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MonashBioinformaticsPlatform / polyApipe

polyApipe
GNU Lesser General Public License v2.1
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Problematic Installation in R #5

Closed ntsopoul closed 7 months ago

ntsopoul commented 8 months ago

Hi,

I have a problem installing polyapiper via BiocManager::install("MonashBioinformaticsPlatform/polyApipe/polyApiper"). This is the error I am getting:

Error: object ‘colMeans’ is not exported by 'namespace:BiocGenerics' Execution halted ERROR: lazy loading failed for package ‘polyApiper’

any advice?

Thanks, Nick

################Session Info####################### R version 4.3.3 (2024-02-29) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.6.1

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York tzcode source: internal

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

other attached packages: [1] EnsDb.Mmusculus.v79_2.99.0 ensembldb_2.26.0 AnnotationFilter_1.26.0 GenomicFeatures_1.54.4
[5] AnnotationDbi_1.64.1 Biobase_2.62.0 GenomicRanges_1.54.1 GenomeInfoDb_1.38.8
[9] IRanges_2.36.0 S4Vectors_0.40.2 BiocGenerics_0.48.1 ggplot2_3.5.0
[13] PASTA_0.0.0.9000 Signac_1.13.0 Seurat_5.0.3 SeuratObject_5.0.1
[17] sp_2.1-3

loaded via a namespace (and not attached): [1] RcppAnnoy_0.0.22 splines_4.3.3 later_1.3.2
[4] BiocIO_1.12.0 filelock_1.0.3 bitops_1.0-7
[7] tibble_3.2.1 polyclip_1.10-6 XML_3.99-0.16.1
[10] fastDummies_1.7.3 lifecycle_1.0.4 processx_3.8.4
[13] globals_0.16.3 lattice_0.22-6 MASS_7.3-60.0.1
[16] magrittr_2.0.3 plotly_4.10.4 yaml_2.3.8
[19] remotes_2.5.0 httpuv_1.6.15 sctransform_0.4.1
[22] spam_2.10-0 pkgbuild_1.4.4 spatstat.sparse_3.0-3
[25] reticulate_1.35.0 cowplot_1.1.3 pbapply_1.7-2
[28] DBI_1.2.2 RColorBrewer_1.1-3 abind_1.4-5
[31] zlibbioc_1.48.2 Rtsne_0.17 purrr_1.0.2
[34] RCurl_1.98-1.14 rappdirs_0.3.3 GenomeInfoDbData_1.2.11
[37] ggrepel_0.9.5 irlba_2.3.5.1 listenv_0.9.1
[40] spatstat.utils_3.0-4 goftest_1.2-3 RSpectra_0.16-1
[43] spatstat.random_3.2-3 fitdistrplus_1.1-11 parallelly_1.37.1
[46] leiden_0.4.3.1 codetools_0.2-20 DelayedArray_0.28.0
[49] RcppRoll_0.3.0 xml2_1.3.6 tidyselect_1.2.1
[52] BiocFileCache_2.10.2 matrixStats_1.2.0 spatstat.explore_3.2-7
[55] GenomicAlignments_1.38.2 jsonlite_1.8.8 progressr_0.14.0
[58] ggridges_0.5.6 survival_3.5-8 progress_1.2.3
[61] tools_4.3.3 ica_1.0-3 Rcpp_1.0.12
[64] glue_1.7.0 gridExtra_2.3 SparseArray_1.2.4
[67] MatrixGenerics_1.14.0 dplyr_1.1.4 withr_3.0.0
[70] BiocManager_1.30.22 fastmap_1.1.1 fansi_1.0.6
[73] callr_3.7.6 digest_0.6.35 R6_2.5.1
[76] mime_0.12 colorspace_2.1-0 scattermore_1.2
[79] tensor_1.5 biomaRt_2.58.2 spatstat.data_3.0-4
[82] RSQLite_2.3.6 utf8_1.2.4 tidyr_1.3.1
[85] generics_0.1.3 data.table_1.15.4 rtracklayer_1.62.0
[88] prettyunits_1.2.0 httr_1.4.7 htmlwidgets_1.6.4
[91] S4Arrays_1.2.1 uwot_0.1.16 pkgconfig_2.0.3
[94] gtable_0.3.4 blob_1.2.4 lmtest_0.9-40
[97] XVector_0.42.0 htmltools_0.5.8.1 dotCall64_1.1-1
[100] ProtGenerics_1.34.0 plyranges_1.22.0 scales_1.3.0
[103] png_0.1-8 rstudioapi_0.16.0 reshape2_1.4.4
[106] rjson_0.2.21 curl_5.2.1 nlme_3.1-164
[109] cachem_1.0.8 zoo_1.8-12 stringr_1.5.1
[112] KernSmooth_2.23-22 parallel_4.3.3 miniUI_0.1.1.1
[115] desc_1.4.3 restfulr_0.0.15 pillar_1.9.0
[118] grid_4.3.3 vctrs_0.6.5 RANN_2.6.1
[121] promises_1.3.0 dbplyr_2.5.0 xtable_1.8-4
[124] cluster_2.1.6 cli_3.6.2 compiler_4.3.3
[127] Rsamtools_2.18.0 rlang_1.1.3 crayon_1.5.2
[130] future.apply_1.11.2 ps_1.7.6 plyr_1.8.9
[133] stringi_1.8.3 viridisLite_0.4.2 deldir_2.0-4
[136] BiocParallel_1.36.0 munsell_0.5.1 Biostrings_2.70.3
[139] MGLM_0.2.1 lazyeval_0.2.2 spatstat.geom_3.2-9
[142] Matrix_1.6-5 RcppHNSW_0.6.0 hms_1.1.3
[145] patchwork_1.2.0 bit64_4.0.5 future_1.33.2
[148] KEGGREST_1.42.0 shiny_1.8.1.1 SummarizedExperiment_1.32.0 [151] ROCR_1.0-11 igraph_2.0.3 memoise_2.0.1
[154] fastmatch_1.1-4 bit_4.0.5

pfh commented 7 months ago

Thanks @ntsopoul. I've removed the problematic imports from BiocGenerics, and it should now install.

Note this package is not actively developed at the moment.