mikejiang
commented
1 year ago looks like there was an upgrade from RcppArmadillo https://github.com/RcppCore/RcppArmadillo/blob/master/ChangeLog which might be the cause. Given bioconductor still has the previous version 0.12.0.1.0, the quick work around for you is to downgrade RcppArmadillo. In the meantime, I will be working on the patch for the latest RcppArmadillo
When I tried to install flowCore by:
devtools::install_github("RGLab/flowCore")
In file included from /public/software/R/lib64/R/library/RcppArmadillo/include/RcppArmadillo.h:29:0, from pairVectorRcppWrap.h:13, from flowCore_types.h:12, from RcppExports.cpp:4: /public/software/R/lib64/R/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:68:45: error: ‘subview_cols’ in namespace ‘arma’ does not name a type
sessionInfo():
sessionInfo()here: R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)Matrix products: default BLAS: /public/software/R/lib64/R/lib/libRblas.so LAPACK: /public/software/R/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.UTF-8
[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_IDENTIFICATION=C
attached base packages: [1] grid stats graphics grDevices utils datasets methods base
other attached packages: [1] cytolib_2.11.1 RcppParallel_5.1.7 RcppArmadillo_0.12.2.0.0 SeuratWrappers_0.3.1
[5] ComplexHeatmap_2.10.0 CellChat_1.4.0 igraph_1.3.5 harmony_0.1.1
[9] Rcpp_1.0.10 BuenColors_0.5.6 MASS_7.3-58.3 stringr_1.5.0
[13] magrittr_2.0.3 sp_1.5-0 SeuratObject_4.1.3 Seurat_4.3.0
[17] reticulate_1.25 dplyr_1.1.0 RColorBrewer_1.1-3 paletteer_1.5.0
[21] data.table_1.14.8 gtools_3.9.4 ggpubr_0.6.0 ggplot2_3.4.1
[25] bigmemory_4.6.1 Biobase_2.54.0 BiocGenerics_0.40.0
loaded via a namespace (and not attached): [1] utf8_1.2.3 spatstat.explore_3.1-0 R.utils_2.12.2 tidyselect_1.2.0 htmlwidgets_1.6.2
[6] Rtsne_0.16 devtools_2.4.5 munsell_0.5.0 codetools_0.2-19 ica_1.0-3
[11] future_1.27.0 miniUI_0.1.1.1 withr_2.5.0 spatstat.random_3.1-4 colorspace_2.1-0
[16] progressr_0.10.1 ggalluvial_0.12.3 uuid_1.1-0 rstudioapi_0.14 stats4_4.1.2
[21] ROCR_1.0-11 ggsignif_0.6.4 tensor_1.5 listenv_0.9.0 NMF_0.26
[26] labeling_0.4.2 polyclip_1.10-4 farver_2.1.1 rprojroot_2.0.3 coda_0.19-4
[31] parallelly_1.32.0 vctrs_0.5.2 generics_0.1.3 R6_2.5.1 doParallel_1.0.17
[36] clue_0.3-64 rsvd_1.0.5 spatstat.utils_3.0-2 cachem_1.0.7 promises_1.2.0.1
[41] scales_1.2.1 gtable_0.3.1 globals_0.16.2 processx_3.6.1 goftest_1.2-3
[46] RProtoBufLib_2.6.0 rlang_1.0.6 systemfonts_1.0.4 GlobalOptions_0.1.2 splines_4.1.2
[51] rstatix_0.7.2 lazyeval_0.2.2 spatstat.geom_3.1-0 broom_1.0.4 BiocManager_1.30.20
[56] reshape2_1.4.4 abind_1.4-5 backports_1.4.1 httpuv_1.6.9 usethis_2.1.6
[61] tools_4.1.2 gridBase_0.4-7 statnet.common_4.6.0 ellipsis_0.3.2 sessioninfo_1.2.2
[66] ggridges_0.5.4 plyr_1.8.8 purrr_1.0.1 ps_1.7.3 prettyunits_1.1.1
[71] deldir_1.0-6 pbapply_1.7-0 GetoptLong_1.0.5 urlchecker_1.0.1 cowplot_1.1.1
[76] S4Vectors_0.32.4 zoo_1.8-11 ggrepel_0.9.3 cluster_2.1.3 fs_1.6.1
[81] RSpectra_0.16-1 sna_2.7 scattermore_0.8 circlize_0.4.15 lmtest_0.9-40
[86] RANN_2.6.1 fitdistrplus_1.1-8 matrixStats_0.63.0 pkgload_1.3.2 patchwork_1.1.2
[91] mime_0.12 xtable_1.8-4 IRanges_2.28.0 gridExtra_2.3 shape_1.4.6
[96] compiler_4.1.2 tibble_3.2.1 KernSmooth_2.23-20 crayon_1.5.2 R.oo_1.25.0
[101] htmltools_0.5.5 later_1.3.0 tidyr_1.3.0 DBI_1.1.3 Matrix_1.5-3
[106] car_3.1-1 cli_3.6.1 R.methodsS3_1.8.2 parallel_4.1.2 pkgconfig_2.0.3
[111] bigmemory.sri_0.1.6 registry_0.5-1 plotly_4.10.1 spatstat.sparse_3.0-1 foreach_1.5.2
[116] svglite_2.1.0 rngtools_1.5.2 callr_3.7.3 digest_0.6.31 sctransform_0.3.5
[121] RcppAnnoy_0.0.20 spatstat.data_3.0-1 leiden_0.4.2 uwot_0.1.14 curl_4.3.3
[126] shiny_1.7.4 rjson_0.2.21 lifecycle_1.0.3 nlme_3.1-158 jsonlite_1.8.4
[131] carData_3.0-5 network_1.18.1 desc_1.4.2 limma_3.50.3 viridisLite_0.4.1
[136] fansi_1.0.4 pillar_1.9.0 lattice_0.20-45 fastmap_1.1.1 httr_1.4.5
[141] pkgbuild_1.4.0 survival_3.5-5 glue_1.6.2 remotes_2.4.2 FNN_1.1.3.2
[146] png_0.1-7 iterators_1.0.14 profvis_0.3.7 stringi_1.7.8 rematch2_2.1.2
[151] memoise_2.0.1 irlba_2.3.5.1 future.apply_1.9.1