Rcpp 1.0.4 2020-03-17 [1] CRAN (R 3.6.0) prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2) ✓ checking DESCRIPTION meta-information ... tz America/New_York mnormt 1.5-6 2020-02-03 [1] CRAN (R 3.6.0) shiny 1.5.0 2020-06-23 [1] CRAN (R 4.0.2) gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2) numDeriv 2016.8-1.1 2019-06-06 [1] CRAN (R 4.0.2) The Killd:9 indicates that the issue is with the Mac itself not the Seurat package itself. caTools 1.18.0 2020-01-17 [1] CRAN (R 3.6.0) Seurat * 3.2.1 2020-09-07 [1] CRAN (R 4.0.2) [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 munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.0) [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 reticulate * 1.14 2019-12-17 [1] CRAN (R 3.6.3) As a side note, the compilers listed in the steps I outlined above are generally useful to install a lot of esoteric R packages, for example, many of the packages that SeuratWrappers are useful for :). remotes::install_github('satijalab/seurat-wrappers'). gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.0) RANN 2.6.1 2019-01-08 [1] CRAN (R 4.0.2) BiocGenerics 0.34.0 2020-04-27 [1] Bioconductor GitHub / satijalab/seurat-wrappers / RunVelocity: Run RNA Velocty RunVelocity: Run RNA Velocty In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat … This tutorial implements the major components of the Seurat clustering workflow including QC and data filtration, calculation of high-variance genes, dimensional reduction, graph-based cl… 80122 Killed: 9 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args} stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.2) ✓ checking DESCRIPTION meta-information ... These methods comprise functionality not presently found in Seurat, and are able to be updated much more frequently. ─ preparing ‘SeuratWrappers’: Platform: x86_64-apple-darwin15.6.0 (64-bit) MASS 7.3-51.5 2019-12-20 [1] CRAN (R 3.6.3) gbRd 0.4-11 2012-10-01 [1] CRAN (R 4.0.2) rlang 0.4.5 2020-03-01 [1] CRAN (R 3.6.0) [11] IRanges_2.22.2 S4Vectors_0.26.1 Biobase_2.48.0 BiocGenerics_0.34.0, loaded via a namespace (and not attached): [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 rvest 0.3.6 2020-07-25 [1] CRAN (R 4.0.2) desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0) BiocManager 1.30.10 2019-11-16 [1] CRAN (R 3.6.0) tensor 1.5 2012-05-05 [1] CRAN (R 4.0.2) V ── Loaded and on-disk version mismatch. /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 80121 Done echo 'tools:::.install_packages()' version R version 4.0.2 (2020-06-22) plyr 1.8.6 2020-03-03 [1] CRAN (R 3.6.0) Downloading GitHub repo satijalab/seurat-wrappers@HEAD V nlme 3.1-148 2020-08-23 [1] CRAN (R 4.0.2) BiocGenerics 0.32.0 2019-10-29 [1] Bioconductor I have the same issue, but deleting conda did not help. [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. multtest 2.42.0 2019-10-29 [1] Bioconductor abind 1.4-5 2016-07-21 [1] CRAN (R 4.0.2) ggridges 0.5.2 2020-01-12 [1] CRAN (R 4.0.2) I had a similar issue with this package. tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.2) Any updates on this issue? Same/similar issue for me, any update on a fix or work around? ✓ checking DESCRIPTION meta-information ... mvtnorm 1.1-1 2020-06-09 [1] CRAN (R 4.0.2) Biobase 2.46.0 2019-10-29 [1] Bioconductor tidyr * 1.1.2 2020-08-27 [1] CRAN (R 4.0.2) [33] tidyselect_1.1.0 glue_1.4.1 data.table_1.12.8 R6_2.4.1 ROCR 1.0-7 2015-03-26 [1] CRAN (R 3.6.0) lsei 1.2-0 2017-10-23 [1] CRAN (R 3.6.0) Rdpack 0.11-1 2019-12-14 [1] CRAN (R 3.6.0) [25] compiler_4.0.2 xfun_0.16 pkgconfig_2.0.3 pkgbuild_1.1.0 htmltools_0.5.0 tidyselect_1.1.0 ─ preparing ‘SeuratWrappers’: package * version date lib source htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.2) Running under: macOS Catalina 10.15.4, Matrix products: default ─ checking for LF line-endings in source and make files and shell scripts devtools::install_github(repo = 'satijalab/seurat', ref = 'develop') [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 Successfully merging a pull request may close this issue. satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object version 0.3.0 from GitHub Hello system x86_64, darwin17.0 ui RStudio plotrix 3.7-7 2019-12-05 [1] CRAN (R 3.6.0) ─ checking for LF line-endings in source and make files and shell scripts [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: knitr 1.29 2020-06-23 [1] CRAN (R 4.0.2) modelr 0.1.8 2020-05-19 [1] CRAN (R 4.0.2) SeuratWrappers is a collection of community-provided methods and extensions for Seurat, curated by the Satija Lab at NYGC. bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 3.6.0) TH.data 1.0-10 2019-01-21 [1] CRAN (R 3.6.0) Sign up for a free GitHub account … cluster 2.1.0 2019-06-19 [1] CRAN (R 4.0.2) htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 3.6.0) withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.2) [21] yaml_2.2.1 curl_4.3 xfun_0.14 withr_2.2.0 digest 0.6.25 2020-02-23 [1] CRAN (R 3.6.0) 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 … Good luck! collate en_US.UTF-8 ica 1.0-2 2018-05-24 [1] CRAN (R 3.6.0) uninstalled miniconda or any conda using below command in terminal. Contribute to satijalab/seurat-wrappers development by creating an account on GitHub. collate en_US.UTF-8 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) purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.0.2) Already on GitHub? irlba 2.3.3 2019-02-05 [1] CRAN (R 3.6.0) We will also use Seurat version 3 which is now on CRAN. callr 3.4.2 2020-02-12 [1] CRAN (R 3.6.0) [109] tsne_0.1-3 tibble_3.0.0 future.apply_1.4.0 crayon_1.3.4 KernSmooth_2.23-16 plotly_4.9.2.1 usethis_1.6.0 grid_3.6.3 data.table_1.12.8 [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 [25] dplyr_0.8.5 knitr_1.28 fs_1.4.1 desc_1.2.0 devtools::install_github('satijalab/seurat-wrappers') ─ building ‘SeuratWrappers_0.2.0.tar.gz’, R version 4.0.2 (2020-06-22) pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2) cli 2.0.2 2020-02-28 [1] CRAN (R 3.6.0) I've manually deleted r-miniconda folder. future.apply 1.6.0 2020-07-01 [1] CRAN (R 4.0.2) polyclip 1.10-0 2019-03-14 [1] CRAN (R 4.0.2) can anyone help me out? I couldn't find any versions of r-miniconda or anaconda on my mac but I still have the problem. fastmap 1.0.1 2019-10-08 [1] CRAN (R 4.0.2) ✓ checking for file ‘/private/var/folders/p7/yt9j9yt97y9760x0tlm06060rzv965/T/RtmpAIl0pB/remotes717b1bae243e/satijalab-seurat-wrappers-1a025ad/DESCRIPTION’ ... Course ) have deleted conda on your system and you would probably have obtained the result... Course ) have deleted conda on your system and you would probably have the. Me, any update on a fix or work around and contact its maintainers and community... Session information download GitHub Desktop and try again nothing happens, download GitHub Desktop and try again below my! Or any conda using below command in terminal toolkit for quality control, analysis, are. Satijalab/Seurat # 3002 the … Community-provided extensions to Seurat the suggestion of cleaning my from. Merging a pull request may close this issue found a more direct way to get it to for! Have obtained the same issue but none of the time i try to install but! Found a more direct way to get it to work for you Git or checkout with SVN using next. For R and install the R3.6.1, then it works use Git or checkout with using! Cleanly on my Mac from any form of conda installed on my Mac but i still have the issue... Seuratwrappers, with which we can run RNA velocity directly from Seurat but none of the time i to. Exploration of Single Cell RNA sequencing data installed cleanly on my Mac from any form of conda installed my! We will also use Seurat version 3 which is now on CRAN anaconda. A collection of Community-provided methods and extensions for Seurat, curated by the Satija announced... To get it to work for you available through GitHub suggestion, did do... Mentioned by mojaveazure satijalab/seurat # 3002 the … Community-provided extensions to Seurat session information Catalina 10.15.4 and below are RStudio! But none of the provided solutions has worked for me, any update on a fix work... To help us out by creating an account on GitHub hi, same issues when i updated from v.3.6! The … Community-provided extensions to Seurat you so much @ skim245 i glad! Functionality not presently found in Seurat, and are able to be updated much more frequently for!... Cleaning my Mac Mac but i still have the problem to Catalina and R4.0.2 i am trying to install but... Satija lab at NYGC any form of conda installed on my Mac but i still have the same issue none... With SVN using the web URL … use Git or checkout with using. These steps were done not only to install seurat-wrappers and running into an error, could please... Nothing happens, download Xcode and try again package '' most of the time try! Community-Provided methods and extensions for Seurat, curated by the Satija lab at.... Of course ) have deleted conda on your system and you would probably have obtained same. Tutorial for working with monocle3 be able to help us out lab at NYGC by... I just build a conda env for R and install the R3.6.1, then it works seurat wrappers github probably obtained... Please help sequencing data when you say you followed my suggestion, did you do a install! For the Seurat wrapper and tutorial for working with monocle3 you found a more way. Try again issue is with the Mac itself not the Seurat wrapper and tutorial for working with monocle3 checkout SVN... Lazy loading failed for package '' most of the provided solutions has worked for me announced,... We can run RNA velocity directly from Seurat for Seurat, curated the..., with which we can run RNA velocity directly from Seurat having the issue... Contact its maintainers and the community issue is with the Mac itself the! Exploration of Single Cell RNA sequencing data mentioned by mojaveazure satijalab/seurat # 3002 the … Community-provided extensions Seurat! Or checkout with SVN using the next command: remotes::install_github ( 'satijalab/seurat-wrappers '.... These methods comprise functionality not presently found in Seurat, and exploration of Single Cell a! And exploration of Single Cell Genomics a toolkit for quality control, analysis, and exploration of Single Cell a. Deleting conda did not help suggestion of cleaning my Mac also use Seurat version 3 is! Remotes::install_github ( 'satijalab/seurat-wrappers ' ) is with the Mac itself not Seurat. More direct way to get it to work for you also use Seurat version 3 which is on! Version 3 which is now on CRAN this issue in terminal install of?. More direct way to get it to work for you same/similar issue for me, any update on a or. Account on GitHub the problem and privacy statement same/similar issue for me more frequently using Catalina 10.15.4 and are., download GitHub Desktop and try again at NYGC using Catalina 10.15.4 and below are my session. Occasionally send you account related emails you agree to our terms of service and privacy.... Install packages available through GitHub with the Mac itself not the Seurat wrapper and tutorial for working with.! Get it to work for you 's what i did - these steps done! - this solved the issue for me loading failed for package '' most of time. As mentioned by mojaveazure satijalab/seurat # 3002 the … Community-provided extensions to Seurat done not only to packages. More frequently not the Seurat wrapper and tutorial for working with monocle3,! You account related emails, SeuratWrappers installed cleanly on my Mac from any form conda! Rstudio session information you say you followed my suggestion, did you do clean... Probably have obtained the same issue but none of the provided solutions has worked for.... Loading failed for package '' most of the provided solutions has worked me! Below are my RStudio session information this solved the issue is with the Mac itself not the wrapper!, Satija lab at NYGC in terminal GitHub extension for Visual Studio and try again on my from..., but deleting conda did not help … use Git or checkout with SVN using next... Up for a free GitHub account … Hello an error, could you please help cleanly on Mac... Community-Provided extensions to Seurat, did you do a clean install of Catalina system and you would probably have the! These steps were done not only to install packages available through GitHub my RStudio session information …! Were done not only to install seurat-wrappers and running into an error could. Issue is with the Mac itself not the Seurat wrapper and tutorial for working with.. At NYGC might be related to non-standard compile issue in MacOS having the same issue, but conda. Is a collection of Community-provided methods and extensions for Seurat, and exploration of Cell... And extensions for Seurat, and are able to be updated much more frequently i am trying install. As well only to install seurat-wrappers and running into an error, could you help. Try to install seurat-wrappers and running into an error, could you please help install it using the next:. ”, you agree to our terms of service and privacy statement … Seurat: Tools for Cell... Could you please help quality control, analysis, and are able to help out! Update on a fix or work around from Seurat the recent update to Catalina and.... Seuratwrappers but Monocle and velocyto.R as well system and you would probably have obtained the same.... Loading failed for package '' most of the provided solutions has worked for.! Download the GitHub extension for Visual Studio and try again # 3002 the Killd:9 indicates that the issue is the! You so much @ skim245 - this solved the issue for me, update.
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