Error in .os_py_path(envname = path) : Assertion on 'path' failed: Directory '/home/dl2373/.local/share/r-miniconda' does not exist.

[13954380607]

library(Giotto)
Loading required package: GiottoClass
Giotto Suite 4.1.0

installGiottoEnvironment()
Error in .os_py_path(envname = path) :
Assertion on 'path' failed: Directory '/home/dl2373/.local/share/r-miniconda' does not exist.

[RubD]

Can you provide more information? What operating system are you working on? And was there any other installation message before this error?

[NJNataren]

I have the same error on Ubuntu (22.04.4 LTS),

R session info below:

sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C

time zone: Australia/Adelaide
tzcode source: system (glibc)

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] Giotto_4.1.0 GiottoClass_0.3.4 rstatix_0.7.2 arrow_17.0.0 lubridate_1.9.3 forcats_1.0.0
[7] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[13] ggplot2_3.5.1 tidyverse_2.0.0

loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.16.0 jsonlite_1.8.8
[4] magrittr_2.0.3 magick_2.8.4 rmarkdown_2.28
[7] fs_1.6.4 zlibbioc_1.50.0 vctrs_0.6.5
[10] memoise_2.0.1 GiottoUtils_0.1.11 terra_1.7-78
[13] htmltools_0.5.8.1 S4Arrays_1.4.1 usethis_3.0.0
[16] curl_5.2.1 broom_1.0.6 SparseArray_1.4.8
[19] htmlwidgets_1.6.4 desc_1.4.3 plyr_1.8.9
[22] plotly_4.10.4 cachem_1.1.0 igraph_2.0.3
[25] mime_0.12 lifecycle_1.0.4 pkgconfig_2.0.3
[28] Matrix_1.6-5 R6_2.5.1 fastmap_1.2.0
[31] GenomeInfoDbData_1.2.12 MatrixGenerics_1.16.0 shiny_1.9.1
[34] digest_0.6.37 colorspace_2.1-1 S4Vectors_0.42.1
[37] ps_1.7.7 pkgload_1.4.0 GenomicRanges_1.56.1
[40] fansi_1.0.6 timechange_0.3.0 httr_1.4.7
[43] abind_1.4-5 compiler_4.4.1 remotes_2.5.0
[46] bit64_4.0.5 withr_3.0.1 backports_1.5.0
[49] carData_3.0-5 pkgbuild_1.4.4 R.utils_2.12.3
[52] rappdirs_0.3.3 DelayedArray_0.30.1 sessioninfo_1.2.2
[55] rjson_0.2.22 gtools_3.9.5 GiottoVisuals_0.2.4
[58] tools_4.4.1 httpuv_1.6.15 R.oo_1.26.0
[61] glue_1.7.0 dbscan_1.2-0 callr_3.7.6
[64] promises_1.3.0 grid_4.4.1 checkmate_2.3.2
[67] reshape2_1.4.4 generics_0.1.3 gtable_0.3.5
[70] tzdb_0.4.0 R.methodsS3_1.8.2 data.table_1.15.4
[73] hms_1.1.3 sp_2.1-4 car_3.1-2
[76] utf8_1.2.4 XVector_0.44.0 BiocGenerics_0.50.0
[79] ggrepel_0.9.5 pillar_1.9.0 vroom_1.6.5
[82] later_1.3.2 lattice_0.22-5 bit_4.0.5
[85] deldir_2.0-4 tidyselect_1.2.1 SingleCellExperiment_1.26.0
[88] miniUI_0.1.1.1 knitr_1.48 IRanges_2.38.1
[91] SummarizedExperiment_1.34.0 scattermore_1.2 stats4_4.4.1
[94] xfun_0.47 Biobase_2.64.0 devtools_2.4.5
[97] matrixStats_1.3.0 stringi_1.8.4 UCSC.utils_1.0.0
[100] lazyeval_0.2.2 yaml_2.3.10 evaluate_0.24.0
[103] codetools_0.2-19 archive_1.1.8 colorRamp2_0.1.0
[106] cli_3.6.3 xtable_1.8-4 reticulate_1.38.0
[109] munsell_0.5.1 processx_3.8.4 Rcpp_1.0.13
[112] GenomeInfoDb_1.40.1 png_0.1-8 parallel_4.4.1
[115] ellipsis_0.3.2 assertthat_0.2.1 profvis_0.3.8
[118] urlchecker_1.0.1 SpatialExperiment_1.14.0 viridisLite_0.4.2
[121] scales_1.3.0 crayon_1.5.3 rlang_1.1.4
[124] cowplot_1.1.3

[jiajic]

I think this should be solved now on the GiottoClass dev branch. It should be merged soon.

[jiajic]

This should be solved after updating to GiottoClass 0.3.5