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MagpiePKU / EpiTrace

Cell age determination by scATAC-seq and bulk-ATAC-seq
https://epitrace.readthedocs.io
GNU General Public License v3.0
21 stars 1 forks source link

install error #2

Open z2hospitalcardio opened 1 month ago

z2hospitalcardio commented 1 month ago

Here is error information pak::pkg_install('MagpiePKU/EpiTrace')

→ Will install 1 package. → Will download 1 package with unknown size.

ℹ Getting 1 pkg with unknown size ✔ Cached copy of EpiTrace 0.0.1.3 (source) is the latest build ✔ No downloads needed, all packages are cached
ℹ Building EpiTrace 0.0.1.3 ✖ Failed to build EpiTrace 0.0.1.3 (35.7s)
Error:
! error in pak subprocess Caused by error in stop_task_build(state, worker): ! Failed to build source package EpiTrace. Type .Last.error to see the more details.

.Last.error <callr_error/rlib_error_3_0/rlib_error/error> Error: ! error in pak subprocess Caused by error in stop_task_build(state, worker): ! Failed to build source package EpiTrace.

Backtrace:

  1. pak::pkg_install("MagpiePKU/EpiTrace")
  2. pak:::remote(function(...) get("pkg_install_do_plan", asNamespace("…

  3. err$throw(res$error)

    Subprocess backtrace:

    1. base::withCallingHandlers(cli_message = function(msg) { …
    2. get("pkg_install_do_plan", asNamespace("pak"))(...)
    3. proposal$install()
    4. pkgdepends::install_package_plan(plan, lib = private$library, num_workers…
    5. base::withCallingHandlers({ …
    6. pkgdepends:::handle_events(state, events)
    7. pkgdepends:::handle_event(state, i)
    8. pkgdepends:::stop_task(state, worker)
    9. pkgdepends:::stop_task_build(state, worker)
  4. base::throw(pkg_error("Failed to build source package {.pkg {pkg}}.…
  5. | base::signalCondition(cond)
  6. global (function (e) …

sessionInfo() R version 4.3.3 (2024-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/liblapack.so.3; LAPACK version 3.9.0

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

time zone: Asia/Shanghai tzcode source: system (glibc)

attached base packages: [1] stats4 stats graphics grDevices utils datasets [7] methods base

other attached packages: [1] pak_0.7.2 SummarizedExperiment_1.32.0 [3] Biobase_2.62.0 GenomicRanges_1.54.1
[5] GenomeInfoDb_1.38.8 IRanges_2.36.0
[7] S4Vectors_0.40.2 BiocGenerics_0.48.1
[9] MatrixGenerics_1.14.0 matrixStats_1.3.0

loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 shape_1.4.6.1
[3] rstudioapi_0.16.0 jsonlite_1.8.8
[5] magrittr_2.0.3 spatstat.utils_3.0-4
[7] GlobalOptions_0.1.2 zlibbioc_1.48.2
[9] vctrs_0.6.5 ROCR_1.0-11
[11] Rsamtools_2.18.0 spatstat.explore_3.2-7 [13] RCurl_1.98-1.14 RcppRoll_0.3.0
[15] htmltools_0.5.8.1 S4Arrays_1.2.1
[17] SparseArray_1.2.4 sctransform_0.3.5
[19] parallelly_1.37.1 KernSmooth_2.23-22
[21] htmlwidgets_1.6.4 ica_1.0-3
[23] plyr_1.8.9 plotly_4.10.4
[25] zoo_1.8-12 igraph_2.0.3
[27] iterators_1.0.14 mime_0.12
[29] lifecycle_1.0.4 pkgconfig_2.0.3
[31] Matrix_1.6-5 R6_2.5.1
[33] fastmap_1.1.1 clue_0.3-65
[35] GenomeInfoDbData_1.2.11 fitdistrplus_1.1-11
[37] future_1.33.2 shiny_1.8.1.1
[39] digest_0.6.35 colorspace_2.1-0
[41] patchwork_1.2.0 Seurat_4.3.0
[43] tensor_1.5 irlba_2.3.5.1
[45] progressr_0.14.0 fansi_1.0.6
[47] spatstat.sparse_3.0-3 httr_1.4.7
[49] polyclip_1.10-6 abind_1.4-5
[51] compiler_4.3.3 doParallel_1.0.17
[53] withr_3.0.0 BiocParallel_1.36.0
[55] R.utils_2.12.3 MASS_7.3-60.0.1
[57] DelayedArray_0.28.0 rjson_0.2.21
[59] tools_4.3.3 lmtest_0.9-40
[61] httpuv_1.6.15 future.apply_1.11.2
[63] goftest_1.2-3 R.oo_1.26.0
[65] glue_1.7.0 R.cache_0.16.0
[67] nlme_3.1-164 promises_1.3.0
[69] grid_4.3.3 Rtsne_0.17
[71] cluster_2.1.6 reshape2_1.4.4
[73] generics_0.1.3 gtable_0.3.4
[75] spatstat.data_3.0-4 R.methodsS3_1.8.2
[77] tidyr_1.3.1 data.table_1.15.4
[79] sp_2.1-3 utf8_1.2.4
[81] XVector_0.42.0 spatstat.geom_3.2-9
[83] RcppAnnoy_0.0.22 foreach_1.5.2
[85] ggrepel_0.9.5 RANN_2.6.1
[87] pillar_1.9.0 stringr_1.5.1
[89] later_1.3.2 circlize_0.4.16
[91] splines_4.3.3 dplyr_1.1.4
[93] lattice_0.22-6 renv_1.0.5
[95] survival_3.5-8 deldir_2.0-4
[97] tidyselect_1.2.1 ComplexHeatmap_2.18.0
[99] Biostrings_2.70.3 miniUI_0.1.1.1
[101] pbapply_1.7-2 gridExtra_2.3
[103] scattermore_1.2 pheatmap_1.0.12
[105] stringi_1.8.3 lazyeval_0.2.2
[107] codetools_0.2-20 tibble_3.2.1
[109] BiocManager_1.30.22 cli_3.6.2
[111] uwot_0.2.2 xtable_1.8-4
[113] reticulate_1.36.0 munsell_0.5.1
[115] Rcpp_1.0.12 globals_0.16.3
[117] spatstat.random_3.2-3 png_0.1-8
[119] parallel_4.3.3 ggplot2_3.5.0
[121] bitops_1.0-7 listenv_0.9.1
[123] viridisLite_0.4.2 scales_1.3.0
[125] ggridges_0.5.6 SeuratObject_4.1.3
[127] leiden_0.4.3.1 purrr_1.0.2
[129] crayon_1.5.2 GetoptLong_1.0.5
[131] rlang_1.1.3 cowplot_1.1.3

MagpiePKU commented 1 month ago

Hi, it seems in the sessionInfo() there's no Signac, ape, WGCNA, among other dependencies pre-installed.

If you could try

BiocManager::install(c('Signac','WGCNA','ggtree')) (and other dependencies listed on the https://epitrace.readthedocs.io/en/latest/installation.html site)

and have a look at whether it still stops building? There's no compiling effort for the package itself. Should be problems on compiling the dependencies.