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Docker-based Geospatial toolkit for R, built on versioned Rocker images

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Building container fails.

Anyone who could help me pinpoint this error?

I think it fails on the installation of "BiocManager" but I have no idea why.

<SNIP>
Setting up postgis (2.3.1+dfsg-2) ...
Processing triggers for libc-bin (2.24-11+deb9u4) ...
also installing the dependencies ‘backports’, ‘ellipsis’, ‘zeallot’, ‘stringi’, ‘assertthat’, ‘utf8’, ‘vctrs’, ‘plyr’, ‘stringr’, ‘cli’, ‘fansi’, ‘pillar’, ‘pkgconfig’, ‘httpuv’, ‘xtable’, ‘sourcetools’, ‘later’, ‘promises’, ‘crayon’, ‘fastmap’, ‘gtable’, ‘reshape2’, ‘tibble’, ‘withr’, ‘colorspace’, ‘glue’, ‘gtools’, ‘lazyeval’, ‘shiny’, ‘ggplot2’, ‘xfun’, ‘mime’, ‘farver’, ‘labeling’, ‘munsell’, ‘lifecycle’, ‘gridExtra’, ‘bit’, ‘gdata’, ‘dichromat’, ‘XML’, ‘digest’, ‘rlang’, ‘jsonlite’, ‘yaml’, ‘base64enc’, ‘crosstalk’, ‘markdown’, ‘png’, ‘scales’, ‘viridis’, ‘leaflet.providers’, ‘RandomFieldsUtils’, ‘e1071’, ‘zoo’, ‘FNN’, ‘R6’, ‘bit64’, ‘Rcpp’, ‘units’, ‘maps’, ‘data.table’, ‘BH’, ‘DBI’, ‘magrittr’, ‘xts’, ‘intervals’, ‘spatstat.data’, ‘spatstat.utils’, ‘abind’, ‘tensor’, ‘polyclip’, ‘goftest’, ‘spData’, ‘expm’, ‘coda’, ‘LearnBayes’, ‘gmodels’, ‘tmaptools’, ‘viridisLite’, ‘htmltools’, ‘htmlwidgets’, ‘leaflet’, ‘leafsync’, ‘splancs’

trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/backports_1.1.5.tar.gz'
Content type 'application/octet-stream' length 14798 bytes (14 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/ellipsis_0.3.0.tar.gz'
Content type 'application/octet-stream' length 7371 bytes
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/zeallot_0.1.0.tar.gz'
Content type 'application/octet-stream' length 32549 bytes (31 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/stringi_1.4.3.tar.gz'
Content type 'application/octet-stream' length 7290890 bytes (7.0 MB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/assertthat_0.2.1.tar.gz'
Content type 'application/octet-stream' length 12742 bytes (12 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/utf8_1.1.4.tar.gz'
Content type 'application/octet-stream' length 218882 bytes (213 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/vctrs_0.2.0.tar.gz'
Content type 'application/octet-stream' length 668258 bytes (652 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/plyr_1.8.4.tar.gz'
Content type 'application/octet-stream' length 392451 bytes (383 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/stringr_1.4.0.tar.gz'
Content type 'application/octet-stream' length 135777 bytes (132 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/cli_1.1.0.tar.gz'
Content type 'application/octet-stream' length 40232 bytes (39 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/fansi_0.4.0.tar.gz'
Content type 'application/octet-stream' length 266123 bytes (259 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/pillar_1.4.2.tar.gz'
Content type 'application/octet-stream' length 228815 bytes (223 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/pkgconfig_2.0.3.tar.gz'
Content type 'application/octet-stream' length 6080 bytes
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downloaded 6080 bytes

trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/httpuv_1.5.2.tar.gz'
Content type 'application/octet-stream' length 1763900 bytes (1.7 MB)
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downloaded 1.7 MB

trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/xtable_1.8-4.tar.gz'
Content type 'application/octet-stream' length 564589 bytes (551 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/sourcetools_0.1.7.tar.gz'
Content type 'application/octet-stream' length 24155 bytes (23 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/later_1.0.0.tar.gz'
Content type 'application/octet-stream' length 56563 bytes (55 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/promises_1.1.0.tar.gz'
Content type 'application/octet-stream' length 2659515 bytes (2.5 MB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/crayon_1.3.4.tar.gz'
Content type 'application/octet-stream' length 658694 bytes (643 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/fastmap_1.0.1.tar.gz'
Content type 'application/octet-stream' length 36802 bytes (35 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/gtable_0.3.0.tar.gz'
Content type 'application/octet-stream' length 368081 bytes (359 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/reshape2_1.4.3.tar.gz'
Content type 'application/octet-stream' length 36405 bytes (35 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/tibble_2.1.3.tar.gz'
Content type 'application/octet-stream' length 310774 bytes (303 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/withr_2.1.2.tar.gz'
Content type 'application/octet-stream' length 53578 bytes (52 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/colorspace_1.4-1.tar.gz'
Content type 'application/octet-stream' length 2152594 bytes (2.1 MB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/glue_1.3.1.tar.gz'
Content type 'application/octet-stream' length 122950 bytes (120 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/gtools_3.8.1.tar.gz'
Content type 'application/octet-stream' length 187516 bytes (183 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/lazyeval_0.2.2.tar.gz'
Content type 'application/octet-stream' length 83482 bytes (81 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/shiny_1.4.0.tar.gz'
Content type 'application/octet-stream' length 3168035 bytes (3.0 MB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/ggplot2_3.2.1.tar.gz'
Content type 'application/octet-stream' length 3204655 bytes (3.1 MB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/xfun_0.11.tar.gz'
Content type 'application/octet-stream' length 57700 bytes (56 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/mime_0.7.tar.gz'
Content type 'application/octet-stream' length 13130 bytes (12 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/farver_2.0.1.tar.gz'
Content type 'application/octet-stream' length 1280565 bytes (1.2 MB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/labeling_0.3.tar.gz'
Content type 'application/octet-stream' length 10722 bytes (10 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/munsell_0.5.0.tar.gz'
Content type 'application/octet-stream' length 182653 bytes (178 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/lifecycle_0.1.0.tar.gz'
Content type 'application/octet-stream' length 150752 bytes (147 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/gridExtra_2.3.tar.gz'
Content type 'application/octet-stream' length 1062844 bytes (1.0 MB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/bit_1.1-14.tar.gz'
Content type 'application/octet-stream' length 54779 bytes (53 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/gdata_2.18.0.tar.gz'
Content type 'application/octet-stream' length 1058430 bytes (1.0 MB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/dichromat_2.0-0.tar.gz'
Content type 'application/octet-stream' length 84320 bytes (82 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/XML_3.98-1.20.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/digest_0.6.23.tar.gz'
Content type 'application/octet-stream' length 143316 bytes (139 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/rlang_0.4.2.tar.gz'
Content type 'application/octet-stream' length 807983 bytes (789 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/jsonlite_1.6.tar.gz'
Content type 'application/octet-stream' length 1052728 bytes (1.0 MB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/yaml_2.2.0.tar.gz'
Content type 'application/octet-stream' length 89447 bytes (87 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/base64enc_0.1-3.tar.gz'
Content type 'application/octet-stream' length 7833 bytes
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/crosstalk_1.0.0.tar.gz'
Content type 'application/octet-stream' length 563474 bytes (550 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/markdown_1.1.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/png_0.1-7.tar.gz'
Content type 'application/octet-stream' length 24990 bytes (24 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/scales_1.1.0.tar.gz'
Content type 'application/octet-stream' length 510666 bytes (498 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/viridis_0.5.1.tar.gz'
Content type 'application/octet-stream' length 1906320 bytes (1.8 MB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/leaflet.providers_1.9.0.tar.gz'
Content type 'application/octet-stream' length 30210 bytes (29 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/RandomFieldsUtils_0.5.3.tar.gz'
Content type 'application/octet-stream' length 137236 bytes (134 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/e1071_1.7-3.tar.gz'
Content type 'application/octet-stream' length 582517 bytes (568 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/zoo_1.8-6.tar.gz'
Content type 'application/octet-stream' length 853504 bytes (833 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/FNN_1.1.3.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/R6_2.4.1.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/bit64_0.9-7.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/Rcpp_1.0.3.tar.gz'
Content type 'application/octet-stream' length 2749025 bytes (2.6 MB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/units_0.6-5.tar.gz'
Content type 'application/octet-stream' length 959970 bytes (937 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/maps_3.3.0.tar.gz'
Content type 'application/octet-stream' length 2493744 bytes (2.4 MB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/data.table_1.12.6.tar.gz'
Content type 'application/octet-stream' length 4944372 bytes (4.7 MB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/BH_1.69.0-1.tar.gz'
Content type 'application/octet-stream' length 12378154 bytes (11.8 MB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/DBI_1.0.0.tar.gz'
Content type 'application/octet-stream' length 931812 bytes (909 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/magrittr_1.5.tar.gz'
Content type 'application/octet-stream' length 200504 bytes (195 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/xts_0.11-2.tar.gz'
Content type 'application/octet-stream' length 537024 bytes (524 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/intervals_0.15.1.tar.gz'
Content type 'application/octet-stream' length 393014 bytes (383 KB)
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/spatstat.data_1.4-0.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/spatstat.utils_1.15-0.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/abind_1.4-5.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/tensor_1.5.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/polyclip_1.10-0.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/goftest_1.2-2.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/spData_0.3.2.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/expm_0.999-4.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/coda_0.19-3.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/LearnBayes_2.15.1.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/gmodels_2.18.1.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/tmaptools_2.0-2.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/viridisLite_0.3.0.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/htmltools_0.4.0.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/htmlwidgets_1.5.1.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/leaflet_2.0.3.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/leafsync_0.1.0.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/splancs_2.01-40.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/RandomFields_3.3.6.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/RNetCDF_2.1-1.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/classInt_0.4-2.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/deldir_0.1-23.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/gstat_2.0-3.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/hdf5r_1.3.0.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/lwgeom_0.1-7.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/mapdata_2.3.0.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/ncdf4_1.17.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/proj4_1.0-8.1.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/raster_3.0-7.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/rgdal_1.4-8.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/rgeos_0.5-2.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/rlas_1.3.4.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/spacetime_1.2-2.tar.gz'
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trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/spatstat_1.61-0.tar.gz'
Content type 'application/octet-stream' length 6647139 bytes (6.3 MB)
==================================================
downloaded 6.3 MB

trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/spatialreg_1.1-5.tar.gz'
Content type 'application/octet-stream' length 176655 bytes (172 KB)
==================================================
downloaded 172 KB

trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/spdep_1.1-3.tar.gz'
Content type 'application/octet-stream' length 1230873 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/tmap_2.3-1.tar.gz'
Content type 'application/octet-stream' length 2928306 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/geoR_1.7-5.2.1.tar.gz'
Content type 'application/octet-stream' length 413766 bytes (404 KB)
==================================================
downloaded 404 KB

trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/geosphere_1.5-10.tar.gz'
Content type 'application/octet-stream' length 774048 bytes (755 KB)
==================================================
downloaded 755 KB

trying URL 'https://mran.microsoft.com/snapshot/2019-12-06/src/contrib/BiocManager_1.30.10.tar.gz'
Content type 'application/octet-stream' length 40205 bytes (39 KB)
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downloaded 39 KB

* installing *source* package ‘backports’ ...
** package ‘backports’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dotsElt.c -o dotsElt.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dotsLength.c -o dotsLength.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o backports.so dotsElt.o dotsLength.o init.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-backports/00new/backports/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (backports)
* installing *source* package ‘zeallot’ ...
** package ‘zeallot’ successfully unpacked and MD5 sums checked
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (zeallot)
* installing *source* package ‘stringi’ ...
** package ‘stringi’ successfully unpacked and MD5 sums checked
** using staged installation
checking for R_HOME... /usr/local/lib/R
checking for R... /usr/local/lib/R/bin/R
checking for endianness... little
checking for R >= 3.1.0 for C++11 use... yes
checking for R < 3.4.0 for CXX1X flag use... no
checking for cat... /bin/cat
checking for local ICUDT_DIR... icu61/data
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... g++ -std=gnu++11 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking elf.h usability... yes
checking elf.h presence... yes
checking for elf.h... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking whether the C++ compiler supports the long long type... yes
checking whether the compiler implements namespaces... yes
checking whether the compiler supports Standard Template Library... yes
checking whether std::map is available... yes
checking for pkg-config... /usr/bin/pkg-config
checking with pkg-config for the system ICU4C... 57.1
checking for ICU4C >= 52... yes
checking for additional required CPPFLAGS, LDFLAGS, and LIBS... done
checking whether we may build an ICU4C-based project... yes
checking programmatically for sufficient U_ICU_VERSION_MAJOR_NUM... yes
checking programmatically if U_CHARSET_IS_UTF8 is defined and set... no
checking for available ICU data library (ucnv, uloc, utrans)... yes
checking for available ICU data library (ucol)... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/uconfig_local.h
config.status: creating src/install.libs.R

*** stringi configure summary:
    ICU_FOUND=1
    STRINGI_CXXSTD=CXX_STD=CXX11
    STRINGI_CFLAGS=   -fpic
    STRINGI_CPPFLAGS=-I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H
    STRINGI_CXXFLAGS=   -fpic
    STRINGI_LDFLAGS=-L/usr/lib/x86_64-linux-gnu  
    STRINGI_LIBS=-licui18n -licuuc -licudata  

*** compiler settings used:
    CC=gcc
    CPP=g++ -std=gnu++11 -E
    LD=g++ -std=gnu++11
    CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic  
    CPPFLAGS=-I/usr/local/include   -UDEBUG -DNDEBUG
    CXX=g++ -std=gnu++11
    CXXFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic  
    LDFLAGS=  
    LIBS=  

** libs
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include -fpic -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stri_brkiter.cpp -o stri_brkiter.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include -fpic -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stri_collator.cpp -o stri_collator.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include -fpic -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stri_common.cpp -o stri_common.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include -fpic -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stri_compare.cpp -o stri_compare.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include -fpic -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stri_container_base.cpp -o stri_container_base.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include -fpic -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stri_container_bytesearch.cpp -o stri_container_bytesearch.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include -fpic -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stri_container_listint.cpp -o stri_container_listint.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include -fpic -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stri_container_listraw.cpp -o stri_container_listraw.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include -fpic -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stri_container_listutf8.cpp -o stri_container_listutf8.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include -fpic -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stri_container_regex.cpp -o stri_container_regex.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include -fpic -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stri_container_usearch.cpp -o stri_container_usearch.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include -fpic -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stri_container_utf16.cpp -o stri_container_utf16.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include -fpic -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stri_container_utf8.cpp -o stri_container_utf8.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include -fpic -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stri_container_utf8_indexable.cpp -o stri_container_utf8_indexable.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include -fpic -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stri_encoding_conversion.cpp -o stri_encoding_conversion.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include -fpic -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stri_encoding_detection.cpp -o stri_encoding_detection.o
Killed
The command '/bin/sh -c apt-get update   && apt-get install -y --no-install-recommends     lbzip2     libfftw3-dev     libgdal-dev     libgeos-dev     libgsl0-dev     libgl1-mesa-dev     libglu1-mesa-dev     libhdf4-alt-dev     libhdf5-dev     libjq-dev     liblwgeom-dev     libpq-dev     libproj-dev     libprotobuf-dev     libnetcdf-dev     libsqlite3-dev     libssl-dev     libudunits2-dev     netcdf-bin     postgis     protobuf-compiler     sqlite3     tk-dev     unixodbc-dev   && install2.r --error     RColorBrewer     RandomFields     RNetCDF     classInt     deldir     gstat     hdf5r     lwgeom     mapdata     maptools     ncdf4     proj4     raster     rgdal     rgeos     rlas     sf     sp     spacetime     spatstat     spatialreg     spdep     tmap     geoR     geosphere     BiocManager     && R -e "BiocManager::install('rhdf5')"' returned a non-zero code: 137

lwgeom not on latest build

After pulling-down the latest version of the image (see below), I get:

> library(sf)
Linking to GEOS 3.5.1, GDAL 2.1.2, PROJ 4.9.3
> library(lwgeom)
Error in library(lwgeom) : there is no package called ‘lwgeom’

May be fixed with #16

Docker image pull message:

PS E:\repos> docker pull rocker/geospatial
Using default tag: latest
latest: Pulling from rocker/geospatial
54f7e8ac135a: Already exists
021dd68904f6: Pull complete
8d3e964cf18d: Pull complete
81bbbedbef33: Pull complete
c7878d347b3f: Pull complete
a7aae3dbd958: Pull complete
da950bb11a69: Pull complete
9802011fbe26: Pull complete
334f65727953: Pull complete
e506f9195a59: Pull complete
Digest: sha256:c3158846628b07d4616fafa30ef1d97cdc1b706d1c9aa30d62e7862ffd75703e
Status: Downloaded newer image for rocker/geospatial:latest
PS E:\repos> docker run -e PASSWORD=notrealpassword -d -p 8788:8787 -v ${pwd}:/home/rstudio/data rocker/geospatial
fb494143ce66c7cf45d9e4415c5fbad699d5626a950e17abe3eac6d23afdd39d

Build is failing

Heads-up @cboettig I noticed just now the build is failing on docker: https://hub.docker.com/r/rocker/geospatial/builds/

My geocompr docker build which builds FROM rocker/geospatial is also failing FYI - noticed a few weeks ago but though it worth leaving a while before looking-into the issue. Not sure how to fix it but suspect this may be something to do with the solution: r-spatial/sf@34f655a#diff-354f30a63fb0907d4ad57269548329e3

consider adding ggsn?

https://cran.r-project.org/web/packages/ggsn/
http://oswaldosantos.github.io/ggsn/

(maybe tmap already addresses this sufficiently?)

Request: rocker/geoverse = rocker/geospatial + rocker/verse additions

Happy to try my hand at a PR of this if you think its OK.

Installation of `sf` R package fails

e.g. running:

docker run --rm -ti rocker/geospatial bash
install2.r sf

gives:

checking for unistd.h... yes
checking gdal.h usability... yes
checking gdal.h presence... yes
checking for gdal.h... yes
checking GDAL: linking with --libs only... yes
checking GDAL: /usr/local/share/gdal/pcs.csv readable... yes
checking GDAL: checking whether PROJ.4 is available for linking:... yes
checking GDAL: checking whether PROJ.4 is available fur running:... yes
checking proj_api.h usability... yes
checking proj_api.h presence... yes
checking for proj_api.h... yes
checking for pj_init_plus in -lproj... yes
checking PROJ.4: epsg found and readable... yes
proj_conf_test.c: In function 'main':
proj_conf_test.c:5:5: error: unknown type name 'PAFile'
     PAFile fp;
     ^
proj_conf_test.c:8:5: warning: implicit declaration of function 'pj_open_lib' [-Wimplicit-function-declaration]
     fp = pj_open_lib(ctx, "conus", "rb");
     ^
proj_conf_test.c:9:12: warning: comparison between pointer and integer
     if (fp == NULL) exit(1);
            ^
proj_conf_test.c:10:5: warning: implicit declaration of function 'pj_ctx_fclose' [-Wimplicit-function-declaration]
     pj_ctx_fclose(ctx, fp);
     ^
./configure: line 3833: ./proj_conf_test: No such file or directory
checking PROJ.4: conus found and readable... yes
checking geos-config usability... yes
configure: GEOS: 3.4.2
checking GEOS version >= 3.3.0... yes
checking geos_c.h usability... yes
checking geos_c.h presence... yes
checking for geos_c.h... yes
checking geos: linking with -lgeos_c... yes
checking liblwgeom.h usability... yes
checking liblwgeom.h presence... yes
checking for liblwgeom.h... yes
checking for lwgeom_version in -llwgeom... no
configure: lwgeom (only needed for st_make_valid) was not found; on ubuntu, liblwgeom-dev provides this
configure: Package CPP flags:  -I/usr/local/include -I/usr/include
configure: Package LIBS:  -L/usr/local/lib -lgdal -L/usr/lib -lgeos_c -lproj
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=c++11 -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -I/usr/include -I/usr/local/include -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=c++11 -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -I/usr/include -I/usr/local/include -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bbox.cpp -o bbox.o
g++ -std=c++11 -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -I/usr/include -I/usr/local/include -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gdal.cpp -o gdal.o
g++ -std=c++11 -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -I/usr/include -I/usr/local/include -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gdal_geom.cpp -o gdal_geom.o
g++ -std=c++11 -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -I/usr/include -I/usr/local/include -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gdal_read.cpp -o gdal_read.o
^g++ -std=c++11 -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -I/usr/include -I/usr/local/include -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gdal_write.cpp -o gdal_write.o
g++ -std=c++11 -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -I/usr/include -I/usr/local/include -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c geos.cpp -o geos.o
geos.cpp: In function ‘Rcpp::LogicalVector CPL_geos_is_valid(Rcpp::List, bool)’:
geos.cpp:294:5: error: ‘GEOSMessageHandler_r’ was not declared in this scope
    (GEOSMessageHandler_r) __emptyNoticeHandler, (void *) &notice);
     ^
geos.cpp:294:65: error: ‘GEOSContext_setNoticeMessageHandler_r’ was not declared in this scope
    (GEOSMessageHandler_r) __emptyNoticeHandler, (void *) &notice);
                                                                 ^
geos.cpp:296:27: error: expected ‘)’ before ‘__emptyErrorHandler’
    (GEOSMessageHandler_r) __emptyErrorHandler, (void *) &notice); 
                           ^
geos.cpp:296:64: error: ‘GEOSContext_setErrorMessageHandler_r’ was not declared in this scope
    (GEOSMessageHandler_r) __emptyErrorHandler, (void *) &notice); 
                                                                ^
/usr/local/lib/R/etc/Makeconf:141: recipe for target 'geos.o' failed
make: *** [geos.o] Error 1
ERROR: compilation failed for package ‘sf’
* removing ‘/usr/local/lib/R/site-library/sf’

The downloaded source packages are in
        ‘/tmp/downloaded_packages’
Warning message:
In install.packages(pkgs = f, lib = lib, repos = if (isMatchingFile(f)) NULL else rep,  :
  installation of package ‘sf’ had non-zero exit status

so the error seems to be related to the geos libs somehow?

Builds for different versions of GDAL, PROJ, GEOS

As discussed in r-spatial/discuss#35 it's useful to be able to control the upstream spatial libraries on which R's geographic infrastructure builds, for reproducibility and development work. I have created an issue in our geocompr book project to support this: https://github.com/Robinlovelace/geocompr/issues/476

To minimise re-inventing the wheel, I wonder if it would be possible to build from version-tags of rocker/geospatial e.g.

FROM rocker/geospatial:proj7 # for proj 7 support
FROM rocker/geospatial:ubuntugis-unstable # for the latest version of the ubuntugis-instable repo
# ...

spatialreg package support

Spatial regression models that used to be in spdep have been moved to a new package spatialreg. Could this package be included in the geospatial library please?

ERROR_CONNECTION_REFUSED when trying to open Rstudio server in browser

Firstly thanks to the developers for providing these great Rstudio containers! I'm having an issue with rocker/geospatial:3.5.2 on Ubuntu 18.04. I run the docker container using the following command:

sudo docker run -it --rm \
     -v "$(pwd)":/home/files \
     -e USER=usrname \
     -e PASSWORD=pwrd \
     -p 8666:8787 \
     rocker/geospatial:3.5.2

When I navigate to http://localhost:8787 I'm confronted with the following error:

localhost refused to connect Try:
Checking the connection
Checking the proxy and the firewall
ERR_CONNECTION_REFUSED

(The same problem exists with rocker/tidyverse images as well.)

I've checked to see if the port is open after running the container using the following:
sudo netstat -tulpn
Here's the output: (not sure exactly how to interpret this)

Active Internet connections (only servers)
Proto Recv-Q Send-Q Local Address Foreign Address State PID/Program name
tcp 0 0 127.0.0.53:53 0.0.0.0:* LISTEN 859/systemd-resolve
tcp 0 0 127.0.0.1:631 0.0.0.0:* LISTEN 1057/cupsd
tcp 0 0 127.0.0.1:28731 0.0.0.0:* LISTEN 19178/rsession
tcp 0 0 127.0.0.1:21469 0.0.0.0:* LISTEN 19178/rsession
tcp6 0 0 ::1:631 :::* LISTEN 1057/cupsd
tcp6 0 0 :::8666 :::* LISTEN 29016/docker-proxy
tcp6 0 0 :::4125 :::* LISTEN 19178/rsession
udp 0 0 224.0.0.251:5353 0.0.0.0:* 12976/chrome --type
udp 0 0 224.0.0.251:5353 0.0.0.0:* 12932/chrome
udp 0 0 224.0.0.251:5353 0.0.0.0:* 12932/chrome
udp 0 0 0.0.0.0:5353 0.0.0.0:* 1069/avahi-daemon:
udp 0 0 0.0.0.0:56883 0.0.0.0:* 1069/avahi-daemon:
udp 0 0 127.0.0.53:53 0.0.0.0:* 859/systemd-resolve
udp 0 0 0.0.0.0:68 0.0.0.0:* 3075/dhclient
udp 0 0 0.0.0.0:631 0.0.0.0:* 1152/cups-browsed
udp6 0 0 :::5353 :::* 1069/avahi-daemon:
udp6 0 0 :::34104 :::* 1069/avahi-daemon:

This issue does not appear when accessing other docker containers through a local port (netdata, for example). I have run rocker/geospatial successfully on this machine in the past, so I'm not sure if this has to do with some inadvertently-changed setting... I'm not running through any proxy servers or VPNs, in case that is relevant.

Other info

docker version:

Docker version 18.09.4, build d14af54266

OS:
Ubuntu 18.04

These rocker images have been awesome and super useful, so I'm hoping to get back up and running as soon as I can. Thanks for any help!

proj6

add support for proj6, (e.g. 6.2.1) since buster is shipping proj v5 (r-spatial/discuss#28 (comment))

Start image without starting RStudio

I have Dockerfile that builds off of your's (recently rocker/geospatial:3.6.0). I often want to run two (or ten) of these Dockers simultaneously on the same machine. The jobs running inside of each depends heavily on having all the geospatial libraries you've nicely aligned in your image, but doesn't require RStudio. (Rstudio is nice to have when we develop on this same image, but it not required in production). In fact, the Rstudio component is kind of a headache in production, as we pass in "fake" port numbers to get the containers to run (but RStudio is not actually accessible unless 8787 is used).

As I understand it right now (or can find in documentation), one cannot run this image (with docker run) without starting RStudio -p 8787:8787. Is that true? If it is true, have you considered how one might use this image without starting RStudio?

GDAL, GEOS and PROJ versions

This isn't a bug per se, but a question: are there any plans for updating the GDAL and PROJ versions shipped in rocker/geospatial? Both are evolving, as outlined here: r-spatial/sf#988

I think documentation on this may also be useful. One resource that I've found useful, that may be of use/interest for updating GDAL versions, is this (although it builds on Ubuntu not Debian, should be similar): https://github.com/GeographicaGS/Docker-GDAL2

Plans to update to python 3.6 or 3.7?

I'm using typing with python 3.7, but I also use a lot of geospatial tools and munging in R. I am running in circles a bit trying to get python upgraded to 3.7 on a container that has R working with geospatial tools. Hints?

Add tmap

A powerful pkg for visualisation.

The current version doesn't allow it to be installed - it needs libprotobuf-dev, libjq-dev and maybe a few other system dependencies to work I think. Could put in a PR for this if I get 👍 that this is a good idea...

Declaration of vested interest: I'm thinking of user rocker/geospatial as the basis of https://hub.docker.com/r/robinlovelace/geocompr/ which currently uses the larger but less frequently updated ropensci container.

Remove build-deps after install to reduce image size

With GDAL and other tools compiled from source, we end up installing a lot of dev libraries only needed at compile time. We can remove these after install as we do in rocker/r-ver to reduce image size. Obviously care must be taken to avoid removing any runtime dependencies.

Mapping linux tools to R packages

This geospatial Docker image is awesome; I made my own before realising this existed - mine was 8GB, while this one is more like 4.5GB.

To understand this package a bit better, but also remove necessary linux tools and R packages from my own build, does there exist any documentation on how each "apt-get" package relates to each R package? Perhaps a simple mapping diagram would be useful in the Readme. I would be happy to help. I've never made such a diagram, so suggestions welcome.

cannot read hdf4file

the nasa has some hdf files are in hdf4 , which request for gdal-bin installation. can you consider adding this as default.
thank you.

Failing builds on versioned images

These are failing in the geospatial container:

https://hub.docker.com/r/rocker/geospatial/builds/

But not in the parent rocker/verse https://hub.docker.com/r/rocker/verse/builds/ builds that were done on the same day. Perhaps the geospatial builds just need to be re-launched?

Shiny Application Not Exposing Port 3838 in Docker Swarm

Hi @cboettig and @eddelbuettel... Firstly, thank you for all the Rocker images you guys put together, they're fantastic. Also, I apologize as this isn't really an issue with the Rocker image, but the firewall security at my employer prevents me from posting (although I can view) on Stack Overflow so I am hoping I can make some progress here...

We have been using the geospatial image for close to a year now and it had been working fine. We host multiple Shiny applications on a Docker EE swarm, using Traefik as a reverse proxy. Recently, upon redeploying a Shiny application with a minor R parameter change the URL for this Shiny application started returning "Bad Gateway." There are a bunch of other Shiny applications running on the swarm, but all of a sudden if we deploy (or redeploy) anything new we get a bad gateway error. We are quite confused and have been looking at this for a week: our Docker installation hasn't been updated since August, Traefik has been frozen since February and the R/Shiny code in question has also been frozen since June.

One quirky phenomenon is that we can access the RStudio server application for the particular deployment but not a Shiny application. That is, if I go to implementation.qa.gswarm.XXX.com I get a bad gateway error. If I redeploy the application and open up Traefik port 8787 instead of 3838 and go to implementation.qa.gswarm.XXX.com then RStudio server comes up without any issues.

I can see on the docker_gwbridge bridge network that the implementation_qa_pm_app is registered as a container, and I can see that Traefik is up and running for this container/service like it is for all the other applications we have running. We really have no idea why our Shiny deployment started failing even though we are unaware of anything changing "under the hood..."

Here is the application's stack file:

version: '3'

services:
  pm_app:
    image: gitlab.XXX.com:5005/gaashiny/implementationreport:${APP_ENV}  
    environment:
      - APP_ENV=${APP_ENV}
    volumes:
      - /sfofileserver/global:/sfofileserver/global
    networks:
      - traefik_public
    deploy:
      placement:
        constraints: 
          - node.hostname == mcsfvlidokas01d.XXX.com
      mode: replicated
      replicas: 1
      labels:
        traefik.port: 3838
        traefik.frontend.rule: Host:implementation.${APP_ENV}.gswarm.XXX.com
        traefik.docker.network: traefik_public

networks:
  traefik_public:
    external: true

The start_shiny.sh file:

#!/bin/bash
echo "export GAAMAHI_APP_ENV=$APP_ENV" >> /etc/profile
eval "$@"

And the shiny-server.conf file:

run_as shiny;

server {
  listen 3838;

  location / {

    app_dir /srv/shiny-server/implementation;

    log_dir /sfofileserver/global/srv/implementation/log;

  }
}

Sorry for blasting this out on here, but we're really scratching our heads on this so any ideas would be most appreciated...

Add ncdf4?

The ncdf4 package was available in previous releases (through 3.3.3 https://github.com/rocker-org/geospatial/search?utf8=%E2%9C%93&q=ncdf4&type=) and then appears to have been removed. There have been a lot of modifications so I wanted to check if this was intentionally removed from the geospatial container, or if it just got lost.

If it wasn't intentionally removed, could you please re-add it?

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