install error, invalid pointer

[wt12318]

Hi,

When I installed the package from source (download from Github), the error has occoured:

> install.packages("~/software/leiden/",repos=NULL,type="source")
Installing package into ‘/home/data/public/R/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘leiden’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
sh: line 1: 14006 Aborted                 R_TESTS= '/home/data/R/R-4.1.0/bin/R' --no-save --no-restore --no-echo 2>&1 < '/tmp/Rtmpy9CnbD/file36a31114d884'
*** Error in `/home/data/R/R-4.1.0/bin/exec/R': free(): invalid pointer: 0x00000000040ec778 ***
======= Backtrace: =========
....
ERROR: loading failed
* removing ‘/home/data/public/R/library/leiden’
Warning in install.packages :
  installation of package ‘/home/wt/software/leiden/’ had non-zero exit status

(Because the body cannot exceed 65536 characters, the full messages was attached in the file below, error.txt)

The session info was :

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /home/data/R/R-4.1.0/lib/libRblas.so
LAPACK: /home/data/R/R-4.1.0/lib/libRlapack.so

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       

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

other attached packages:
[1] reticulate_1.24

loaded via a namespace (and not attached):
 [1] MatrixGenerics_1.6.0        Biobase_2.54.0              tidyr_1.2.0                
 [4] pkgload_1.2.4               jsonlite_1.8.0              NeoEnrichment_0.1.0        
 [7] brio_1.1.3                  assertthat_0.2.1            stats4_4.1.0               
[10] BSgenome_1.62.0             GenomeInfoDbData_1.2.7      Rsamtools_2.10.0           
[13] yaml_2.3.5                  remotes_2.4.2               sessioninfo_1.2.2          
[16] pillar_1.7.0                lattice_0.20-45             glue_1.6.1                 
[19] GenomicRanges_1.46.1        XVector_0.34.0              colorspace_2.0-3           
[22] Matrix_1.4-0                XML_3.99-0.6                pkgconfig_2.0.3            
[25] devtools_2.4.3              zlibbioc_1.36.0             purrr_0.3.4                
[28] scales_1.1.1                processx_3.5.2              BiocParallel_1.28.3        
[31] tibble_3.1.6                generics_0.1.2              IRanges_2.28.0             
[34] ggplot2_3.3.5               usethis_2.1.5               ellipsis_0.3.2             
[37] cachem_1.0.6                withr_2.4.3                 SummarizedExperiment_1.24.0
[40] BiocGenerics_0.40.0         cli_3.2.0                   magrittr_2.0.2             
[43] crayon_1.5.0                memoise_2.0.1               ps_1.6.0                   
[46] fs_1.5.2                    fansi_1.0.2                 pkgbuild_1.3.1             
[49] data.table_1.14.2           tools_4.1.0                 prettyunits_1.1.1          
[52] BiocIO_1.4.0                lifecycle_1.0.1             matrixStats_0.61.0         
[55] S4Vectors_0.32.3            munsell_0.5.0               DelayedArray_0.20.0        
[58] callr_3.7.0                 Biostrings_2.62.0           compiler_4.1.0             
[61] GenomeInfoDb_1.30.1         rlang_1.0.1                 grid_4.1.0                 
[64] RCurl_1.98-1.6              rstudioapi_0.13             rappdirs_0.3.3             
[67] rjson_0.2.21                bitops_1.0-7                testthat_3.1.2             
[70] restfulr_0.0.13             gtable_0.3.0                DBI_1.1.2                  
[73] curl_4.3.2                  R6_2.5.1                    GenomicAlignments_1.30.0   
[76] dplyr_1.0.8                 rtracklayer_1.54.0          fastmap_1.1.0              
[79] utf8_1.2.2                  rprojroot_2.0.2             desc_1.4.0                 
[82] stringi_1.7.6               Rcpp_1.0.8                  parallel_4.1.0             
[85] EasyBioinfo_0.0.0.9000      png_0.1-7                   vctrs_0.3.8                
[88] tidyselect_1.1.2           

error.txt

[PiaoyangGuohai1]

Have you resolved this problem? I got same.

[wt12318]

No, but I change to another machine and worked.