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ropensci / CoordinateCleaner

Automated flagging of common spatial and temporal errors in biological and palaeontological collection data, for the use in conservation, ecology and palaeontology.

Home Page:https://docs.ropensci.org/CoordinateCleaner/

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Error installing CoordinateCleaner

dylancraven opened this issue · comments

commented

Hi Alex,

I've been having trouble updating CoordinateCleaner due to problems with "rnaturalearth". Do you have any suggestions?

Here are the errors and sessionInfo():

install.packages("rnaturalearth")
Aborted (core dumped)
ERROR: lazy loading failed for package ‘rnaturalearth’

  • removing ‘/home/dylan/R/x86_64-pc-linux-gnu-library/4.2/rnaturalearth’
    Warning in install.packages :
    installation of package ‘rnaturalearth’ had non-zero exit status

and for

install.packages("rnaturalearth", repos = "http://packages.ropensci.org", type = "source")

*** caught segfault ***
address 0x55b654000000, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
ERROR: lazy loading failed for package ‘rnaturalearth’

  • removing ‘/home/dylan/R/x86_64-pc-linux-gnu-library/4.2/rnaturalearth’
    Warning in install.packages :
    installation of package ‘rnaturalearth’ had non-zero exit status

Here is the sessionInfo

R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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

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

loaded via a namespace (and not attached):
[1] Rcpp_1.0.8.3 plyr_1.8.7 pillar_1.7.0 compiler_4.2.0 rgnparser_0.2.0
[6] iterators_1.0.14 class_7.3-20 sys_3.4 tools_4.2.0 uuid_1.1-0
[11] nlme_3.1-157 jsonlite_1.8.0 lifecycle_1.0.1 tibble_3.1.7 lattice_0.20-45
[16] pkgconfig_2.0.3 rlang_1.0.2 foreach_1.5.2 DBI_1.1.2 cli_3.3.0
[21] curl_4.3.2 crul_1.2.0 parallel_4.2.0 e1071_1.7-9 xml2_1.3.3
[26] dplyr_1.0.9 stringr_1.4.0 generics_0.1.2 vctrs_0.4.1 hms_1.1.1
[31] classInt_0.4-3 grid_4.2.0 tidyselect_1.1.2 data.table_1.14.2 reshape_0.8.9
[36] httpcode_0.3.0 glue_1.6.2 sf_1.0-7 R6_2.5.1 fansi_1.0.3
[41] conditionz_0.1.0 tzdb_0.3.0 readr_2.1.2 purrr_0.3.4 magrittr_2.0.3
[46] codetools_0.2-18 ellipsis_0.3.2 units_0.8-0 bold_1.2.0 assertthat_0.2.1
[51] taxize_0.9.100 ape_5.6-2 utf8_1.2.2 KernSmooth_2.23-20 stringi_1.7.6
[56] proxy_0.4-26 crayon_1.5.1 zoo_1.8-10

commented

Hi Dylan,

thanks for the report. As you say this seems like a problem with rnaturalearth or specific to your setup, which may have been solved by the latest update of this package. Can you try again and see if the problem persists?

commented

Thanks for your response Alex. I had a problem with my libraries, and so had to do a complete re-install, but at least now I was able to install the new version.

commented

Thanks for your response Alex. I had a problem with my libraries, and so had to do a complete re-install, but at least now I was able to install the new version.