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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.
https://docs.ropensci.org/CoordinateCleaner/
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Error installing CoordinateCleaner #72

Closed dylancraven closed 2 years ago

dylancraven commented 2 years ago

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’

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’

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

azizka commented 2 years ago

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?

dylancraven commented 2 years ago

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.

dylancraven commented 2 years ago

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.