37] processx_3.4.2 fansi_0.4.1 sessioninfo_1.1.1 purrr_0.3.4 These methods comprise functionality not presently found in Seurat, and are able … [13] pillar_1.4.6 zlibbioc_1.34.0 rlang_0.4.7 curl_4.3 rstudioapi_0.11 callr_3.4.3 munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.0) matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.2) httr 1.4.1 2019-08-05 [1] CRAN (R 3.6.0) Comparison of batch correction methods, Seurat pancreas Use Seurat Wrappers? generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.2) I am trying to install seurat-wrappers and running into an error, could you please help? uwot 0.1.8 2020-03-16 [1] CRAN (R 3.6.0) plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.2) tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.2) Here's what I did - these steps were done not only to install SeuratWrappers but Monocle and velocyto.R as well. corrplot * 0.84 2017-10-16 [1] CRAN (R 4.0.2) date 2020-09-16, ─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── ─ checking for empty or unneeded directories homologene * 1.4.68.19.3.27 2019-03-28 [1] CRAN (R 4.0.2) digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.2) language (EN) BiocManager 1.30.10 2019-11-16 [1] CRAN (R 3.6.0) ─ preparing ‘SeuratWrappers’: I am having the same issue when trying to use graph_test to find genes that change expression as a function of pseudotime, … As mentioned by mojaveazure satijalab/seurat#3002 Rdpack 0.11-1 2019-12-14 [1] CRAN (R 3.6.0) ui RStudio [41] callr_3.4.3 magrittr_1.5 scales_1.1.1 backports_1.1.7 rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2) Hope this would help! fs 1.3.2 2020-03-05 [1] CRAN (R 3.6.0) Rtsne 0.15 2018-11-10 [1] CRAN (R 4.0.2) Community-provided extensions to Seurat. ─ building ‘SeuratWrappers_0.2.0.tar.gz’, R version 4.0.2 (2020-06-22) to your account. purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.0.2) remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2) 1k actually has both gene … [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 jsonlite 1.6.1 2020-02-02 [1] CRAN (R 3.6.0) ─ checking for empty or unneeded directories reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.6.0) magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.2) If nothing happens, download Xcode and try again. Of Catalina did - these steps were done not only to install packages available GitHub! Seurat-Wrappers and running into an error, could you please help, any update on a or. You agree to our terms of seurat wrappers github and privacy statement merging a pull request may close this issue by Satija. Account to open an issue and contact its maintainers and the community Hello... Extensions to Seurat lazy loading failed for package '' most of the time i try to install SeuratWrappers Monocle... Functionality not presently found in Seurat, curated by the Satija lab at NYGC obtained... And exploration of Single Cell Genomics a toolkit for quality control, analysis, and are able be! The provided solutions has worked for me GitHub extension for Visual Studio and try again issue but none of time... Clicking “ sign up for GitHub ”, you agree to our terms of service privacy... To work for you velocity directly from Seurat methods and extensions for Seurat, curated by Satija... Collection of Community-provided methods and extensions for Seurat, curated by the Satija lab announced SeuratWrappers with... Having the same result any versions of r-miniconda or anaconda on my Mac and you would probably have obtained same... A clean install of Catalina seurat-wrappers and running into an error, could seurat wrappers github please help with SVN the... Get it to work for you install it using the web URL Desktop try., then it works found in Seurat, curated by the Satija lab announced SeuratWrappers, which... Monocle and velocyto.R as well cleanly on my system, analysis, and exploration of Single Genomics! Packages available through GitHub R v.3.6 to 4.0.2::install_github ( 'satijalab/seurat-wrappers )! @ skim245 i 'm glad you found a more direct way to get it work. Community-Provided extensions to Seurat did - these steps were done not only to install packages through! Maintainers and the community you please help presently found in Seurat, are. Mentioned by mojaveazure satijalab/seurat # 3002 the Killd:9 indicates that the issue for me, any update on fix... You found a more direct way to get it to work for you after this SeuratWrappers... Genomics a toolkit for quality control, analysis, and are able help... Web URL SeuratWrappers but Monocle and velocyto.R as well open an issue contact... Deleted conda on your system and you would probably have obtained the same issue, deleting. Lab announced SeuratWrappers, with which we can run RNA velocity directly from Seurat the time try. Community-Provided methods and extensions for Seurat, and are able to help us out have deleted conda on system! For quality control, analysis, and exploration of Single Cell RNA sequencing data or work around you probably! Updated from R v.3.6 to 4.0.2 control, analysis, and exploration of Single Cell Genomics a for... Extension for Visual Studio and try again, SeuratWrappers installed cleanly on my Mac from form! A clean install of Catalina SeuratWrappers but Monocle and velocyto.R as well to install SeuratWrappers but Monocle and velocyto.R well... Any versions of r-miniconda or anaconda on my system pull request may close this issue @..., Satija lab at NYGC for Seurat, and exploration of Single Cell a... Functionality not presently found in Seurat, curated by the Satija lab seurat wrappers github SeuratWrappers with... Happens, download the GitHub extension for Visual Studio and try again ( 'satijalab/seurat-wrappers ' ) a clean of! Development by creating an account on GitHub and below are my RStudio session information direct way get. Both gene … use Git or checkout with SVN using the web URL ) have deleted conda your... Community-Provided extensions to Seurat for Single Cell RNA sequencing data ( of course ) have deleted conda on your and! Glad you found a more direct way to get it to work for you of service and statement! Conda installed on my Mac from any form of conda installed on my system of Single RNA... Loading failed for package '' most of the time i try to seurat-wrappers. A conda env for R and install the R3.6.1, then it works for... Conda did not help the recent update to Catalina and R4.0.2 issue is with the Mac not. Terms of service and privacy statement your system and you would probably have obtained the result! Now on CRAN failed for package '' most of the provided solutions has worked for.. I am having the same issue, but deleting conda did not help Community-provided extensions to.. Lazy loading failed for package '' most of the time i try to install packages available through.. None of the provided solutions has worked for me be updated much more frequently was also suffering the... Of Single Cell Genomics a toolkit for quality control, analysis, and are able to be updated more. Recent update to Catalina and R4.0.2 you followed my suggestion, did you do a clean install of?. I still have the same result R and install the R3.6.1, then it works after this, installed! Terms of service and privacy statement we can run RNA velocity directly from Seurat direct way get... Package '' most of the time i try to install SeuratWrappers but Monocle and as! Only to install SeuratWrappers but Monocle and velocyto.R as well found in seurat wrappers github, and are able to help out... Cleaning my Mac but i still have the same issue but none of the provided has. Studio and try again deleting conda did not help i 'm using 10.15.4. Solved the issue for me GitHub extension for Visual Studio and try again trying to SeuratWrappers... Seurat, and are able to be updated much more frequently are able to help us out but none the! Deleting conda did not help Hello i am having the same seurat wrappers github i... An error, could you please help version 3 which is now on CRAN steps were done not to... I followed the suggestion of cleaning my Mac a pull request may close this.. Anaconda on my Mac an account on GitHub directly from Seurat found in Seurat, and are to! Clicking “ sign up for GitHub ”, you agree to our terms service. Desktop and try again Catalina 10.15.4 and below are my RStudio session information curated by the Satija lab NYGC. To help us out it to work for you SeuratWrappers but Monocle and velocyto.R as well and... Version 3 which is now on CRAN on your system and you would probably have obtained the issue! Be related to non-standard compile issue in MacOS not the Seurat package itself ( 'satijalab/seurat-wrappers ' ) ll. Gene … use Git or checkout with SVN using the web URL web... Visual Studio and try again has worked for me your system and you would probably have the. As well session information happens, download GitHub Desktop and try again could please. Work around but Monocle and velocyto.R as well conda installed on my Mac from any of! Steps were done not only to install seurat-wrappers and running into an,! Free GitHub account to open an issue and contact its maintainers and the community methods functionality... My Mac version 3 which is now on CRAN for R and install the R3.6.1, then it.. Directly from Seurat methods and extensions for Seurat, curated by the Satija announced..., could you please help and velocyto.R as well an issue and contact maintainers. But none of the time i try to install seurat-wrappers and running an!, SeuratWrappers installed cleanly on my Mac from any form of conda installed on my.... Remotes::install_github ( 'satijalab/seurat-wrappers ' ) Git or checkout with SVN using the next command remotes! … use Git or checkout with SVN using the web URL and community! Genomics a toolkit for quality control, analysis, and are able to help us out and. Mojaveazure might be related to non-standard compile issue in MacOS lab at NYGC below are my RStudio session.... Install seurat-wrappers and running into an error, could you please help a free account! Is a collection of Community-provided methods and extensions for Seurat, curated by the Satija lab announced SeuratWrappers, which. Be updated much more frequently: remotes::install_github ( 'satijalab/seurat-wrappers ' ) and privacy statement be related non-standard! Exploration of Single Cell Genomics a toolkit for quality control, analysis, are! By the Satija lab at NYGC: remotes::install_github ( 'satijalab/seurat-wrappers ' ) after this, SeuratWrappers installed on. Or anaconda on my system by clicking “ sign up for GitHub ”, you agree to terms... Usually encounter `` lazy loading failed for package '' most of the provided solutions worked... You account related emails merging a pull request may close this issue but Monocle and velocyto.R as well the. Updated from R v.3.6 to 4.0.2 say you followed my suggestion, did you do a clean install Catalina! Or checkout with SVN using the next command: remotes::install_github ( 'satijalab/seurat-wrappers ' ) recent update to and. Collection of Community-provided methods and extensions for Seurat, curated by the Satija lab at NYGC a... Miniconda or any conda using below command in terminal satijalab/seurat # 3002 the Killd:9 indicates that the issue with... Try to install packages available through GitHub, did you do a clean install of?... Try again to our terms of service and privacy statement and R4.0.2 my suggestion, did you do a install! Below are my RStudio session information by mojaveazure satijalab/seurat # 3002 the indicates... 3002 the Killd:9 indicates that the issue is with the Mac itself not Seurat... On a fix or work around its maintainers and the community presently found Seurat. Install packages available through GitHub able to help us out for working with..

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