can not be installed in centos stream 9

[luying616]

remotes::install_github("r-spatial/spdep", INSTALL_opts = "--no-byte-compile")
Downloading GitHub repo r-spatial/spdep@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: Rcpp (1.0.14 -> 1.1.0) [CRAN]

Enter one or more numbers, or an empty line to skip updates:
── R CMD build ────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/tmp/Rtmpj0lHI9/remotes3085731f8ca932/r-spatial-spdep-e3e6199/DESCRIPTION’ ...
─ preparing ‘spdep’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts (446ms)
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘spdep_1.4-1.tar.gz’

将程序包安装入‘/home/luying/R/x86_64-pc-linux-gnu-library/4.4’
(因为‘lib’没有被指定)
Attaching SeuratObject

• installing source package ‘spdep’ ...
  ** using staged installation
  ** libs
  using C compiler: ‘gcc (GCC) 11.5.0 20240719 (Red Hat 11.5.0-9)’
  gcc -I"/usr/local/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c card.c -o card.o
  gcc -I"/usr/local/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dfs_ncomp.c -o dfs_ncomp.o
  gcc -I"/usr/local/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dnn.c -o dnn.o
  gcc -I"/usr/local/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c gabriel.c -o gabriel.o
  gcc -I"/usr/local/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c gearyw.c -o gearyw.o
  gcc -I"/usr/local/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c gsymtest.c -o gsymtest.o
  gcc -I"/usr/local/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o
  gcc -I"/usr/local/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c insiders.c -o insiders.o
  gcc -I"/usr/local/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c jc.c -o jc.o
  gcc -I"/usr/local/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c knn.c -o knn.o
  gcc -I"/usr/local/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c lagw.c -o lagw.o
  gcc -I"/usr/local/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c listw2sn.c -o listw2sn.o
  gcc -I"/usr/local/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c nbdists.c -o nbdists.o
  gcc -I"/usr/local/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c perm_no_replace.c -o perm_no_replace.o
  gcc -I"/usr/local/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c polypoly.c -o polypoly.o
  gcc -I"/usr/local/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c relative.c -o relative.o
  gcc -I"/usr/local/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c skater.c -o skater.o
  gcc -I"/usr/local/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c symtest.c -o symtest.o
  gcc -shared -L/usr/local/lib64/R/lib -L/usr/local/lib64 -o spdep.so card.o dfs_ncomp.o dnn.o gabriel.o gearyw.o gsymtest.o init.o insiders.o jc.o knn.o lagw.o listw2sn.o nbdists.o perm_no_replace.o polypoly.o relative.o skater.o symtest.o -L/usr/local/lib64/R/lib -lRlapack -L/usr/local/lib64/R/lib -lRblas -lgfortran -lm -lquadmath -L/usr/local/lib64/R/lib -lR
  installing to /home/luying/R/x86_64-pc-linux-gnu-library/4.4/00LOCK-spdep/00new/spdep/libs
  ** R
  ** data
  ** inst
  ** preparing package for lazy loading
  Attaching SeuratObject
  free(): invalid pointer
  ERROR: lazy loading failed for package ‘spdep’
• removing ‘/home/luying/R/x86_64-pc-linux-gnu-library/4.4/spdep’
  警告信息:
  In i.p(...) :
  安装程序包‘/tmp/Rtmpj0lHI9/file30857374968787/spdep_1.4-1.tar.gz’时退出狀態的值不是0

sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: CentOS Stream 9

Matrix products: default
BLAS: /usr/local/lib64/R/lib/libRblas.so
LAPACK: /usr/local/lib64/R/lib/libRlapack.so; LAPACK version 3.12.0

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

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

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

other attached packages:
[1] sp_2.2-0

loaded via a namespace (and not attached):
[1] deldir_2.0-4 pbapply_1.7-2 gridExtra_2.3 remotes_2.5.0
[5] rlang_1.1.6 magrittr_2.0.3 RcppAnnoy_0.0.22 matrixStats_1.5.0
[9] ggridges_0.5.6 compiler_4.4.1 spatstat.geom_3.4-1 callr_3.7.6
[13] png_0.1-8 vctrs_0.6.5 reshape2_1.4.4 stringr_1.5.1
[17] pkgconfig_2.0.3 fastmap_1.2.0 promises_1.3.2 rmarkdown_2.29
[21] ps_1.9.1 purrr_1.0.4 xfun_0.52 jsonlite_2.0.0
[25] goftest_1.2-3 later_1.4.2 spatstat.utils_3.1-4 irlba_2.3.5.1
[29] parallel_4.4.1 cluster_2.1.6 R6_2.6.1 ica_1.0-3
[33] stringi_1.8.7 RColorBrewer_1.1-3 spatstat.data_3.1-6 reticulate_1.42.0
[37] parallelly_1.44.0 spatstat.univar_3.1-3 lmtest_0.9-40 scattermore_1.2
[41] Rcpp_1.0.14 knitr_1.50 tensor_1.5 future.apply_1.11.3
[45] zoo_1.8-14 sctransform_0.4.2 httpuv_1.6.16 Matrix_1.7-0
[49] splines_4.4.1 igraph_2.1.4 tidyselect_1.2.1 rstudioapi_0.17.1
[53] dichromat_2.0-0.1 abind_1.4-8 yaml_2.3.10 spatstat.explore_3.4-3
[57] codetools_0.2-20 spatstat.random_3.4-1 miniUI_0.1.2 processx_3.8.6
[61] curl_6.3.0 pkgbuild_1.4.7 listenv_0.9.1 lattice_0.22-6
[65] tibble_3.2.1 plyr_1.8.9 shiny_1.10.0 ROCR_1.0-11
[69] evaluate_1.0.3 Rtsne_0.17 desc_1.4.3 future_1.49.0
[73] survival_3.6-4 polyclip_1.10-7 fitdistrplus_1.2-2 pillar_1.10.2
[77] rsconnect_1.4.1 Seurat_4.4.0 KernSmooth_2.23-24 plotly_4.10.4
[81] generics_0.1.4 ggplot2_3.5.2 scales_1.4.0 globals_0.18.0
[85] xtable_1.8-4 glue_1.8.0 lazyeval_0.2.2 tools_4.4.1
[89] data.table_1.17.2 RANN_2.6.2 leiden_0.4.3.1 cowplot_1.1.3
[93] grid_4.4.1 tidyr_1.3.1 nlme_3.1-164 patchwork_1.3.0
[97] cli_3.6.5 spatstat.sparse_3.1-0 viridisLite_0.4.2 dplyr_1.1.4
[101] uwot_0.2.3 gtable_0.3.6 digest_0.6.37 progressr_0.15.1
[105] ggrepel_0.9.6 htmlwidgets_1.6.4 SeuratObject_4.1.4 farver_2.1.2
[109] htmltools_0.5.8.1 lifecycle_1.0.4 httr_1.4.7 mime_0.13
[113] MASS_7.3-60.2

[luying616]

gdb -ex run --args R --vanilla

inside gdb

(gdb) bt
GNU gdb (CentOS Stream) 16.3-2.el9
Copyright (C) 2024 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Type "show copying" and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
https://www.gnu.org/software/gdb/bugs/.
Find the GDB manual and other documentation resources online at:
http://www.gnu.org/software/gdb/documentation/.

For help, type "help".
Type "apropos word" to search for commands related to "word"...
"/usr/local/bin/R": not in executable format: file format not recognized
Starting program: --vanilla
No executable file specified.
Use the "file" or "exec-file" command.

[rsbivand]

There is no direct connection between spdep and Seurat, but you had already loaded an outdated version of Seurat before starting the installation. Seurat is currently at version 5.3.0, and there may be pathways between the myriad packages you have loaded and Seurat and spdep. There is no need to install from github for CRAN packages - install from CRAN, but in a fresh session. Do consider updating other packages. For me in a fresh session:

> library(spdep)
Loading required package: spData
Loading required package: sf
Linking to GEOS 3.13.1, GDAL 3.11.3, PROJ 9.6.2; sf_use_s2() is TRUE
> sessionInfo()
R version 4.5.1 (2025-06-13)
Platform: x86_64-pc-linux-gnu
Running under: Fedora Linux 42 (Workstation Edition)

Matrix products: default
BLAS/LAPACK: FlexiBLAS LIBFLEXIBLAS_OPENBLAS-SERIAL.SO;  LAPACK version 3.12.0

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

time zone: Europe/Oslo
tzcode source: system (glibc)

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

other attached packages:
[1] spdep_1.4-1  sf_1.0-21    spData_2.3.4

loaded via a namespace (and not attached):
 [1] s2_1.1.9           lattice_0.22-7     e1071_1.7-16       magrittr_2.0.3    
 [5] spDataLarge_2.0.6  KernSmooth_2.23-26 deldir_2.0-4       wk_0.9.4          
 [9] classInt_0.4-11    grid_4.5.1         DBI_1.2.3          proxy_0.4-27      
[13] class_7.3-23       compiler_4.5.1     boot_1.3-31        tools_4.5.1       
[17] sp_2.2-0           Rcpp_1.1.0         units_0.8-7