Closed jenellewallace closed 1 year ago
Hi @jenellewallace, I just pushed an update to the develop branch that should fix this issue, can you try installing from the develop branch and see if you still get this error?
remotes::install_github("stuart-lab/signac", ref = "develop")
Thanks very much, this update solves the problem for me!
Hi, I think I have the same problem as issue #1394 - thanks for any help you can provide! Here is my code:
During the FeatureMatrix step, I get the output and error:
I also tried
in the call to FeatureMatrix, but that gave the same error. I do not get the error if I call FeatureMatrix on each fragment object individually instead of the whole list.
My session info is: R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)
Matrix products: default BLAS: /wynton/home/cbi/shared/software/CBI/R-4.2.0-gcc10/lib64/R/lib/libRblas.so LAPACK: /wynton/home/cbi/shared/software/CBI/R-4.2.0-gcc10/lib64/R/lib/libRlapack.so
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US$ [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C $ [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATIO$
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] Signac_1.9.0 SeuratObject_4.1.3 Seurat_4.3.0
loaded via a namespace (and not attached): [1] Rtsne_0.16 colorspace_2.1-0 deldir_1.0-6 ellipsis_0.3.2 ggri$ [6] XVector_0.38.0 GenomicRanges_1.50.2 rstudioapi_0.14 spatstat.data_3.0-1 leid$ [11] listenv_0.9.0 ggrepel_0.9.3 fansi_1.0.4 codetools_0.2-19 spli$ [16] RcppRoll_0.3.0 polyclip_1.10-4 jsonlite_1.8.4 Rsamtools2.14.0 ica$ [21] cluster_2.1.4 png_0.1-8 uwot_0.1.14 shiny_1.7.4 sctr$ [26] spatstat.sparse_3.0-1 compiler_4.2.0 httr_1.4.6 Matrix_1.5-4 fast$ [31] lazyeval_0.2.2 cli_3.6.1 later_1.3.1 htmltools_0.5.5 tool$ [36] igraph_1.4.2 gtable_0.3.3 glue_1.6.2 GenomeInfoDbData_1.2.9 RANN$ [41] reshape2_1.4.4 dplyr_1.1.2 fastmatch_1.1-3 Rcpp_1.0.10 scat$ [46] Biostrings_2.66.0 vctrs_0.6.2 spatstat.explore_3.2-1 nlme_3.1-162 prog$ [51] lmtest_0.9-40 spatstat.random_3.1-5 stringr_1.5.0 globals_0.16.2 mime$ [56] miniUI_0.1.1.1 lifecycle_1.0.3 irlba_2.3.5.1 goftest_1.2-3 futu$ [61] zlibbioc_1.44.0 MASS_7.3-60 zoo_1.8-12 scales_1.2.1 prom$ [66] spatstat.utils_3.0-3 parallel_4.2.0 RColorBrewer_1.1-3 reticulate_1.28 pbap$ [71] gridExtra_2.3 ggplot2_3.4.2 stringi_1.7.12 S4Vectors_0.36.2 Bioc$ [76] BiocParallel_1.32.6 GenomeInfoDb_1.34.9 rlang_1.1.1 pkgconfig_2.0.3 matr$ [81] bitops_1.0-7 lattice_0.21-8 ROCR_1.0-11 purrr_1.0.1 tens$ [86] patchwork_1.1.2 htmlwidgets_1.6.2 cowplot_1.1.1 tidyselect_1.2.0 para$ [91] RcppAnnoy_0.0.20 plyr_1.8.8 magrittr_2.0.3 R6_2.5.1 IRan$ [96] generics_0.1.3 pillar_1.9.0 fitdistrplus_1.1-11 survival_3.5-5 abin$ [101] RCurl_1.98-1.12 sp_1.6-0 tibble_3.2.1 future.apply_1.10.0 cray$ [106] KernSmooth_2.23-21 utf8_1.2.3 spatstat.geom_3.2-1 plotly_4.10.1 grid$ [111] data.table_1.14.8 digest_0.6.31 xtable_1.8-4 tidyr_1.3.0 http$ [116] stats4_4.2.0 munsell_0.5.0 viridisLite_0.4.2