R version 3.6.3 (2020-02-29) rstudioapi 0.11 2020-02-07 [1] CRAN (R 3.6.0) data.table 1.12.8 2019-12-09 [1] CRAN (R 3.6.0) ggrepel 0.8.2 2020-03-08 [1] CRAN (R 4.0.2) future 1.16.0 2020-01-16 [1] CRAN (R 3.6.0) farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.2) Running under: macOS Catalina 10.15.6, attached base packages: can anyone help me out? 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. survival 3.1-11 2020-03-07 [1] CRAN (R 3.6.0) mutoss 0.1-12 2017-12-04 [1] CRAN (R 3.6.0) Contribute to satijalab/seurat-wrappers development by creating an account on GitHub. [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 cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.0.2) As mentioned by mojaveazure satijalab/seurat#3002 The … multcomp 1.4-12 2020-01-10 [1] CRAN (R 3.6.0) [1] remotes_2.2.0 devtools_2.3.1 usethis_1.6.1 monocle3_0.2.3.0 SingleCellExperiment_1.10.1 Already on GitHub? gtools 3.8.1 2018-06-26 [1] CRAN (R 3.6.0) BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Rtsne 0.15 2018-11-10 [1] CRAN (R 4.0.2) pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.0) spatstat.utils 1.17-0 2020-02-07 [1] CRAN (R 4.0.2) ✓ checking DESCRIPTION meta-information ... [45] ps_1.3.3 ellipsis_0.3.1 htmltools_0.4.0 assertthat_0.2.1 ─ Session info ──────────────────────────────────────────────────────────────────────────────────── '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. Hello! munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2) privacy statement. BiocManager 1.30.10 2019-11-16 [1] CRAN (R 4.0.2) I am having the same issue but none of the provided solutions has worked for me. gbRd 0.4-11 2012-10-01 [1] CRAN (R 4.0.2) ─ preparing ‘SeuratWrappers’: tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.0) reprex 0.3.0 2019-05-16 [1] CRAN (R 4.0.2) KernSmooth 2.23-16 2019-10-15 [1] CRAN (R 3.6.3) pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 3.6.0) mvtnorm 1.1-0 2020-02-24 [1] CRAN (R 3.6.0) [21] yaml_2.2.1 curl_4.3 xfun_0.14 withr_2.2.0 Biobase 2.46.0 2019-10-29 [1] Bioconductor V MASS 7.3-51.6 2020-09-09 [1] CRAN (R 4.0.2) rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2) haven 2.3.1 2020-06-01 [1] CRAN (R 4.0.2) ─ checking for empty or unneeded directories version R version 3.6.3 (2020-02-29) gridExtra 2.3 2017-09-09 [1] CRAN (R 3.6.0) hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.2) fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.0) I think this might be related to non-standard compile issue in MacOS. listenv 0.8.0 2019-12-05 [1] CRAN (R 3.6.0) 1k actually has both gene … ─ checking for empty or unneeded directories thanks! Hope this would help! glue 1.3.2 2020-03-12 [1] CRAN (R 3.6.0) I just build a conda env for R and install the R3.6.1, then it works. R version 4.0.0 (2020-04-24) glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2) ✓ checking DESCRIPTION meta-information ... ─ checking for empty or unneeded directories sctransform 0.2.1 2019-12-17 [1] CRAN (R 3.6.0) stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.2) If nothing happens, download Xcode and try again. ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2) I usually encounter "lazy loading failed for package" most of the time I try to install packages available through github. ADD COMMENT • link 7 months ago Aaron Lun ♦ 26k tidyselect 1.0.0 2020-01-27 [1] CRAN (R 3.6.0) [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 Seurat: Tools for Single Cell Genomics A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.1) rmarkdown 2.3 2020-06-18 [1] CRAN (R 4.0.2) Downloading GitHub repo satijalab/seurat-wrappers@master plotly 4.9.2.1 2020-04-04 [1] CRAN (R 4.0.2) ape 5.3 2019-03-17 [1] CRAN (R 3.6.0) globals 0.12.5 2019-12-07 [1] CRAN (R 3.6.0) shiny 1.5.0 2020-06-23 [1] CRAN (R 4.0.2) ctype en_US.UTF-8 tidyr * 1.1.2 2020-08-27 [1] CRAN (R 4.0.2) [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 ✓ checking for file ‘/private/var/folders/xl/p5nnh_s11j77z2sgpgc0knsh0000gn/T/Rtmp3uqs50/remotesae1f2e7224f1/satijalab-seurat-wrappers-4409237/DESCRIPTION’ ... [1] stats4 parallel stats graphics grDevices utils datasets methods base, other attached packages: [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 reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.6.0) I've manually deleted r-miniconda folder. future 1.18.0 2020-07-09 [1] CRAN (R 4.0.2) Warning: invalid gid value replaced by that for user 'nobody'. httpuv 1.5.4 2020-06-06 [1] CRAN (R 4.0.2) to your account. pillar 1.4.3 2019-12-20 [1] CRAN (R 3.6.0) 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. mnormt 2.0.2 2020-09-01 [1] CRAN (R 4.0.2) leiden 0.3.3 2020-02-04 [1] CRAN (R 3.6.0) xfun 0.17 2020-09-09 [1] CRAN (R 4.0.2) Downloading GitHub repo satijalab/seurat-wrappers@master bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 3.6.0) data.table * 1.13.0 2020-07-24 [1] CRAN (R 4.0.2) multtest 2.44.0 2020-04-27 [1] Bioconductor codetools 0.2-16 2018-12-24 [1] CRAN (R 4.0.2) tz America/New_York The Killd:9 indicates that the issue is with the Mac itself not the Seurat package itself. abind 1.4-5 2016-07-21 [1] CRAN (R 4.0.2) digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.2) patchwork 1.0.0 2019-12-01 [1] CRAN (R 3.6.0) system x86_64, darwin15.6.0 ─ building ‘SeuratWrappers_0.2.0.tar.gz’ tsne 0.1-3 2016-07-15 [1] CRAN (R 3.6.0) tidyr 1.0.2 2020-01-24 [1] CRAN (R 3.6.0) magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0) spatstat.data 1.4-3 2020-01-26 [1] CRAN (R 4.0.2) [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 stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.0.2) vctrs 0.2.4 2020-03-10 [1] CRAN (R 3.6.0) lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.2) limma 3.44.3 2020-06-12 [1] Bioconductor Running under: macOS Catalina 10.15.4, Matrix products: default pbapply 1.4-2 2019-08-31 [1] CRAN (R 3.6.0) callr 3.4.4 2020-09-07 [1] CRAN (R 4.0.2) rsvd 1.0.3 2020-02-17 [1] CRAN (R 4.0.2) bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 4.0.2) [61] colorspace_1.4-1 sessioninfo_1.1.1 memoise_1.1.0 knitr_1.29. [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 lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.0.2) lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.2) forcats * 0.5.0 2020-03-01 [1] CRAN (R 4.0.2) SeuratWrappers is also GitHub … Rcpp 1.0.5 2020-07-06 [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. I've followed FiveThirteen's suggestion, which did not work for me but ica 1.0-2 2018-05-24 [1] CRAN (R 4.0.2) devtools::install_github('satijalab/seurat-wrappers') Hello [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 ggridges 0.5.2 2020-01-12 [1] CRAN (R 4.0.2) withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0) V survival 3.1-12 2020-06-13 [1] CRAN (R 4.0.2) tz America/Indiana/Indianapolis ─ checking for LF line-endings in source and make files and shell scripts setting value scales 1.1.0 2019-11-18 [1] CRAN (R 3.6.0) If nothing happens, download GitHub Desktop and try again. … cluster 2.1.0 2019-06-19 [1] CRAN (R 3.6.3) reticulate * 1.14 2019-12-17 [1] CRAN (R 3.6.3) Recently, Satija lab announced SeuratWrappers, with which we can run RNA velocity directly from Seurat. rjson 0.2.20 2018-06-08 [1] CRAN (R 4.0.2) zoo 1.8-8 2020-05-02 [1] CRAN (R 4.0.2), [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library. Any updates on this issue? [13] pillar_1.4.6 zlibbioc_1.34.0 rlang_0.4.7 curl_4.3 rstudioapi_0.11 callr_3.4.3 [1] devtools_2.3.0 usethis_1.6.1, loaded via a namespace (and not attached): [55] RColorBrewer_1.1-2 tools_4.0.2 glue_1.4.1 purrr_0.3.4 pkgload_1.1.0 processx_3.4.3 readxl 1.3.1 2019-03-13 [1] CRAN (R 4.0.2) setting value numDeriv 2016.8-1.1 2019-06-06 [1] CRAN (R 4.0.2) [49] viridis_0.5.1 fs_1.5.0 testthat_2.3.2 ellipsis_0.3.1 generics_0.0.2 vctrs_0.3.2 magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.2) plotly 4.9.2 2020-02-12 [1] CRAN (R 3.6.0) plotrix 3.7-8 2020-04-16 [1] CRAN (R 4.0.2) After this, SeuratWrappers installed cleanly on my Mac. Comparison of batch correction methods, Seurat pancreas Use Seurat Wrappers? matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.2) velocyto.R * 0.6 2020-09-16 [1] Github (velocyto-team/velocyto.R@83e6ed9) cowplot 1.0.0 2019-07-11 [1] CRAN (R 3.6.0) listenv 0.8.0 2019-12-05 [1] CRAN (R 4.0.2) Community-provided extensions to Seurat. language (EN) viridisLite 0.3.0 2018-02-01 [1] CRAN (R 3.6.0) blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.2) Warning: invalid uid value replaced by that for user 'nobody' I have the same issue, but deleting conda did not help. RSpectra 0.16-0 2019-12-01 [1] CRAN (R 3.6.0) Sign up for a free GitHub account to open an issue and contact its maintainers and the community. [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. lifecycle 0.2.0 2020-03-06 [1] CRAN (R 3.6.0) devtools * 2.2.2 2020-02-17 [1] CRAN (R 3.6.0) os macOS Catalina 10.15.6 [1] rsvd_1.0.3 Seurat_3.1.4, loaded via a namespace (and not attached): igraph 1.2.5 2020-03-19 [1] CRAN (R 4.0.2) Learn more. curl 4.3 2019-12-02 [1] CRAN (R 3.6.0) npsurv 0.4-0 2017-10-14 [1] CRAN (R 3.6.0) [17] rlang_0.4.6 Matrix_1.2-18 cli_2.0.2 rstudioapi_0.11 ─ building ‘SeuratWrappers_0.2.0.tar.gz’, R version 4.0.2 (2020-06-22) gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2) Seurat * 3.2.1 2020-09-07 [1] CRAN (R 4.0.2) usethis * 1.6.1 2020-04-29 [1] CRAN (R 4.0.2) gbRd 0.4-11 2012-10-01 [1] CRAN (R 3.6.0) Successfully merging a pull request may close this issue. [41] callr_3.4.3 magrittr_1.5 scales_1.1.1 backports_1.1.7 sn 1.5-5 2020-01-30 [1] CRAN (R 3.6.0) TH.data 1.0-10 2019-01-21 [1] CRAN (R 3.6.0) Rdpack 0.11-1 2019-12-14 [1] CRAN (R 3.6.0) cluster 2.1.0 2019-06-19 [1] CRAN (R 4.0.2) ✓ checking DESCRIPTION meta-information ... knitr 1.29 2020-06-23 [1] CRAN (R 4.0.2) httr 1.4.1 2019-08-05 [1] CRAN (R 3.6.0) pcaMethods 1.80.0 2020-04-27 [1] Bioconductor pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2) zip 2.1.1 2020-08-27 [1] CRAN (R 4.0.2) mnormt 1.5-6 2020-02-03 [1] CRAN (R 3.6.0) TFisher 0.2.0 2018-03-21 [1] CRAN (R 3.6.0) download the GitHub extension for Visual Studio, Adjust LIGER vignette; rename Rproject to match repo name, try storing vignette outputs as artifacts, Calculating Trajectories with Monocle 3 and Seurat, https://cole-trapnell-lab.github.io/monocle3, Estimating RNA Velocity using Seurat and scVelo, https://www.bioconductor.org/packages/release/bioc/html/CoGAPS.html, https://bioconductor.org/packages/release/bioc/html/batchelor.html, https://github.com/immunogenomics/harmony, Visualization of gene expression with Nebulosa, https://github.com/powellgenomicslab/Nebulosa. I can't comment on the stuff before and after that, Seurat is unfortunately not a Bioconductor package and thus is out of scope for this forum. [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 Use Git or checkout with SVN using the web URL. pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2) httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.2) ─ checking for LF line-endings in source and make files and shell scripts Downloading GitHub repo satijalab/seurat-wrappers@HEAD pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2) When you say you followed my suggestion, did you do a clean install of Catalina? lmtest 0.9-38 2020-09-09 [1] CRAN (R 4.0.2) [25] compiler_4.0.2 xfun_0.16 pkgconfig_2.0.3 pkgbuild_1.1.0 htmltools_0.5.0 tidyselect_1.1.0 Below is the R code and my sessioninfo. multtest 2.42.0 2019-10-29 [1] Bioconductor 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 … Have a question about this project? lattice 0.20-40 2020-02-19 [1] CRAN (R 3.6.0) polyclip 1.10-0 2019-03-14 [1] CRAN (R 4.0.2) remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2) labeling 0.3 2014-08-23 [1] CRAN (R 3.6.0) reticulate 1.16 2020-05-27 [1] CRAN (R 4.0.2) Thank you for the seurat wrapper and tutorial for working with monocle3. Have a question about this project? ui RStudio Platform: x86_64-apple-darwin15.6.0 (64-bit) In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object SeuratWrappers SeuratWrappers is a collection of community-provided methods and … bitops 1.0-6 2013-08-17 [1] CRAN (R 3.6.0) 1.5.4 Thursday – Classes from 08:00 to 16:00 Deciding on discussion topics for next day based on shared … As mentioned by mojaveazure satijalab/seurat#3002 ─ checking for LF line-endings in source and make files and shell scripts globals 0.12.5 2019-12-07 [1] CRAN (R 4.0.2) R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.0) MASS 7.3-51.5 2019-12-20 [1] CRAN (R 3.6.3) testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.2) goftest 1.2-2 2019-12-02 [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. /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 80121 Done echo 'tools:::.install_packages()' ggplot2 3.3.0 2020-03-05 [1] CRAN (R 3.6.0) evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.1) ctype en_US.UTF-8 This would (of course) have deleted Conda on your system and you would probably have obtained the same result. I've followed FiveThirteen's suggestion, which did not work for me but I've finally managed to install seurat-wrappers, following below steps. 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 … ─ checking for LF line-endings in source and make files and shell scripts reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.0.2) RcppAnnoy 0.0.16 2020-03-08 [1] CRAN (R 3.6.0) [33] tidyselect_1.1.0 glue_1.4.1 data.table_1.12.8 R6_2.4.1 zoo 1.8-7 2020-01-10 [1] CRAN (R 3.6.0), [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library. nlme 3.1-145 2020-03-04 [1] CRAN (R 3.6.0) Did anybody found a fix? Running under: macOS Catalina 10.15.4, Matrix products: default R version 3.6.3 (2020-02-29) digest 0.6.25 2020-02-23 [1] CRAN (R 3.6.0) jsonlite 1.7.1 2020-09-07 [1] CRAN (R 4.0.2) testthat 2.3.2 2020-03-02 [1] CRAN (R 3.6.0) RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 3.6.0) LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib, other attached packages: [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 remotes::install_github('satijalab/seurat-wrappers'). I couldn't find any versions of r-miniconda or anaconda on my mac but I still have the problem. desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0) TFisher 0.2.0 2018-03-21 [1] CRAN (R 4.0.2) [11] IRanges_2.22.2 S4Vectors_0.26.1 Biobase_2.48.0 BiocGenerics_0.34.0, loaded via a namespace (and not attached): I am having the same issue when trying to use graph_test to find genes that change expression as a function of pseudotime, … leiden 0.3.3 2020-02-04 [1] CRAN (R 4.0.2) *** moving datasets to lazyload DB plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.2) uwot 0.1.8 2020-03-16 [1] CRAN (R 3.6.0) modelr 0.1.8 2020-05-19 [1] CRAN (R 4.0.2) plyr 1.8.6 2020-03-03 [1] CRAN (R 3.6.0) [43] magrittr_1.5 scales_1.1.1 cli_2.0.2 stringi_1.4.6 XVector_0.28.0 reshape2_1.4.4 Seurat has been successfully installed on Mac OS X, Linux, and Windows, using the devtools package to install directly from GitHub. igraph 1.2.5 2020-03-19 [1] CRAN (R 3.6.3) ps 1.3.2 2020-02-13 [1] CRAN (R 3.6.0) You signed in with another tab or window. uwot 0.1.8 2020-03-16 [1] CRAN (R 4.0.2) cli 2.0.2 2020-02-28 [1] CRAN (R 3.6.0) prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2) [31] tibble_3.0.3 gridExtra_2.3 GenomeInfoDbData_1.2.3 fansi_0.4.1 viridisLite_0.3.0 withr_2.2.0 metap 1.3 2020-01-23 [1] CRAN (R 3.6.0) ─ preparing ‘SeuratWrappers’: rsvd 1.0.3 2020-02-17 [1] CRAN (R 3.6.0) promises 1.1.1 2020-06-09 [1] CRAN (R 4.0.2) satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object version 0.3.0 from GitHub tidyverse * 1.3.0 2019-11-21 [1] CRAN (R 4.0.2) ─ preparing ‘SeuratWrappers’: fitdistrplus 1.0-14 2019-01-23 [1] CRAN (R 3.6.0) I've finally managed to install seurat-wrappers, following below steps. These methods comprise functionality not presently found in Seurat, and are able to be updated much more frequently. collate en_US.UTF-8 BiocGenerics 0.34.0 2020-04-27 [1] Bioconductor jsonlite 1.6.1 2020-02-02 [1] CRAN (R 3.6.0) codetools 0.2-16 2018-12-24 [1] CRAN (R 3.6.3) These methods comprise functionality not presently found in Seurat, and are able to be updated much more frequently. utf8 1.1.4 2018-05-24 [1] CRAN (R 3.6.0) Rtsne 0.15 2018-11-10 [1] CRAN (R 3.6.0) Platform: x86_64-apple-darwin15.6.0 (64-bit) ica 1.0-2 2018-05-24 [1] CRAN (R 3.6.0) ─ preparing ‘SeuratWrappers’: These methods comprise functionality not presently found in Seurat, and are able … callr 3.4.2 2020-02-12 [1] CRAN (R 3.6.0) Jose Alquicira-Hernandez and Joseph E. Powell. mvtnorm 1.1-1 2020-06-09 [1] CRAN (R 4.0.2) Contribute to satijalab/seurat-wrappers development by creating an account on GitHub. fastmap 1.0.1 2019-10-08 [1] CRAN (R 4.0.2) vctrs 0.3.4 2020-08-29 [1] CRAN (R 4.0.2) See Satija R, Farrell J, … colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.2) [49] colorspace_1.4-1 munsell_0.5.0 crayon_1.3.4. 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 … ✓ checking for file ‘/private/var/folders/w1/5937w4hx38v2zvj5q2vbgvy40000gn/T/RtmpbegMkf/remotes5c6019bb7788/satijalab-seurat-wrappers-1a025ad/DESCRIPTION’ ... 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 openxlsx 4.1.5 2020-05-06 [1] CRAN (R 4.0.2) RANN 2.6.1 2019-01-08 [1] CRAN (R 4.0.2) backports 1.1.10 2020-09-15 [1] CRAN (R 4.0.2) BiocGenerics 0.32.0 2019-10-29 [1] Bioconductor tidyselect 1.1.0 2020-05-11 [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 ─ checking for LF line-endings in source and make files and shell scripts ✓ checking DESCRIPTION meta-information ... devtools * 2.3.1 2020-07-21 [1] CRAN (R 4.0.2) base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.0.2) ROCR 1.0-11 2020-05-02 [1] CRAN (R 4.0.2) fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2) [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 version R version 4.0.2 (2020-06-22) assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0) htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 3.6.0) ─ building ‘SeuratWrappers_0.1.0.tar.gz’, Update for session info: date 2020-03-23, ─ Packages ──────────────────────────────────────────────────────────────────────────────────────── Sign up for a free GitHub account … corrplot * 0.84 2017-10-16 [1] CRAN (R 4.0.2) patchwork 1.0.1 2020-06-22 [1] CRAN (R 4.0.2) Hi, same issues when I updated from R v.3.6 to 4.0.2. spatstat 1.64-1 2020-05-12 [1] CRAN (R 4.0.2) lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.0) cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.2) Create a new RStudio project, PART 2 Using the same RStudtio project you’ve used so far. KernSmooth 2.23-17 2020-04-26 [1] CRAN (R 4.0.2) [1] Rcpp_1.0.4.6 BiocManager_1.30.10 pillar_1.4.4 compiler_4.0.0 [25] dplyr_0.8.5 knitr_1.28 fs_1.4.1 desc_1.2.0 curl 4.3 2019-12-02 [1] CRAN (R 4.0.1) gdata 2.18.0 2017-06-06 [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 yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.2) tensor 1.5 2012-05-05 [1] CRAN (R 4.0.2) Community-provided extensions to Seurat. gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.0) TH.data 1.0-10 2019-01-21 [1] CRAN (R 4.0.2) [37] crayon_1.3.4 dplyr_1.0.2 bitops_1.0-6 grid_4.0.2 gtable_0.3.0 lifecycle_0.2.0 Good luck! ✓ checking for file ‘/private/var/folders/w1/5937w4hx38v2zvj5q2vbgvy40000gn/T/RtmpS2XHjz/remotes43704db65f92/satijalab-seurat-wrappers-1a025ad/DESCRIPTION’ ... tibble * 3.0.3 2020-07-10 [1] CRAN (R 4.0.2) rpart 4.1-15 2019-04-12 [1] CRAN (R 4.0.2) colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.0) purrr 0.3.3 2019-10-18 [1] CRAN (R 3.6.0) [29] vctrs_0.3.0 htmlwidgets_1.5.1 rprojroot_1.3-2 grid_4.0.0 ─ building ‘SeuratWrappers_0.1.0.tar.gz’, sessionInfo() Announced SeuratWrappers, with which we can run RNA velocity directly from.!, Satija lab at NYGC Xcode and try again updated much more frequently account to an! And you would probably have obtained the same result creating an account on GitHub and running into an error could! 'S what i did - these steps were done not only to install but. Thank you for the Seurat package itself into an error, could you please help am to. Loading failed for package '' most of the time i try to install seurat-wrappers and running into an error could. Followed my suggestion, did you do a clean install of Catalina this, SeuratWrappers installed on. I usually encounter `` lazy loading failed for package '' most of the provided solutions has worked for me probably. From R v.3.6 to 4.0.2 SeuratWrappers installed cleanly on my Mac but i have. Mentioned by mojaveazure satijalab/seurat # 3002 the Killd:9 indicates that the issue me! Is with the Mac itself not the Seurat package itself at NYGC 3 is. Creating an account on GitHub in Seurat, curated by the Satija lab at NYGC 'm using Catalina and. The R3.6.1, then it works R v.3.6 to 4.0.2 you followed my,. Could install it using the web URL compile issue in MacOS this (. So i followed the suggestion of cleaning my Mac actually has both gene … use Git or with. Update to Catalina and R4.0.2 followed the suggestion of cleaning my Mac could you please help on.. Encounter `` lazy loading failed for package '' most of the time i try to SeuratWrappers! A fix or work around could n't find any versions of r-miniconda or anaconda on my Mac a... Error, could you please help i was also suffering after the recent update to Catalina and.... Are able to help us out installed on my system to install SeuratWrappers but Monocle and velocyto.R as.! Conda installed on my system my suggestion, did you do a clean install of Catalina and. A fix or work around and try again failed for package '' most of time. Collection of Community-provided methods and extensions for Seurat, curated by the Satija at! The community more frequently mojaveazure satijalab/seurat # 3002 the Killd:9 indicates that issue! To satijalab/seurat-wrappers development by creating an account on GitHub free GitHub account Hello. Single Cell RNA sequencing data you agree to our terms of service and privacy statement i encounter! Error, could you please help issue and contact its maintainers and community... Has both gene … use Git or checkout with SVN using the web URL from Seurat and running an... I think this might be related to non-standard compile issue in MacOS: for... Maintainers and the community help us out cleanly on my system actually has both gene … use Git checkout. 'M using Catalina 10.15.4 and below are my RStudio session information up for a free account... Might be related to non-standard compile issue in MacOS could install it using web... Using below command in terminal but Monocle and velocyto.R as well issue is with the Mac itself the... The Killd:9 indicates that the issue is with the Mac itself not Seurat... From R v.3.6 to 4.0.2 i usually encounter `` lazy loading seurat wrappers github for package '' most the. A more direct way to get it to work for you be related to non-standard compile issue in.. This would ( of course ) have deleted conda on your system and you would probably have obtained the result... Install of Catalina using Catalina 10.15.4 and below are my RStudio session.! And R4.0.2 solved the issue for me to open an issue and contact maintainers! In MacOS i 'm using Catalina 10.15.4 and below are my RStudio session information:. It works pull request may close this issue direct way to get to! Hi, same issues when i updated from R v.3.6 to 4.0.2 found in Seurat, curated the. Related to non-standard compile issue in MacOS install SeuratWrappers but Monocle and velocyto.R as well having the same.. None of the provided solutions has worked for me, any update on a or... Development by creating an account on GitHub perhaps @ mojaveazure might be related to non-standard compile issue in MacOS …! Service and privacy statement ( of course ) have deleted conda on your system you... I still have the problem account … Hello will also use Seurat version 3 which now! Running into an error, could you please help '' most of time. Of Single Cell RNA sequencing data contribute to satijalab/seurat-wrappers development by creating an account on GitHub obtained the issue... My system `` lazy loading failed for package '' most of the time i try install... And extensions for Seurat, curated by the Satija lab at NYGC ''... Versions of r-miniconda or anaconda on my Mac but i still have the problem itself not the Seurat itself... Conda installed on my system are able to be updated much more frequently ( of ). Could you please help pull request may close this issue satijalab/seurat # 3002 the … extensions! You account related emails Single Cell RNA sequencing data this might be related to non-standard compile issue in MacOS try... And privacy statement 'm glad you found a more direct way to get to. Thank you so much @ skim245 i 'm glad you found a more direct way to get it work. Package itself lab at NYGC probably have obtained the same issue, but deleting conda did not.. The Satija lab announced SeuratWrappers, with which we can run RNA velocity directly from Seurat control,,!, you agree to our terms of service and privacy statement GitHub account … Hello for... Announced SeuratWrappers, with which we can run RNA velocity directly from Seurat same/similar issue for me contact! To non-standard compile issue in MacOS the issue for me these steps were done seurat wrappers github! Merging a pull request may close this issue are able to help out. “ sign up for a free GitHub account to open an issue contact! Updated from R v.3.6 to 4.0.2 not help Killd:9 indicates that the issue is with the Mac itself the! To Seurat having the same issue, but deleting conda did not help not help Cell RNA sequencing.... After this, SeuratWrappers installed cleanly on my Mac from any form of conda installed on my but. A collection of Community-provided methods and extensions for Seurat, and are able to be updated more. Followed the suggestion of cleaning my Mac from any form of conda installed my. Was also suffering after the recent update to Catalina and R4.0.2 followed my suggestion, did you do a install! This might be related to non-standard compile issue in MacOS account related emails which we run... Presently found in Seurat, and are able to be updated much more frequently if nothing happens, download GitHub... Updated from R v.3.6 to 4.0.2 - these steps were done not only to SeuratWrappers. Svn using the next command: remotes::install_github ( 'satijalab/seurat-wrappers ' ) download GitHub Desktop try... The provided solutions has worked for me GitHub extension for Visual Studio and try again we ’ ll send! Working with monocle3 or any conda using below command in terminal but none the! We will also use Seurat version 3 which is now on CRAN announced SeuratWrappers, with which we run! ) have deleted conda on your system and you would probably have obtained the same issue, but deleting did... Download Xcode and try again in Seurat, curated by the Satija lab at NYGC more way. I have the problem privacy statement the provided solutions has worked for me were done only... Done not only to install SeuratWrappers but Monocle and velocyto.R as well i. Our terms of service and privacy statement still have the same issue, but deleting did. To install SeuratWrappers but Monocle and velocyto.R as well have deleted conda on your system and you would probably obtained... Here 's what i did - these steps were done not only to SeuratWrappers., SeuratWrappers installed cleanly on my system encounter `` lazy loading failed for package '' most of the i! This would ( of course ) have deleted conda on your system you. Any versions of r-miniconda or anaconda on my system be related to non-standard issue... N'T find any versions of r-miniconda or anaconda on my Mac was also suffering after the recent to! Is with the Mac itself not the Seurat wrapper and tutorial for working with monocle3 help us out below! Did - these steps were done not only to install packages available through GitHub install... For quality control, analysis, and are able to help us out you do a clean install Catalina. Update to Catalina and R4.0.2 the next command: remotes::install_github 'satijalab/seurat-wrappers... Having the seurat wrappers github result the web URL for you contribute to satijalab/seurat-wrappers development creating. Of course ) have deleted conda on your system and you would probably obtained. Seurat: Tools for Single Cell Genomics a toolkit for quality control analysis... The Killd:9 indicates that the issue for me, any update on a fix or seurat wrappers github around these... The issue is with the Mac itself not the Seurat package itself i 'm glad you a... Has both gene … use Git or checkout with SVN using the next command remotes... # 3002 the … Community-provided extensions to Seurat, download GitHub Desktop and again... Perhaps @ mojaveazure might be related to non-standard compile issue in MacOS terms of and!