Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Line starting 'Encoding ...' is malformed! #172

Open
alekseybelikov opened this issue Dec 13, 2024 · 1 comment
Open

Line starting 'Encoding ...' is malformed! #172

alekseybelikov opened this issue Dec 13, 2024 · 1 comment

Comments

@alekseybelikov
Copy link

install_github("liulab-dfci/MAESTRO")

Downloading GitHub repo liulab-dfci/MAESTRO@HEAD

Error: Failed to install 'MAESTRO' from GitHub:
Line starting 'Encoding ...' is malformed!
Traceback:

  1. install_github("liulab-dfci/MAESTRO")
  2. pkgbuild::with_build_tools({
    . ellipsis::check_dots_used(action = getOption("devtools.ellipsis_action",
    . rlang::warn))
    . {
    . remotes <- lapply(repo, github_remote, ref = ref, subdir = subdir,
    . auth_token = auth_token, host = host)
    . install_remotes(remotes, auth_token = auth_token, host = host,
    . dependencies = dependencies, upgrade = upgrade, force = force,
    . quiet = quiet, build = build, build_opts = build_opts,
    . build_manual = build_manual, build_vignettes = build_vignettes,
    . repos = repos, type = type, ...)
    . }
    . }, required = FALSE)
  3. install_remotes(remotes, auth_token = auth_token, host = host,
    . dependencies = dependencies, upgrade = upgrade, force = force,
    . quiet = quiet, build = build, build_opts = build_opts, build_manual = build_manual,
    . build_vignettes = build_vignettes, repos = repos, type = type,
    . ...)
  4. tryCatch(res[[i]] <- install_remote(remotes[[i]], ...), error = function(e) {
    . stop(remote_install_error(remotes[[i]], e))
    . })
  5. tryCatchList(expr, classes, parentenv, handlers)
  6. tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. value[3L]
@alekseybelikov
Copy link
Author

R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.5

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale:
[1] C

time zone: Europe/London
tzcode source: internal

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

other attached packages:
[1] devtools_2.4.5 usethis_2.2.3 gridExtra_2.3
[4] cowplot_1.1.3 ensembldb_2.26.1 AnnotationFilter_1.26.0
[7] GenomicFeatures_1.54.4 sva_3.50.0 BiocParallel_1.36.0
[10] genefilter_1.84.0 mgcv_1.9-1 nlme_3.1-165
[13] harmony_1.2.0 Rcpp_1.0.12 AnnotationHub_3.10.1
[16] BiocFileCache_2.10.2 dbplyr_2.5.0 writexl_1.5.1
[19] enrichplot_1.22.0 org.Hs.eg.db_3.18.0 AnnotationDbi_1.64.1
[22] Biobase_2.62.0 clusterProfiler_4.10.1 patchwork_1.2.0
[25] ggplot2_3.5.1 GenomicRanges_1.54.1 GenomeInfoDb_1.38.8
[28] IRanges_2.36.0 S4Vectors_0.40.2 BiocGenerics_0.48.1
[31] Seurat_5.1.0 SeuratObject_5.0.2 sp_2.1-4
[34] Signac_1.14.0

loaded via a namespace (and not attached):
[1] dichromat_2.0-0.1 progress_1.2.3
[3] urlchecker_1.0.1 nnet_7.3-19
[5] goftest_1.2-3 Biostrings_2.70.3
[7] vctrs_0.6.5 spatstat.random_3.2-3
[9] digest_0.6.36 png_0.1-8
[11] ggrepel_0.9.5 IRdisplay_1.1
[13] deldir_2.0-4 parallelly_1.37.1
[15] MASS_7.3-60 reshape2_1.4.4
[17] httpuv_1.6.15 qvalue_2.34.0
[19] withr_3.0.0 xfun_0.45
[21] ggfun_0.1.7 ellipsis_0.3.2
[23] survival_3.7-0 memoise_2.0.1
[25] gson_0.1.0 profvis_0.3.8
[27] tidytree_0.4.6 zoo_1.8-12
[29] pbapply_1.7-2 IRkernel_1.3.2
[31] Formula_1.2-5 prettyunits_1.2.0
[33] KEGGREST_1.42.0 promises_1.3.0
[35] httr_1.4.7 restfulr_0.0.15
[37] globals_0.16.3 fitdistrplus_1.1-11
[39] rstudioapi_0.16.0 miniUI_0.1.1.1
[41] generics_0.1.3 DOSE_3.28.2
[43] base64enc_0.1-3 curl_5.2.1
[45] repr_1.1.7 zlibbioc_1.48.2
[47] ggraph_2.2.1 polyclip_1.10-6
[49] GenomeInfoDbData_1.2.11 SparseArray_1.2.4
[51] interactiveDisplayBase_1.40.0 xtable_1.8-4
[53] stringr_1.5.1 evaluate_0.24.0
[55] S4Arrays_1.2.1 hms_1.1.3
[57] irlba_2.3.5.1 colorspace_2.1-0
[59] filelock_1.0.3 ROCR_1.0-11
[61] reticulate_1.37.0 spatstat.data_3.1-2
[63] magrittr_2.0.3 lmtest_0.9-40
[65] later_1.3.2 viridis_0.6.5
[67] ggtree_3.10.1 lattice_0.22-6
[69] spatstat.geom_3.2-9 future.apply_1.11.2
[71] scattermore_1.2 XML_3.99-0.17
[73] shadowtext_0.1.4 matrixStats_1.3.0
[75] RcppAnnoy_0.0.22 Hmisc_5.2-0
[77] pillar_1.9.0 compiler_4.3.2
[79] RSpectra_0.16-1 stringi_1.8.4
[81] tensor_1.5 SummarizedExperiment_1.32.0
[83] GenomicAlignments_1.38.2 plyr_1.8.9
[85] crayon_1.5.3 abind_1.4-5
[87] BiocIO_1.12.0 gridGraphics_0.5-1
[89] locfit_1.5-9.10 graphlayouts_1.2.1
[91] bit_4.0.5 dplyr_1.1.4
[93] fastmatch_1.1-4 codetools_0.2-20
[95] biovizBase_1.50.0 plotly_4.10.4
[97] mime_0.12 splines_4.3.2
[99] fastDummies_1.7.3 HDO.db_0.99.1
[101] knitr_1.48 blob_1.2.4
[103] utf8_1.2.4 BiocVersion_3.18.1
[105] pbdZMQ_0.3-11 fs_1.6.4
[107] listenv_0.9.1 checkmate_2.3.2
[109] pkgbuild_1.4.4 ggplotify_0.1.2
[111] tibble_3.2.1 Matrix_1.6-5
[113] statmod_1.5.0 tweenr_2.0.3
[115] pkgconfig_2.0.3 tools_4.3.2
[117] cachem_1.1.0 RhpcBLASctl_0.23-42
[119] RSQLite_2.3.7 viridisLite_0.4.2
[121] DBI_1.2.3 fastmap_1.2.0
[123] rmarkdown_2.27 scales_1.3.0
[125] grid_4.3.2 ica_1.0-3
[127] Rsamtools_2.18.0 BiocManager_1.30.23
[129] dotCall64_1.1-1 VariantAnnotation_1.48.1
[131] RANN_2.6.1 rpart_4.1.23
[133] farver_2.1.2 tidygraph_1.3.1
[135] scatterpie_0.2.4 yaml_2.3.9
[137] MatrixGenerics_1.14.0 foreign_0.8-87
[139] rtracklayer_1.62.0 cli_3.6.3
[141] purrr_1.0.2 leiden_0.4.3.1
[143] lifecycle_1.0.4 uwot_0.1.16
[145] sessioninfo_1.2.2 backports_1.5.0
[147] annotate_1.80.0 gtable_0.3.5
[149] rjson_0.2.21 ggridges_0.5.6
[151] progressr_0.14.0 parallel_4.3.2
[153] ape_5.8 limma_3.58.1
[155] jsonlite_1.8.8 edgeR_4.0.16
[157] RcppHNSW_0.6.0 bitops_1.0-7
[159] bit64_4.0.5 Rtsne_0.17
[161] yulab.utils_0.1.8 spatstat.utils_3.0-5
[163] GOSemSim_2.28.1 lazyeval_0.2.2
[165] shiny_1.8.1.1 htmltools_0.5.8.1
[167] GO.db_3.18.0 sctransform_0.4.1
[169] rappdirs_0.3.3 glue_1.7.0
[171] spam_2.10-0 XVector_0.42.0
[173] RCurl_1.98-1.16 treeio_1.26.0
[175] BSgenome_1.70.2 igraph_2.0.3
[177] R6_2.5.1 tidyr_1.3.1
[179] RcppRoll_0.3.1 labeling_0.4.3
[181] cluster_2.1.6 pkgload_1.4.0
[183] aplot_0.2.3 DelayedArray_0.28.0
[185] tidyselect_1.2.1 ProtGenerics_1.34.0
[187] htmlTable_2.4.3 ggforce_0.4.2
[189] xml2_1.3.6 future_1.33.2
[191] munsell_0.5.1 KernSmooth_2.23-24
[193] data.table_1.15.4 htmlwidgets_1.6.4
[195] fgsea_1.28.0 RColorBrewer_1.1-3
[197] biomaRt_2.58.2 rlang_1.1.4
[199] spatstat.sparse_3.1-0 spatstat.explore_3.2-7
[201] remotes_2.5.0 uuid_1.2-0
[203] fansi_1.0.6 Cairo_1.6-2

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant