library(phangorn) error

[wang0430]

hi, when i library phangorn, it presents a error,
library(phangorn)
Loading required package: ape
Error: package or namespace load failed for ‘phangorn’ in .doLoadActions(where, attach):
error in load action .A.1 for package phangorn: loadModule(module = "Fitch_mod", what = TRUE, env = ns, loadNow = TRUE): Unable to load module "Fitch_mod": cannot allocate vector of size 705769.6 Gb
In addition: Warning message:
package ‘ape’ was built under R version 4.3.0

sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /home/wanggl/miniconda3/envs/python3.8/lib/libopenblasp-r0.3.21.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] 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
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] ape_5.7-1

loaded via a namespace (and not attached):
[1] Rcpp_1.0.10 quadprog_1.5-8 lattice_0.20-45 digest_0.6.29
[5] grid_4.2.3 nlme_3.1-159 magrittr_2.0.3 rlang_1.1.0
[9] cli_3.4.1 rstudioapi_0.14 Matrix_1.5-3 generics_0.1.3
[13] fastmatch_1.1-3 igraph_1.3.5 parallel_4.2.3 compiler_4.2.3
[17] pkgconfig_2.0.3

[KlausVigo]

Which version of phangorn have you installed?

[wala-github]

I have encountered the same issue:

> library(phangorn)
Error: package or namespace load failed for ‘phangorn’ in .doLoadActions(where, attach):
 error in load action .__A__.1 for package phangorn: loadModule(module = "Fitch_mod", what = TRUE, env = ns, loadNow = TRUE): Unable to load module "Fitch_mod": cannot allocate vector of size 699477.4 Gb

I have just installed phangorn using:

remotes::install_github("KlausVigo/phangorn")

I had tried installing using install.packages("phangorn"), which I guess is commit 5086adc, but I got the following error preventing the installation:

phangorn testing if installed package can be loaded from temporary location sh: line 1: 8208 Segmentation fault (core dumped) R_TESTS= '/opt/R/4.3.3/lib/R/bin/R' --no-save --no-restore --no-echo 2>&1 < '/tmp/RtmpCb5VYR/file1f933fbef8a5'

 *** caught segfault ***
address 0x20, cause 'memory not mapped'

sessioninfo():

sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so;  LAPACK version 3.8.0

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

time zone: UTC
tzcode source: system (glibc)

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

other attached packages:
 [1] Biostrings_2.70.3   GenomeInfoDb_1.38.8 XVector_0.42.0      IRanges_2.36.0     
 [5] S4Vectors_0.40.2    BiocGenerics_0.48.1 distillR_0.3.0      reshape_0.8.9      
 [9] ape_5.8             ggtree_3.10.1       colorspace_2.1-0    vioplot_0.4.0      
[13] zoo_1.8-12          sm_2.2-6.0          Hmsc_3.0-13         coda_0.19-4        
[17] ggpubr_0.6.0        cowplot_1.1.1       DT_0.33             ggnewscale_0.4.10  
[21] scales_1.2.1        lubridate_1.9.2     forcats_1.0.0       stringr_1.5.0      
[25] dplyr_1.1.2         purrr_1.0.1         readr_2.1.4         tidyr_1.3.0        
[29] tibble_3.2.1        ggplot2_3.4.2       tidyverse_2.0.0    

loaded via a namespace (and not attached):
  [1] rstudioapi_0.15.0       jsonlite_1.8.7          magrittr_2.0.3         
  [4] rmarkdown_2.23          zlibbioc_1.48.2         MCMCpack_1.7-0         
  [7] fs_1.6.2                fields_15.2             vctrs_0.6.3            
 [10] memoise_2.0.1           RCurl_1.98-1.14         rstatix_0.7.2          
 [13] htmltools_0.5.5         usethis_2.2.2           curl_5.0.1             
 [16] truncnorm_1.0-9         broom_1.0.5             gridGraphics_0.5-1     
 [19] pROC_1.18.4             pracma_2.4.4            htmlwidgets_1.6.2      
 [22] desc_1.4.2              plyr_1.8.8              cachem_1.0.8           
 [25] igraph_2.0.3            mime_0.12               lifecycle_1.0.3        
 [28] pkgconfig_2.0.3         Matrix_1.6-5            R6_2.5.1               
 [31] fastmap_1.1.1           GenomeInfoDbData_1.2.11 shiny_1.7.5            
 [34] digest_0.6.33           aplot_0.2.2             patchwork_1.1.2        
 [37] ps_1.7.5                rprojroot_2.0.3         pkgload_1.3.2.1        
 [40] fansi_1.0.4             timechange_0.2.0        abind_1.4-5            
 [43] compiler_4.3.3          remotes_2.4.2           withr_2.5.0            
 [46] backports_1.4.1         carData_3.0-5           pkgbuild_1.4.2         
 [49] maps_3.4.1              ggsignif_0.6.4          MASS_7.3-60            
 [52] quantreg_5.95           sessioninfo_1.2.2       tools_4.3.3            
 [55] httpuv_1.6.11           ggseqlogo_0.2           nnet_7.3-19            
 [58] quadprog_1.5-8          glue_1.6.2              callr_3.7.3            
 [61] nlme_3.1-164            promises_1.2.0.1        grid_4.3.3             
 [64] reshape2_1.4.4          generics_0.1.3          gtable_0.3.3           
 [67] tzdb_0.4.0              hms_1.1.3               sp_2.0-0               
 [70] car_3.1-2               utf8_1.2.3              pillar_1.9.0           
 [73] yulab.utils_0.1.4       spam_2.10-0             later_1.3.1            
 [76] splines_4.3.3           treeio_1.26.0           lattice_0.22-5         
 [79] survival_3.5-8          FNN_1.1.4               SparseM_1.81           
 [82] tidyselect_1.2.0        miniUI_0.1.1.1          knitr_1.43             
 [85] mcmc_0.9-8              xfun_0.39               statmod_1.5.0          
 [88] devtools_2.4.5          matrixStats_1.3.0       stringi_1.7.12         
 [91] lazyeval_0.2.2          ggfun_0.1.5             yaml_2.3.7             
 [94] evaluate_0.21           BiocManager_1.30.21     ggplotify_0.1.2        
 [97] cli_3.6.1               xtable_1.8-4            munsell_0.5.0          
[100] processx_3.8.2          Rcpp_1.0.11             parallel_4.3.3         
[103] MatrixModels_0.5-1      ellipsis_0.3.2          prettyunits_1.1.1      
[106] dotCall64_1.1-1         profvis_0.3.8           urlchecker_1.0.1       
[109] bitops_1.0-7            viridisLite_0.4.2       tidytree_0.4.6         
[112] crayon_1.5.2            rlang_1.1.1             fastmatch_1.1-4        
[115] BayesLogit_2.1

[wala-github]

I have fixed my issue by restarting R, updating ape, loading ape and then running library(phangorn)