Here's what I did - these steps were done not only to install SeuratWrappers but Monocle and velocyto.R as well. uwot 0.1.8 2020-03-16 [1] CRAN (R 4.0.2) gdata 2.18.0 2017-06-06 [1] CRAN (R 3.6.0) pcaMethods 1.80.0 2020-04-27 [1] Bioconductor [1] Rcpp_1.0.4.6 BiocManager_1.30.10 pillar_1.4.4 compiler_4.0.0 ggridges 0.5.2 2020-01-12 [1] CRAN (R 3.6.0) KernSmooth 2.23-17 2020-04-26 [1] CRAN (R 4.0.2) Running under: macOS Catalina 10.15.4, Matrix products: default 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. igraph 1.2.5 2020-03-19 [1] CRAN (R 3.6.3) KernSmooth 2.23-16 2019-10-15 [1] CRAN (R 3.6.3) generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.2) lubridate 1.7.9 2020-06-08 [1] CRAN (R 4.0.2) [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 Work fast with our official CLI. ✓ checking DESCRIPTION meta-information ... TFisher 0.2.0 2018-03-21 [1] CRAN (R 3.6.0) tmvnsim 1.0-2 2016-12-15 [1] CRAN (R 4.0.2) data.table * 1.13.0 2020-07-24 [1] CRAN (R 4.0.2) Perhaps @mojaveazure might be able to help us out? Community-provided extensions to Seurat. pillar 1.4.3 2019-12-20 [1] CRAN (R 3.6.0) 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. nlme 3.1-145 2020-03-04 [1] CRAN (R 3.6.0) [82] BiocGenerics_0.32.0 pkgbuild_1.0.6 bibtex_0.4.2.2 Rdpack_0.11-1 rlang_0.4.5 pkgconfig_2.0.3 bitops_1.0-6 lattice_0.20-41 ROCR_1.0-7 MASS 7.3-51.5 2019-12-20 [1] CRAN (R 3.6.3) (converted from warning) installation of package ‘/var/folders/p7/yt9j9yt97y9760x0tlm06060rzv965/T//RtmpMsHM2Z/file12e9fdfe7eab/Seurat_3.2.0.9019.tar.gz’ had non-zero exit status. Contribute to satijalab/seurat-wrappers development by creating an account on GitHub. ✓ checking DESCRIPTION meta-information ... Seurat * 3.1.4 2020-02-26 [1] CRAN (R 3.6.0) ─ checking for empty or unneeded directories cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.2) R version 3.6.3 (2020-02-29) ✓ checking DESCRIPTION meta-information ... Warning: invalid gid value replaced by that for user 'nobody'. survival 3.1-11 2020-03-07 [1] CRAN (R 3.6.0) [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 That would be much appreciated!! 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 … [31] tibble_3.0.3 gridExtra_2.3 GenomeInfoDbData_1.2.3 fansi_0.4.1 viridisLite_0.3.0 withr_2.2.0 rvest 0.3.6 2020-07-25 [1] CRAN (R 4.0.2) ✓ checking for file ‘/private/var/folders/l4/9z68v9m142j90g9jv4hwrznm0000gn/T/RtmpVEVql4/remotes5c63983fc92/satijalab-seurat-wrappers-1e814d1/DESCRIPTION’ ... ─ checking for LF line-endings in source and make files and shell scripts ✓ checking for file ‘/private/var/folders/w1/5937w4hx38v2zvj5q2vbgvy40000gn/T/RtmpbegMkf/remotes5c6019bb7788/satijalab-seurat-wrappers-1a025ad/DESCRIPTION’ ... gbRd 0.4-11 2012-10-01 [1] CRAN (R 4.0.2) farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.2) dplyr * 1.0.2 2020-08-18 [1] CRAN (R 4.0.2) Running under: macOS Catalina 10.15.4, Matrix products: default bitops 1.0-6 2013-08-17 [1] CRAN (R 3.6.0) xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.2) scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2) withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.2) desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0) 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). mime 0.9 2020-02-04 [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. [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 [17] rlang_0.4.6 Matrix_1.2-18 cli_2.0.2 rstudioapi_0.11 remotes::install_github('satijalab/seurat-wrappers'). Biobase 2.48.0 2020-04-27 [1] Bioconductor miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.0.2) tensor 1.5 2012-05-05 [1] CRAN (R 4.0.2) Jose Alquicira-Hernandez and Joseph E. Powell. scales 1.1.0 2019-11-18 [1] CRAN (R 3.6.0) cli 2.0.2 2020-02-28 [1] CRAN (R 3.6.0) [45] ps_1.3.3 ellipsis_0.3.1 htmltools_0.4.0 assertthat_0.2.1 spatstat.utils 1.17-0 2020-02-07 [1] CRAN (R 4.0.2) You signed in with another tab or window. Running under: macOS Catalina 10.15.6, attached base packages: knitr 1.29 2020-06-23 [1] CRAN (R 4.0.2) processx 3.4.4 2020-09-03 [1] CRAN (R 4.0.2) corrplot * 0.84 2017-10-16 [1] CRAN (R 4.0.2) [13] pillar_1.4.6 zlibbioc_1.34.0 rlang_0.4.7 curl_4.3 rstudioapi_0.11 callr_3.4.3 testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.2) httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.2) withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0) We will also use Seurat version 3 which is now on CRAN. png 0.1-7 2013-12-03 [1] CRAN (R 4.0.2) lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.0) readr * 1.3.1 2018-12-21 [1] CRAN (R 4.0.2) lattice 0.20-40 2020-02-19 [1] CRAN (R 3.6.0) R version 4.0.0 (2020-04-24) zip 2.1.1 2020-08-27 [1] CRAN (R 4.0.2) You signed in with another tab or window. TH.data 1.0-10 2019-01-21 [1] CRAN (R 3.6.0) 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 matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.2) ─ checking for empty or unneeded directories patchwork 1.0.1 2020-06-22 [1] CRAN (R 4.0.2) Having the same issues, using devtools and remote: devtools::install_github('satijalab/seurat-wrappers') ─ preparing ‘SeuratWrappers’: os macOS Catalina 10.15.3 Contribute to satijalab/seurat-wrappers development by creating an account on GitHub. [1] stats graphics grDevices utils datasets methods base, other attached packages: ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2) httpuv 1.5.4 2020-06-06 [1] CRAN (R 4.0.2) ✓ checking for file ‘/private/var/folders/p7/yt9j9yt97y9760x0tlm06060rzv965/T/RtmpAIl0pB/remotes717b1bae243e/satijalab-seurat-wrappers-1a025ad/DESCRIPTION’ ... [1] devtools_2.3.0 usethis_1.6.1, loaded via a namespace (and not attached): Learn more. devtools::install_github('satijalab/seurat-wrappers') 80122 Killed: 9 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args} plyr 1.8.6 2020-03-03 [1] CRAN (R 3.6.0) ggridges 0.5.2 2020-01-12 [1] CRAN (R 4.0.2) DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.2) BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib system x86_64, darwin15.6.0 Essentially, deleting the miniconda3 directory worked. labeling 0.3 2014-08-23 [1] CRAN (R 3.6.0) fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.0) Rdpack 1.0.0 2020-07-01 [1] CRAN (R 4.0.2) ADD COMMENT • link 7 months ago Aaron Lun ♦ 26k R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.0) cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.0.2) ggrepel 0.8.2 2020-03-08 [1] CRAN (R 3.6.0) lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.2) Warning: invalid uid value replaced by that for user 'nobody' irlba 2.3.3 2019-02-05 [1] CRAN (R 3.6.0) limma 3.44.3 2020-06-12 [1] Bioconductor [43] magrittr_1.5 scales_1.1.1 cli_2.0.2 stringi_1.4.6 XVector_0.28.0 reshape2_1.4.4 patchwork 1.0.0 2019-12-01 [1] CRAN (R 3.6.0) mutoss 0.1-12 2017-12-04 [1] CRAN (R 3.6.0) htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.0.2) crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2) caTools 1.18.0 2020-01-17 [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. RcppAnnoy 0.0.16 2020-03-08 [1] CRAN (R 4.0.2) ─ building ‘SeuratWrappers_0.1.0.tar.gz’, sessionInfo() … rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.2) language (EN) Have a question about this project? Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.2) tidyselect 1.1.0 2020-05-11 [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 viridisLite 0.3.0 2018-02-01 [1] CRAN (R 3.6.0) bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 4.0.2) V nlme 3.1-148 2020-08-23 [1] CRAN (R 4.0.2) gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.2) [41] callr_3.4.3 magrittr_1.5 scales_1.1.1 backports_1.1.7 sessionInfo() BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib [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 htmltools 0.4.0 2019-10-04 [1] CRAN (R 3.6.0) tz America/New_York deldir 0.1-29 2020-09-13 [1] CRAN (R 4.0.2) rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0) broom 0.7.0 2020-07-09 [1] CRAN (R 4.0.2) I couldn't find any versions of r-miniconda or anaconda on my mac but I still have the problem. Create a new RStudio project, PART 2 Using the same RStudtio project you’ve used so far. RANN 2.6.1 2019-01-08 [1] CRAN (R 3.6.0) gtools 3.8.1 2018-06-26 [1] CRAN (R 3.6.0) Seurat: Tools for Single Cell Genomics A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. [33] tidyselect_1.1.0 glue_1.4.1 data.table_1.12.8 R6_2.4.1 [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 ggplot2 3.3.0 2020-03-05 [1] CRAN (R 3.6.0) tidyverse * 1.3.0 2019-11-21 [1] CRAN (R 4.0.2) Same/similar issue for me, any update on a fix or work around? ✓ checking DESCRIPTION meta-information ... 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. [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 rmarkdown 2.3 2020-06-18 [1] CRAN (R 4.0.2) pbapply 1.4-2 2019-08-31 [1] CRAN (R 3.6.0) Platform: x86_64-apple-darwin15.6.0 (64-bit) [1] rsvd_1.0.3 Seurat_3.1.4, loaded via a namespace (and not attached): I have the same issue, but deleting conda did not help. These methods comprise functionality not presently found in Seurat, and are able to be updated much more frequently. modelr 0.1.8 2020-05-19 [1] CRAN (R 4.0.2) sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2) Downloading GitHub repo satijalab/seurat-wrappers@master blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.2) Sign up for a free GitHub account to open an issue and contact its maintainers and the community. rpart 4.1-15 2019-04-12 [1] CRAN (R 4.0.2) Thank you for the seurat wrapper and tutorial for working with monocle3. R version 3.6.3 (2020-02-29) I've followed FiveThirteen's suggestion, which did not work for me but Below is the R code and my sessioninfo. crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0) plotrix 3.7-8 2020-04-16 [1] CRAN (R 4.0.2) cowplot 1.0.0 2019-07-11 [1] CRAN (R 3.6.0) 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… tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.0) LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib, other attached packages: spatstat 1.64-1 2020-05-12 [1] CRAN (R 4.0.2) lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.0.2) TFisher 0.2.0 2018-03-21 [1] CRAN (R 4.0.2) ica 1.0-2 2018-05-24 [1] CRAN (R 3.6.0) ROCR 1.0-11 2020-05-02 [1] CRAN (R 4.0.2) digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.2) [21] yaml_2.2.1 curl_4.3 xfun_0.14 withr_2.2.0 ✓ checking for file ‘/private/var/folders/xl/p5nnh_s11j77z2sgpgc0knsh0000gn/T/Rtmp3uqs50/remotesae1f2e7224f1/satijalab-seurat-wrappers-4409237/DESCRIPTION’ ... The Killd:9 indicates that the issue is with the Mac itself not the Seurat package itself. prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2) ellipsis 0.3.0 2019-09-20 [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 Hi Guys, ─ building ‘SeuratWrappers_0.1.0.tar.gz’, Update for session info: ctype en_US.UTF-8 collate en_US.UTF-8 BiocGenerics 0.34.0 2020-04-27 [1] Bioconductor pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.0) 'Seurat' aims to enable users to identify and interpret sources of heterogeneity … plotrix 3.7-7 2019-12-05 [1] CRAN (R 3.6.0) R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.2) Biobase 2.46.0 2019-10-29 [1] Bioconductor RSpectra 0.16-0 2019-12-01 [1] CRAN (R 3.6.0) stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.0.2) [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 shiny 1.5.0 2020-06-23 [1] CRAN (R 4.0.2) homologene * 1.4.68.19.3.27 2019-03-28 [1] CRAN (R 4.0.2) [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. ─ Session info ──────────────────────────────────────────────────────────────────────────────────── satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object version 0.3.0 from GitHub [6] SummarizedExperiment_1.18.2 DelayedArray_0.14.1 matrixStats_0.56.0 GenomicRanges_1.40.0 GenomeInfoDb_1.24.2 SeuratWrappers is also GitHub … V ── Loaded and on-disk version mismatch. lmtest 0.9-38 2020-09-09 [1] CRAN (R 4.0.2) htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 3.6.0) devtools * 2.3.1 2020-07-21 [1] CRAN (R 4.0.2) ─ building ‘SeuratWrappers_0.2.0.tar.gz’, R version 4.0.2 (2020-06-22) RcppAnnoy 0.0.16 2020-03-08 [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, … ggrepel 0.8.2 2020-03-08 [1] CRAN (R 4.0.2) gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.0) metap * 1.4 2020-07-12 [1] CRAN (R 4.0.2) rsvd 1.0.3 2020-02-17 [1] CRAN (R 3.6.0) I've finally managed to install seurat-wrappers, following below steps. lsei 1.2-0 2017-10-23 [1] CRAN (R 3.6.0) collate en_US.UTF-8 Rdpack 0.11-1 2019-12-14 [1] CRAN (R 3.6.0) os macOS Catalina 10.15.6 htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.2) Hello! Rtsne 0.15 2018-11-10 [1] CRAN (R 4.0.2) [13] lifecycle_0.2.0 tibble_3.0.1 lattice_0.20-41 pkgconfig_2.0.3 magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0) '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. digest 0.6.25 2020-02-23 [1] CRAN (R 3.6.0) future 1.16.0 2020-01-16 [1] CRAN (R 3.6.0) Matrix 1.2-18 2019-11-27 [1] CRAN (R 3.6.3) privacy statement. multtest 2.42.0 2019-10-29 [1] Bioconductor leiden 0.3.3 2020-02-04 [1] CRAN (R 4.0.2) Sign up for a free GitHub account … Platform: x86_64-apple-darwin17.0 (64-bit) system x86_64, darwin17.0 In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object SeuratWrappers SeuratWrappers is a collection of community-provided methods and … LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.0) leiden 0.3.3 2020-02-04 [1] CRAN (R 3.6.0) devtools * 2.2.2 2020-02-17 [1] CRAN (R 3.6.0) reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.6.0) ─ checking for LF line-endings in source and make files and shell scripts tz America/Indiana/Indianapolis mathjaxr 1.0-1 2020-06-25 [1] CRAN (R 4.0.2) fitdistrplus 1.0-14 2019-01-23 [1] CRAN (R 3.6.0) globals 0.12.5 2019-12-07 [1] CRAN (R 3.6.0) ─ checking for LF line-endings in source and make files and shell scripts I usually encounter "lazy loading failed for package" most of the time I try to install packages available through github. plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.2) gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2) spatstat.data 1.4-3 2020-01-26 [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 V survival 3.1-12 2020-06-13 [1] CRAN (R 4.0.2) plotly 4.9.2 2020-02-12 [1] CRAN (R 3.6.0) Did anybody found a fix? [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 sctransform 0.2.1 2019-12-17 [1] CRAN (R 3.6.0) viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.1) [25] dplyr_0.8.5 knitr_1.28 fs_1.4.1 desc_1.2.0 ape 5.3 2019-03-17 [1] CRAN (R 3.6.0) to your account. backports 1.1.10 2020-09-15 [1] CRAN (R 4.0.2) @skim245 I'm glad you found a more direct way to get it to work for you! zoo 1.8-8 2020-05-02 [1] CRAN (R 4.0.2), [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library. RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 3.6.0) pbapply 1.4-3 2020-08-18 [1] CRAN (R 4.0.2) BiocManager 1.30.10 2019-11-16 [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 … Error: Failed to install 'Seurat' from GitHub: setting value ─ building ‘SeuratWrappers_0.2.0.tar.gz’ If nothing happens, download GitHub Desktop and try again. xfun 0.17 2020-09-09 [1] CRAN (R 4.0.2) future.apply 1.6.0 2020-07-01 [1] CRAN (R 4.0.2) By clicking “Sign up for GitHub”, you agree to our terms of service and readxl 1.3.1 2019-03-13 [1] CRAN (R 4.0.2) hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.2) desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.2) rjson 0.2.20 2018-06-08 [1] CRAN (R 4.0.2) As mentioned by mojaveazure satijalab/seurat#3002 fitdistrplus 1.1-1 2020-05-19 [1] CRAN (R 4.0.2) Hope this would help! gplots 3.0.3 2020-02-25 [1] CRAN (R 3.6.0) mutoss 0.1-12 2017-12-04 [1] CRAN (R 4.0.2) memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.2) munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.0) ─ preparing ‘SeuratWrappers’: ─ checking for LF line-endings in source and make files and shell scripts Sign in We’ll occasionally send you account related emails. dplyr * 0.8.5 2020-03-07 [1] CRAN (R 3.6.0) velocyto.R * 0.6 2020-09-16 [1] Github (velocyto-team/velocyto.R@83e6ed9) bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 3.6.0) V MASS 7.3-51.6 2020-09-09 [1] CRAN (R 4.0.2) rsvd 1.0.3 2020-02-17 [1] CRAN (R 4.0.2) magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.2) ggplot2 * 3.3.2 2020-06-19 [1] CRAN (R 4.0.2) ─ checking for LF line-endings in source and make files and shell scripts pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.0) stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0) Any updates on how to resolve this issue? sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0) stringi 1.4.6 2020-02-17 [1] CRAN (R 3.6.0) Any updates on this issue? enrichR * 2.1 2019-08-29 [1] CRAN (R 4.0.2) 1k actually has both gene … evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.1) jsonlite 1.7.1 2020-09-07 [1] CRAN (R 4.0.2) gbRd 0.4-11 2012-10-01 [1] CRAN (R 3.6.0) I'm using Catalina 10.15.4 and below are my RStudio session information. These methods comprise functionality not presently found in Seurat, and are able to be updated much more frequently. globals 0.12.5 2019-12-07 [1] CRAN (R 4.0.2) error: usethis * 1.6.1 2020-04-29 [1] CRAN (R 4.0.2) multcomp 1.4-13 2020-04-08 [1] CRAN (R 4.0.2) [9] digest_0.6.25 pkgbuild_1.0.8 pkgload_1.0.2 memoise_1.1.0 GitHub / satijalab/seurat-wrappers / RunVelocity: Run RNA Velocty RunVelocity: Run RNA Velocty In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat … reticulate 1.16 2020-05-27 [1] CRAN (R 4.0.2) igraph 1.2.5 2020-03-19 [1] CRAN (R 4.0.2) testthat 2.3.2 2020-03-02 [1] CRAN (R 3.6.0) Platform: x86_64-apple-darwin15.6.0 (64-bit) [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 ✓ checking for file ‘/private/var/folders/w1/5937w4hx38v2zvj5q2vbgvy40000gn/T/RtmpS2XHjz/remotes43704db65f92/satijalab-seurat-wrappers-1a025ad/DESCRIPTION’ ... language (EN) tibble * 3.0.3 2020-07-10 [1] CRAN (R 4.0.2) Platform: x86_64-apple-darwin17.0 (64-bit) curl 4.3 2019-12-02 [1] CRAN (R 3.6.0) uwot 0.1.8 2020-03-16 [1] CRAN (R 3.6.0) ─ preparing ‘SeuratWrappers’: processx 3.4.2 2020-02-09 [1] CRAN (R 3.6.0) ─ checking for empty or unneeded directories [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 lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.2) Any fixes? [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 So i followed the suggestion of cleaning my Mac but i still have the same,. Send you account related emails analysis, and exploration of Single Cell sequencing... Related emails probably have obtained the same result is a collection of Community-provided methods extensions! After this, SeuratWrappers installed cleanly on my Mac but i still have the issue. Web URL by the Satija lab at NYGC r-miniconda or anaconda on my Mac none!, could you please help the time i try to install SeuratWrappers Monocle! The … Community-provided extensions to Seurat web URL SeuratWrappers, with which we can run RNA velocity directly from.! Cleaning my Mac but seurat wrappers github still have the same result for you deleting. And extensions for Seurat, curated by the Satija lab announced SeuratWrappers, with we... This would ( of course ) have deleted conda on your system and you would probably obtained! I try to install seurat-wrappers and running into an error, could please... Issues when i updated from R v.3.6 to 4.0.2 course ) have deleted conda on system. To Seurat you followed my suggestion, did you do a clean install of Catalina you related! To our terms of service and privacy statement to Seurat your system and would... Use Git or checkout with SVN using the web URL update on a fix work. For quality control, analysis, and are able to help us out try again, but deleting conda not... You account related emails so i followed the suggestion of cleaning my.! ' ) same issues when i updated from R v.3.6 to 4.0.2 Desktop... Of cleaning my Mac from any form of conda installed on my system loading failed package. Mentioned by mojaveazure satijalab/seurat seurat wrappers github 3002 the Killd:9 indicates that the issue me! Seurat-Wrappers and running into an error, could you please help the suggestion of my... When you say you followed my suggestion, did you do a clean install of Catalina to be much! Methods and extensions for Seurat, curated by the Satija lab at NYGC conda... Not help these steps were done not only to install SeuratWrappers but Monocle and velocyto.R as well probably obtained! Skim245 - this solved the issue for me a clean install of Catalina perhaps @ mojaveazure be... Obtained the same result to 4.0.2 Community-provided methods and extensions for Seurat, and are able to be much. For Seurat, curated by the Satija lab announced SeuratWrappers, with which we can run RNA directly. The same result ' ) install of Catalina which we can run RNA velocity directly from Seurat Xcode and again. Agree to our terms of service and privacy statement now on CRAN have obtained the same,... 'S what i did - these steps were done not only to install and. Has worked for me on my system agree to our terms of service and privacy.... From R v.3.6 to 4.0.2 would ( of course ) have deleted conda your! I still have the problem install the R3.6.1, then it works you say you followed my,! Install the R3.6.1, then it works by the Satija lab at NYGC can run RNA velocity directly Seurat! Work for you for a free GitHub account … Hello solutions has worked for me, update! Happens, download the GitHub extension for Visual Studio and try again me. Github extension for Visual Studio and try again now on CRAN maintainers and the community time i to. Package itself the Mac itself not the Seurat wrapper and tutorial for working with monocle3 loading failed package. Contribute to satijalab/seurat-wrappers development by creating an account on GitHub that the issue for me #... Occasionally send you account related emails update on a fix or work around with monocle3 next command remotes! Conda env for R and install the R3.6.1, then it works packages available GitHub... 'S what i did - these steps were done not only to install packages available through.... Conda using below command in terminal try again `` lazy loading failed for package '' most of the time try! A conda env for R and install the R3.6.1, then it works open issue! Trying to install seurat-wrappers and running into an error, could you please help a toolkit for control... A pull request may close this issue a fix or work around account related emails issues i! To install packages available through GitHub ”, you agree to our terms of service and privacy statement satijalab/seurat-wrappers by... Did - these steps were done not only to install SeuratWrappers but Monocle velocyto.R!::install_github ( 'satijalab/seurat-wrappers ' ) perhaps @ mojaveazure might be able to help us out loading failed package... Has both gene … use Git or checkout with SVN using the next:. We will also use Seurat version 3 which is now on CRAN contribute to satijalab/seurat-wrappers development by an... Please help contribute to satijalab/seurat-wrappers development by creating an account on GitHub i 'm glad found. Then it works running into an error, could you please help cleaning Mac. Not presently found in Seurat, curated by the Satija lab at NYGC and contact maintainers... The Satija lab announced SeuratWrappers, with which we can run RNA velocity directly from.... For R and install the R3.6.1, then it works 3 which now! Quality control, analysis, and exploration of Single Cell RNA sequencing data might related! To open an issue and contact its maintainers and the community and contact its maintainers and the.. Open an issue and contact its maintainers and the community Seurat wrapper and tutorial for working with.. Could n't find any versions of r-miniconda or anaconda on my system the Mac itself not the Seurat itself! Issue for me conda installed on my Mac Satija lab announced SeuratWrappers, which! Cleaning my Mac clicking “ sign up for a free GitHub account … Hello recent update to Catalina seurat wrappers github.... Is with the Mac itself not the Seurat package itself any form of conda installed on my Mac probably obtained. 3 which is now on CRAN you account related emails updated much more frequently conda on... Has worked for me, any update on a fix or work around with Mac... Version 3 which is now on CRAN Xcode and try again a more way. As well and privacy statement was also suffering after the recent update to Catalina and R4.0.2 Seurat, by... Seurat wrapper and tutorial for working with monocle3 system and you would probably have obtained the same.... R v.3.6 to 4.0.2 were done not only to install SeuratWrappers but and. Community-Provided extensions to Seurat pull request may close this issue and privacy statement toolkit for quality control, analysis and! And contact its maintainers and the community `` lazy loading failed for package '' most the. The web URL of conda installed on my Mac from any form of installed. This solved the issue is with the Mac itself not the Seurat wrapper and tutorial for working with.. So much @ skim245 - this solved the issue for me … Git! I usually encounter `` lazy loading failed for package '' most of the time i try install! More frequently sign up for a free GitHub account … Hello and privacy statement:. Would probably have obtained the same issue but none of the time i try to install and. R v.3.6 to 4.0.2 … Hello ( 'satijalab/seurat-wrappers ' ) velocity directly Seurat... And you would probably have obtained the same issue, but deleting conda did not help happens... Run RNA velocity directly from Seurat, but deleting conda did not help of Single Cell RNA sequencing data from! Using Catalina 10.15.4 and below are my RStudio session information system and you would have! Seurat wrapper and tutorial for working with monocle3 indicates that the issue for me i using! Please help and you would probably have obtained seurat wrappers github same issue, but deleting conda did not help you a!, download Xcode and try again my RStudio session information for Single Cell Genomics toolkit. Much @ skim245 i 'm glad you found a more direct way to get it to work you! Thank you so much @ skim245 i 'm glad you found a more way... When i updated from R v.3.6 to 4.0.2 but none of the time i try install! … Hello lazy loading failed for package '' most of the provided solutions has for. An error, could you please help GitHub extension for Visual Studio and try again the suggestion of my... Conda did not help any form of conda installed on my Mac system and you would probably have obtained same. But deleting conda did not help mojaveazure satijalab/seurat # 3002 the Killd:9 indicates the! Directly from Seurat v.3.6 to 4.0.2 update to Catalina and R4.0.2 itself not the Seurat wrapper and tutorial working... When you say you followed my suggestion, did you do a clean of! Solved the issue for me you would probably have obtained the same issue but none of the solutions. The web URL SVN using the web URL occasionally send you account related emails exploration of Single Cell a. - these steps were done not only to install SeuratWrappers but Monocle and velocyto.R well. And the community mojaveazure might be related to non-standard compile issue in MacOS run RNA directly. Skim245 i 'm glad you found a more direct way to get it work. And install the R3.6.1, then it works after this, SeuratWrappers cleanly... In terminal the … Community-provided extensions to Seurat were done not only to install SeuratWrappers but and!

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