Help me out: install error #66

Changwan-planet · 2023-06-15T08:11:14Z

Changwan-planet
Jun 15, 2023

Dear RGPR developers,

Hi there,
I tried to install RGPR in Rstuio, but I got this long long error. I really want to use coodinate system in your program to handle GPR data.
Please fix this issue!

Systen envrionment
OS : Ubuntu 22.04.2 LTS
R : R version 4.3.0 (2023-04-21)
Rstudio : 2023.06.0 Build 421

> if(!require("devtools")) install.packages("devtools")
Loading required package: devtools
Installing package into ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
also installing the dependencies ‘Rcpp’, ‘utf8’, ‘askpass’, ‘credentials’, ‘openssl’, ‘sys’, ‘zip’, ‘httr2’, ‘fastmap’, ‘httpuv’, ‘mime’, ‘fontawesome’, ‘sourcetools’, ‘later’, ‘promises’, ‘base64enc’, ‘jquerylib’, ‘sass’, ‘fansi’, ‘systemfonts’, ‘textshaping’, ‘tinytex’, ‘xfun’, ‘pillar’, ‘highr’, ‘diffobj’, ‘rematch2’, ‘curl’, ‘gert’, ‘gh’, ‘glue’, ‘jsonlite’, ‘purrr’, ‘rappdirs’, ‘yaml’, ‘cachem’, ‘shiny’, ‘htmltools’, ‘callr’, ‘processx’, ‘bslib’, ‘digest’, ‘downlit’, ‘httr’, ‘magrittr’, ‘ragg’, ‘rmarkdown’, ‘tibble’, ‘xml2’, ‘htmlwidgets’, ‘stringr’, ‘vctrs’, ‘xopen’, ‘commonmark’, ‘knitr’, ‘stringi’, ‘brio’, ‘ps’, ‘waldo’, ‘usethis’, ‘cli’, ‘desc’, ‘ellipsis’, ‘fs’, ‘lifecycle’, ‘memoise’, ‘miniUI’, ‘pkgbuild’, ‘pkgdown’, ‘pkgload’, ‘profvis’, ‘rcmdcheck’, ‘rlang’, ‘roxygen2’, ‘rversions’, ‘sessioninfo’, ‘testthat’, ‘urlchecker’

trying URL 'https://cloud.r-project.org/src/contrib/Rcpp_1.0.10.tar.gz'
Content type 'application/x-gzip' length 2936173 bytes (2.8 MB)
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downloaded 2.8 MB

trying URL 'https://cloud.r-project.org/src/contrib/utf8_1.2.3.tar.gz'
Content type 'application/x-gzip' length 241412 bytes (235 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/askpass_1.1.tar.gz'
Content type 'application/x-gzip' length 5730 bytes
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trying URL 'https://cloud.r-project.org/src/contrib/credentials_1.3.2.tar.gz'
Content type 'application/x-gzip' length 230070 bytes (224 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/openssl_2.0.6.tar.gz'
Content type 'application/x-gzip' length 1206602 bytes (1.2 MB)
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trying URL 'https://cloud.r-project.org/src/contrib/sys_3.4.2.tar.gz'
Content type 'application/x-gzip' length 20169 bytes (19 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/zip_2.3.0.tar.gz'
Content type 'application/x-gzip' length 110488 bytes (107 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/httr2_0.2.3.tar.gz'
Content type 'application/x-gzip' length 123376 bytes (120 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/fastmap_1.1.1.tar.gz'
Content type 'application/x-gzip' length 46412 bytes (45 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/httpuv_1.6.11.tar.gz'
Content type 'application/x-gzip' length 1874829 bytes (1.8 MB)
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trying URL 'https://cloud.r-project.org/src/contrib/mime_0.12.tar.gz'
Content type 'application/x-gzip' length 12562 bytes (12 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/fontawesome_0.5.1.tar.gz'
Content type 'application/x-gzip' length 1276983 bytes (1.2 MB)
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downloaded 1.2 MB

trying URL 'https://cloud.r-project.org/src/contrib/sourcetools_0.1.7-1.tar.gz'
Content type 'application/x-gzip' length 24095 bytes (23 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/later_1.3.1.tar.gz'
Content type 'application/x-gzip' length 63641 bytes (62 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/promises_1.2.0.1.tar.gz'
Content type 'application/x-gzip' length 3120504 bytes (3.0 MB)
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downloaded 3.0 MB

trying URL 'https://cloud.r-project.org/src/contrib/base64enc_0.1-3.tar.gz'
Content type 'application/x-gzip' length 7833 bytes
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downloaded 7833 bytes

trying URL 'https://cloud.r-project.org/src/contrib/jquerylib_0.1.4.tar.gz'
Content type 'application/x-gzip' length 520207 bytes (508 KB)
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downloaded 508 KB

trying URL 'https://cloud.r-project.org/src/contrib/sass_0.4.6.tar.gz'
Content type 'application/x-gzip' length 3024838 bytes (2.9 MB)
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downloaded 2.9 MB

trying URL 'https://cloud.r-project.org/src/contrib/fansi_1.0.4.tar.gz'
Content type 'application/x-gzip' length 482055 bytes (470 KB)
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downloaded 470 KB

trying URL 'https://cloud.r-project.org/src/contrib/systemfonts_1.0.4.tar.gz'
Content type 'application/x-gzip' length 81757 bytes (79 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/textshaping_0.3.6.tar.gz'
Content type 'application/x-gzip' length 35722 bytes (34 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/tinytex_0.45.tar.gz'
Content type 'application/x-gzip' length 33082 bytes (32 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/xfun_0.39.tar.gz'
Content type 'application/x-gzip' length 135480 bytes (132 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/pillar_1.9.0.tar.gz'
Content type 'application/x-gzip' length 444528 bytes (434 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/highr_0.10.tar.gz'
Content type 'application/x-gzip' length 15084 bytes (14 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/diffobj_0.3.5.tar.gz'
Content type 'application/x-gzip' length 479276 bytes (468 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/rematch2_2.1.2.tar.gz'
Content type 'application/x-gzip' length 13366 bytes (13 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/curl_5.0.1.tar.gz'
Content type 'application/x-gzip' length 714177 bytes (697 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/gert_1.9.2.tar.gz'
Content type 'application/x-gzip' length 121088 bytes (118 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/gh_1.4.0.tar.gz'
Content type 'application/x-gzip' length 41214 bytes (40 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/glue_1.6.2.tar.gz'
Content type 'application/x-gzip' length 106510 bytes (104 KB)
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downloaded 104 KB

trying URL 'https://cloud.r-project.org/src/contrib/jsonlite_1.8.5.tar.gz'
Content type 'application/x-gzip' length 1053106 bytes (1.0 MB)
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downloaded 1.0 MB

trying URL 'https://cloud.r-project.org/src/contrib/purrr_1.0.1.tar.gz'
Content type 'application/x-gzip' length 220628 bytes (215 KB)
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downloaded 215 KB

trying URL 'https://cloud.r-project.org/src/contrib/rappdirs_0.3.3.tar.gz'
Content type 'application/x-gzip' length 12288 bytes (12 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/yaml_2.3.7.tar.gz'
Content type 'application/x-gzip' length 94330 bytes (92 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/cachem_1.0.8.tar.gz'
Content type 'application/x-gzip' length 26510 bytes (25 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/shiny_1.7.4.tar.gz'
Content type 'application/x-gzip' length 2476288 bytes (2.4 MB)
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trying URL 'https://cloud.r-project.org/src/contrib/htmltools_0.5.5.tar.gz'
Content type 'application/x-gzip' length 131880 bytes (128 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/callr_3.7.3.tar.gz'
Content type 'application/x-gzip' length 97813 bytes (95 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/processx_3.8.1.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/bslib_0.5.0.tar.gz'
Content type 'application/x-gzip' length 4917051 bytes (4.7 MB)
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trying URL 'https://cloud.r-project.org/src/contrib/digest_0.6.31.tar.gz'
Content type 'application/x-gzip' length 163502 bytes (159 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/downlit_0.4.2.tar.gz'
Content type 'application/x-gzip' length 37039 bytes (36 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.6.tar.gz'
Content type 'application/x-gzip' length 157621 bytes (153 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/magrittr_2.0.3.tar.gz'
Content type 'application/x-gzip' length 267074 bytes (260 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/ragg_1.2.5.tar.gz'
Content type 'application/x-gzip' length 427859 bytes (417 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/rmarkdown_2.22.tar.gz'
Content type 'application/x-gzip' length 2184560 bytes (2.1 MB)
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downloaded 2.1 MB

trying URL 'https://cloud.r-project.org/src/contrib/tibble_3.2.1.tar.gz'
Content type 'application/x-gzip' length 565982 bytes (552 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/xml2_1.3.4.tar.gz'
Content type 'application/x-gzip' length 272605 bytes (266 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/htmlwidgets_1.6.2.tar.gz'
Content type 'application/x-gzip' length 867472 bytes (847 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/stringr_1.5.0.tar.gz'
Content type 'application/x-gzip' length 175699 bytes (171 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/vctrs_0.6.3.tar.gz'
Content type 'application/x-gzip' length 967338 bytes (944 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/xopen_1.0.0.tar.gz'
Content type 'application/x-gzip' length 11221 bytes (10 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/commonmark_1.9.0.tar.gz'
Content type 'application/x-gzip' length 144922 bytes (141 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/knitr_1.43.tar.gz'
Content type 'application/x-gzip' length 895054 bytes (874 KB)
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downloaded 874 KB

trying URL 'https://cloud.r-project.org/src/contrib/stringi_1.7.12.tar.gz'
Content type 'application/x-gzip' length 7602365 bytes (7.3 MB)
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downloaded 7.3 MB

trying URL 'https://cloud.r-project.org/src/contrib/brio_1.1.3.tar.gz'
Content type 'application/x-gzip' length 12629 bytes (12 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/ps_1.7.5.tar.gz'
Content type 'application/x-gzip' length 129213 bytes (126 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/waldo_0.5.1.tar.gz'
Content type 'application/x-gzip' length 39619 bytes (38 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/usethis_2.2.0.tar.gz'
Content type 'application/x-gzip' length 370918 bytes (362 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/cli_3.6.1.tar.gz'
Content type 'application/x-gzip' length 567293 bytes (553 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/desc_1.4.2.tar.gz'
Content type 'application/x-gzip' length 79249 bytes (77 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/ellipsis_0.3.2.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/fs_1.6.2.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/lifecycle_1.0.3.tar.gz'
Content type 'application/x-gzip' length 106854 bytes (104 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/memoise_2.0.1.tar.gz'
Content type 'application/x-gzip' length 17852 bytes (17 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/miniUI_0.1.1.1.tar.gz'
Content type 'application/x-gzip' length 97958 bytes (95 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/pkgbuild_1.4.1.tar.gz'
Content type 'application/x-gzip' length 46906 bytes (45 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/pkgdown_2.0.7.tar.gz'
Content type 'application/x-gzip' length 871465 bytes (851 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/pkgload_1.3.2.tar.gz'
Content type 'application/x-gzip' length 76704 bytes (74 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/profvis_0.3.8.tar.gz'
Content type 'application/x-gzip' length 149012 bytes (145 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/rcmdcheck_1.4.0.tar.gz'
Content type 'application/x-gzip' length 73522 bytes (71 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/rlang_1.1.1.tar.gz'
Content type 'application/x-gzip' length 762533 bytes (744 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/roxygen2_7.2.3.tar.gz'
Content type 'application/x-gzip' length 279442 bytes (272 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/rversions_2.1.2.tar.gz'
Content type 'application/x-gzip' length 42135 bytes (41 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/sessioninfo_1.2.2.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/testthat_3.1.8.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/urlchecker_1.0.1.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/devtools_2.4.5.tar.gz'
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* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/Rcpp’
Warning in install.packages :
  installation of package ‘Rcpp’ had non-zero exit status
* installing *source* package ‘utf8’ ...
** package ‘utf8’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/utf8’
Warning in install.packages :
  installation of package ‘utf8’ had non-zero exit status
* installing *source* package ‘sys’ ...
** package ‘sys’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/sys’
Warning in install.packages :
  installation of package ‘sys’ had non-zero exit status
* installing *source* package ‘zip’ ...
** package ‘zip’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/zip’
Warning in install.packages :
  installation of package ‘zip’ had non-zero exit status
* installing *source* package ‘fastmap’ ...
** package ‘fastmap’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/fastmap’
Warning in install.packages :
  installation of package ‘fastmap’ had non-zero exit status
* installing *source* package ‘mime’ ...
** package ‘mime’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/mime’
Warning in install.packages :
  installation of package ‘mime’ had non-zero exit status
* installing *source* package ‘sourcetools’ ...
** package ‘sourcetools’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/sourcetools’
Warning in install.packages :
  installation of package ‘sourcetools’ had non-zero exit status
* installing *source* package ‘base64enc’ ...
** package ‘base64enc’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/base64enc’
Warning in install.packages :
  installation of package ‘base64enc’ had non-zero exit status
* installing *source* package ‘fansi’ ...
** package ‘fansi’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/fansi’
Warning in install.packages :
  installation of package ‘fansi’ had non-zero exit status
* installing *source* package ‘systemfonts’ ...
** package ‘systemfonts’ successfully unpacked and MD5 sums checked
** using staged installation
/usr/lib/R/bin/config: 1: eval: make: not found
/usr/lib/R/bin/config: 1: eval: make: not found
/usr/lib/R/bin/config: 1: eval: make: not found
/usr/lib/R/bin/config: 1: eval: make: not found
/usr/lib/R/bin/config: 1: eval: make: not found
/usr/lib/R/bin/config: 1: eval: make: not found
Error in system2(file.path(R.home("bin"), "R"), c("CMD", "config", x),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/systemfonts’
Warning in install.packages :
  installation of package ‘systemfonts’ had non-zero exit status
* installing *source* package ‘xfun’ ...
** package ‘xfun’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/xfun’
Warning in install.packages :
  installation of package ‘xfun’ had non-zero exit status
* installing *source* package ‘diffobj’ ...
** package ‘diffobj’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/diffobj’
Warning in install.packages :
  installation of package ‘diffobj’ had non-zero exit status
* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
/usr/lib/R/bin/config: 1: eval: make: not found
/usr/lib/R/bin/config: 1: eval: make: not found
/usr/lib/R/bin/config: 1: eval: make: not found
/usr/lib/R/bin/config: 1: eval: make: not found
/usr/lib/R/bin/config: 1: eval: make: not found
/usr/lib/R/bin/config: 1: eval: make: not found
Error in system2(file.path(R.home("bin"), "R"), c("CMD", "config", x),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/curl’
Warning in install.packages :
  installation of package ‘curl’ had non-zero exit status
* installing *source* package ‘glue’ ...
** package ‘glue’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/glue’
Warning in install.packages :
  installation of package ‘glue’ had non-zero exit status
* installing *source* package ‘jsonlite’ ...
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/jsonlite’
Warning in install.packages :
  installation of package ‘jsonlite’ had non-zero exit status
* installing *source* package ‘rappdirs’ ...
** package ‘rappdirs’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/rappdirs’
Warning in install.packages :
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* installing *source* package ‘yaml’ ...
** package ‘yaml’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/yaml’
Warning in install.packages :
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* installing *source* package ‘digest’ ...
** package ‘digest’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/digest’
Warning in install.packages :
  installation of package ‘digest’ had non-zero exit status
* installing *source* package ‘magrittr’ ...
** package ‘magrittr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/magrittr’
Warning in install.packages :
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* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
** using staged installation
/usr/lib/R/bin/config: 1: eval: make: not found
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/usr/lib/R/bin/config: 1: eval: make: not found
/usr/lib/R/bin/config: 1: eval: make: not found
/usr/lib/R/bin/config: 1: eval: make: not found
Error in system2(file.path(R.home("bin"), "R"), c("CMD", "config", x),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/xml2’
Warning in install.packages :
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* installing *source* package ‘commonmark’ ...
** package ‘commonmark’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/commonmark’
Warning in install.packages :
  installation of package ‘commonmark’ had non-zero exit status
* installing *source* package ‘stringi’ ...
** package ‘stringi’ successfully unpacked and MD5 sums checked
** using staged installation
/usr/lib/R/bin/config: 1: eval: make: not found
/usr/lib/R/bin/config: 1: eval: make: not found
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/usr/lib/R/bin/config: 1: eval: make: not found
/usr/lib/R/bin/config: 1: eval: make: not found
/usr/lib/R/bin/config: 1: eval: make: not found
Error in system2(file.path(R.home("bin"), "R"), c("CMD", "config", x),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/stringi’
Warning in install.packages :
  installation of package ‘stringi’ had non-zero exit status
* installing *source* package ‘brio’ ...
** package ‘brio’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/brio’
Warning in install.packages :
  installation of package ‘brio’ had non-zero exit status
* installing *source* package ‘ps’ ...
** package ‘ps’ successfully unpacked and MD5 sums checked
** using staged installation
/usr/lib/R/bin/config: 1: eval: make: not found
/usr/lib/R/bin/config: 1: eval: make: not found
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/usr/lib/R/bin/config: 1: eval: make: not found
/usr/lib/R/bin/config: 1: eval: make: not found
/usr/lib/R/bin/config: 1: eval: make: not found
Error in system2(file.path(R.home("bin"), "R"), c("CMD", "config", x),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/ps’
Warning in install.packages :
  installation of package ‘ps’ had non-zero exit status
* installing *source* package ‘cli’ ...
** package ‘cli’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/cli’
Warning in install.packages :
  installation of package ‘cli’ had non-zero exit status
* installing *source* package ‘fs’ ...
** package ‘fs’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/fs’
Warning in install.packages :
  installation of package ‘fs’ had non-zero exit status
* installing *source* package ‘rlang’ ...
** package ‘rlang’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"),  : 
  error in running command
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/rlang’
Warning in install.packages :
  installation of package ‘rlang’ had non-zero exit status
ERROR: dependency ‘sys’ is not available for package ‘askpass’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/askpass’
Warning in install.packages :
  installation of package ‘askpass’ had non-zero exit status
ERROR: dependencies ‘Rcpp’, ‘rlang’ are not available for package ‘later’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/later’
Warning in install.packages :
  installation of package ‘later’ had non-zero exit status
ERROR: dependency ‘systemfonts’ is not available for package ‘textshaping’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/textshaping’
Warning in install.packages :
  installation of package ‘textshaping’ had non-zero exit status
ERROR: dependency ‘xfun’ is not available for package ‘tinytex’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/tinytex’
Warning in install.packages :
  installation of package ‘tinytex’ had non-zero exit status
ERROR: dependency ‘xfun’ is not available for package ‘highr’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/highr’
Warning in install.packages :
  installation of package ‘highr’ had non-zero exit status
ERROR: dependencies ‘rlang’, ‘fastmap’ are not available for package ‘cachem’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/cachem’
Warning in install.packages :
  installation of package ‘cachem’ had non-zero exit status
ERROR: dependency ‘ps’ is not available for package ‘processx’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/processx’
Warning in install.packages :
  installation of package ‘processx’ had non-zero exit status
ERROR: dependency ‘cli’ is not available for package ‘desc’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/desc’
Warning in install.packages :
  installation of package ‘desc’ had non-zero exit status
ERROR: dependency ‘rlang’ is not available for package ‘ellipsis’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/ellipsis’
Warning in install.packages :
  installation of package ‘ellipsis’ had non-zero exit status
ERROR: dependencies ‘cli’, ‘glue’, ‘rlang’ are not available for package ‘lifecycle’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/lifecycle’
Warning in install.packages :
  installation of package ‘lifecycle’ had non-zero exit status
ERROR: dependencies ‘curl’, ‘xml2’ are not available for package ‘rversions’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/rversions’
Warning in install.packages :
  installation of package ‘rversions’ had non-zero exit status
ERROR: dependency ‘cli’ is not available for package ‘sessioninfo’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/sessioninfo’
Warning in install.packages :
  installation of package ‘sessioninfo’ had non-zero exit status
ERROR: dependencies ‘cli’, ‘curl’, ‘xml2’ are not available for package ‘urlchecker’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/urlchecker’
Warning in install.packages :
  installation of package ‘urlchecker’ had non-zero exit status
ERROR: dependency ‘askpass’ is not available for package ‘openssl’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/openssl’
Warning in install.packages :
  installation of package ‘openssl’ had non-zero exit status
ERROR: dependencies ‘Rcpp’, ‘later’, ‘rlang’, ‘magrittr’ are not available for package ‘promises’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/promises’
Warning in install.packages :
  installation of package ‘promises’ had non-zero exit status
ERROR: dependencies ‘digest’, ‘base64enc’, ‘rlang’, ‘fastmap’, ‘ellipsis’ are not available for package ‘htmltools’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/htmltools’
Warning in install.packages :
  installation of package ‘htmltools’ had non-zero exit status
ERROR: dependency ‘processx’ is not available for package ‘callr’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/callr’
Warning in install.packages :
  installation of package ‘callr’ had non-zero exit status
ERROR: dependencies ‘systemfonts’, ‘textshaping’ are not available for package ‘ragg’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/ragg’
Warning in install.packages :
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ERROR: dependencies ‘cli’, ‘glue’, ‘lifecycle’, ‘rlang’ are not available for package ‘vctrs’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/vctrs’
Warning in install.packages :
  installation of package ‘vctrs’ had non-zero exit status
ERROR: dependency ‘processx’ is not available for package ‘xopen’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/xopen’
Warning in install.packages :
  installation of package ‘xopen’ had non-zero exit status
ERROR: dependencies ‘highr’, ‘xfun’, ‘yaml’ are not available for package ‘knitr’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/knitr’
Warning in install.packages :
  installation of package ‘knitr’ had non-zero exit status
ERROR: dependencies ‘rlang’, ‘cachem’ are not available for package ‘memoise’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/memoise’
Warning in install.packages :
  installation of package ‘memoise’ had non-zero exit status
ERROR: dependencies ‘cli’, ‘desc’, ‘fs’, ‘glue’, ‘rlang’ are not available for package ‘pkgload’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/pkgload’
Warning in install.packages :
  installation of package ‘pkgload’ had non-zero exit status
ERROR: dependencies ‘openssl’, ‘sys’, ‘curl’, ‘jsonlite’, ‘askpass’ are not available for package ‘credentials’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/credentials’
Warning in install.packages :
  installation of package ‘credentials’ had non-zero exit status
ERROR: dependencies ‘cli’, ‘curl’, ‘glue’, ‘magrittr’, ‘openssl’, ‘rappdirs’, ‘rlang’ are not available for package ‘httr2’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/httr2’
Warning in install.packages :
  installation of package ‘httr2’ had non-zero exit status
ERROR: dependencies ‘Rcpp’, ‘promises’, ‘later’ are not available for package ‘httpuv’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/httpuv’
Warning in install.packages :
  installation of package ‘httpuv’ had non-zero exit status
ERROR: dependencies ‘rlang’, ‘htmltools’ are not available for package ‘fontawesome’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/fontawesome’
Warning in install.packages :
  installation of package ‘fontawesome’ had non-zero exit status
ERROR: dependency ‘htmltools’ is not available for package ‘jquerylib’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/jquerylib’
Warning in install.packages :
  installation of package ‘jquerylib’ had non-zero exit status
ERROR: dependencies ‘fs’, ‘rlang’, ‘htmltools’, ‘rappdirs’ are not available for package ‘sass’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/sass’
Warning in install.packages :
  installation of package ‘sass’ had non-zero exit status
ERROR: dependencies ‘cli’, ‘fansi’, ‘glue’, ‘lifecycle’, ‘rlang’, ‘utf8’, ‘vctrs’ are not available for package ‘pillar’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/pillar’
Warning in install.packages :
  installation of package ‘pillar’ had non-zero exit status
ERROR: dependencies ‘cli’, ‘lifecycle’, ‘magrittr’, ‘rlang’, ‘vctrs’ are not available for package ‘purrr’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/purrr’
Warning in install.packages :
  installation of package ‘purrr’ had non-zero exit status
ERROR: dependencies ‘brio’, ‘desc’, ‘digest’, ‘fansi’, ‘memoise’, ‘rlang’, ‘vctrs’, ‘yaml’ are not available for package ‘downlit’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/downlit’
Warning in install.packages :
  installation of package ‘downlit’ had non-zero exit status
ERROR: dependencies ‘curl’, ‘jsonlite’, ‘mime’, ‘openssl’ are not available for package ‘httr’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/httr’
Warning in install.packages :
  installation of package ‘httr’ had non-zero exit status
ERROR: dependencies ‘cli’, ‘glue’, ‘lifecycle’, ‘magrittr’, ‘rlang’, ‘stringi’, ‘vctrs’ are not available for package ‘stringr’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/stringr’
Warning in install.packages :
  installation of package ‘stringr’ had non-zero exit status
ERROR: dependencies ‘callr’, ‘cli’, ‘desc’, ‘processx’ are not available for package ‘pkgbuild’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/pkgbuild’
Warning in install.packages :
  installation of package ‘pkgbuild’ had non-zero exit status
ERROR: dependencies ‘askpass’, ‘credentials’, ‘openssl’, ‘sys’, ‘zip’ are not available for package ‘gert’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/gert’
Warning in install.packages :
  installation of package ‘gert’ had non-zero exit status
ERROR: dependencies ‘cli’, ‘httr2’, ‘jsonlite’, ‘rlang’ are not available for package ‘gh’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/gh’
Warning in install.packages :
  installation of package ‘gh’ had non-zero exit status
ERROR: dependencies ‘base64enc’, ‘cachem’, ‘htmltools’, ‘jquerylib’, ‘jsonlite’, ‘memoise’, ‘mime’, ‘rlang’, ‘sass’ are not available for package ‘bslib’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/bslib’
Warning in install.packages :
  installation of package ‘bslib’ had non-zero exit status
ERROR: dependencies ‘fansi’, ‘lifecycle’, ‘magrittr’, ‘pillar’, ‘rlang’, ‘vctrs’ are not available for package ‘tibble’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/tibble’
Warning in install.packages :
  installation of package ‘tibble’ had non-zero exit status
ERROR: dependencies ‘callr’, ‘cli’, ‘curl’, ‘desc’, ‘digest’, ‘pkgbuild’, ‘sessioninfo’, ‘xopen’ are not available for package ‘rcmdcheck’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/rcmdcheck’
Warning in install.packages :
  installation of package ‘rcmdcheck’ had non-zero exit status
ERROR: dependencies ‘cli’, ‘commonmark’, ‘desc’, ‘knitr’, ‘pkgload’, ‘purrr’, ‘rlang’, ‘stringi’, ‘stringr’, ‘xml2’ are not available for package ‘roxygen2’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/roxygen2’
Warning in install.packages :
  installation of package ‘roxygen2’ had non-zero exit status
ERROR: dependency ‘tibble’ is not available for package ‘rematch2’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/rematch2’
Warning in install.packages :
  installation of package ‘rematch2’ had non-zero exit status
ERROR: dependencies ‘httpuv’, ‘mime’, ‘jsonlite’, ‘fontawesome’, ‘htmltools’, ‘sourcetools’, ‘later’, ‘promises’, ‘rlang’, ‘fastmap’, ‘commonmark’, ‘glue’, ‘bslib’, ‘cachem’, ‘ellipsis’, ‘lifecycle’ are not available for package ‘shiny’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/shiny’
Warning in install.packages :
  installation of package ‘shiny’ had non-zero exit status
ERROR: dependencies ‘bslib’, ‘fontawesome’, ‘htmltools’, ‘jquerylib’, ‘jsonlite’, ‘knitr’, ‘stringr’, ‘tinytex’, ‘xfun’, ‘yaml’ are not available for package ‘rmarkdown’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/rmarkdown’
Warning in install.packages :
  installation of package ‘rmarkdown’ had non-zero exit status
ERROR: dependencies ‘cli’, ‘curl’, ‘desc’, ‘fs’, ‘gert’, ‘gh’, ‘glue’, ‘jsonlite’, ‘lifecycle’, ‘purrr’, ‘rappdirs’, ‘rlang’, ‘yaml’ are not available for package ‘usethis’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/usethis’
Warning in install.packages :
  installation of package ‘usethis’ had non-zero exit status
ERROR: dependencies ‘htmltools’, ‘jsonlite’, ‘yaml’, ‘knitr’, ‘rmarkdown’ are not available for package ‘htmlwidgets’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/htmlwidgets’
Warning in install.packages :
  installation of package ‘htmlwidgets’ had non-zero exit status
ERROR: dependencies ‘cli’, ‘diffobj’, ‘fansi’, ‘glue’, ‘rematch2’, ‘rlang’, ‘tibble’ are not available for package ‘waldo’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/waldo’
Warning in install.packages :
  installation of package ‘waldo’ had non-zero exit status
ERROR: dependencies ‘shiny’, ‘htmltools’ are not available for package ‘miniUI’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/miniUI’
Warning in install.packages :
  installation of package ‘miniUI’ had non-zero exit status
ERROR: dependencies ‘bslib’, ‘callr’, ‘cli’, ‘desc’, ‘digest’, ‘downlit’, ‘fs’, ‘httr’, ‘jsonlite’, ‘magrittr’, ‘memoise’, ‘purrr’, ‘ragg’, ‘rlang’, ‘rmarkdown’, ‘tibble’, ‘xml2’, ‘yaml’ are not available for package ‘pkgdown’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/pkgdown’
Warning in install.packages :
  installation of package ‘pkgdown’ had non-zero exit status
ERROR: dependencies ‘htmlwidgets’, ‘purrr’, ‘rlang’, ‘stringr’, ‘vctrs’ are not available for package ‘profvis’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/profvis’
Warning in install.packages :
  installation of package ‘profvis’ had non-zero exit status
ERROR: dependencies ‘brio’, ‘callr’, ‘cli’, ‘desc’, ‘digest’, ‘ellipsis’, ‘jsonlite’, ‘lifecycle’, ‘magrittr’, ‘pkgload’, ‘processx’, ‘ps’, ‘rlang’, ‘waldo’ are not available for package ‘testthat’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/testthat’
Warning in install.packages :
  installation of package ‘testthat’ had non-zero exit status
ERROR: dependencies ‘usethis’, ‘cli’, ‘desc’, ‘ellipsis’, ‘fs’, ‘lifecycle’, ‘memoise’, ‘miniUI’, ‘pkgbuild’, ‘pkgdown’, ‘pkgload’, ‘profvis’, ‘rcmdcheck’, ‘rlang’, ‘roxygen2’, ‘rversions’, ‘sessioninfo’, ‘testthat’, ‘urlchecker’ are not available for package ‘devtools’
* removing ‘/home/csun/R/x86_64-pc-linux-gnu-library/4.3/devtools’
Warning in install.packages :
  installation of package ‘devtools’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/Rtmp6jsxI7/downloaded_packages’
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘devtools’
> devtools::install_github("emanuelhuber/RGPR")
Error in loadNamespace(x) : there is no package called ‘devtools’

Answered by Changwan-planet

Jun 19, 2023

Ok. Great.

I leave some my experiences about issues when installing RGPR.

Those sites help you address your installing issues.

cairo
--> https://www.cairographics.org/download/
--> https://github.com/s-u/Cairo

gdal
-->https://mothergeo-py.readthedocs.io/en/latest/development/how-to/gdal-ubuntu-pkg.html

When you finished to install the above libraries, you would face the last enemy, hdf5r.
I noticed that It is infamous for its install in R.

sudo apt-get install libhdf5-dev

devtools::install_github("hhoeflin/hdf5r")

(https://github.com/hhoeflin/hdf5r)

Those were bad solutions for me.

This command help me a lot to install hdf5r.

conda install -c conda-forge r-hdf5r

(https://anaconda.org/c…

View full answer

emanuelhuber · 2023-06-17T20:59:27Z

emanuelhuber
Jun 17, 2023
Maintainer

Hello @Changwan-planet

Thank you for contacting me.
I think that the problem is that "make" (the application) is not available on your PC (see this issue with the same problem: https://community.rstudio.com/t/unable-to-install-package-for-r-markdown/167999)

I suggest you to install "make" and then to try to install RGPR again.
Here is a tutorial how to install "make": https://www.howtogeek.com/886504/how-to-fix-make-command-not-found-error-in-ubuntu/

Let me know if it solves your problem.

Best,

Emanuel

1 reply

Changwan-planet Jun 18, 2023
Author

Thank you for your answer.
Since your reply,
I tried to install RGPR many times, also read the error massages, and installed some libraries such as libfreetype6-dev, libpng-dev, libtiff5-dev, and libjpeg-dev, that R error messages required.

At this moment, I met another wall.
A core warning message is below.

I strived to install each package, but same error occured.

There were 13 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In i.p(...) : installation of package ‘robustbase’ had non-zero exit status
2: In i.p(...) : installation of package ‘spam’ had non-zero exit status
3: In i.p(...) : installation of package ‘terra’ had non-zero exit status
4: In i.p(...) : installation of package ‘hdf5r’ had non-zero exit status
5: In i.p(...) : installation of package ‘adimpro’ had non-zero exit status
6: In i.p(...) : installation of package ‘Cairo’ had non-zero exit status
7: In i.p(...) : installation of package ‘rgeos’ had non-zero exit status
8: In i.p(...) : installation of package ‘rgdal’ had non-zero exit status
9: In i.p(...) : installation of package ‘robfilter’ had non-zero exit status
10: In i.p(...) : installation of package ‘sf’ had non-zero exit status
11: In i.p(...) : installation of package ‘fields’ had non-zero exit status
12: In i.p(...) : installation of package ‘raster’ had non-zero exit status
13: In i.p(...) :
  installation of package ‘/tmp/RtmpB7iJJs/file1d0ea768bfb09/RGPR_0.0.7.tar.gz’ had non-zero exit status

All the error content is below.

> if(!require("devtools")) install.packages("devtools")
Loading required package: devtools
Loading required package: usethis
> devtools::install_github("emanuelhuber/RGPR")
Downloading GitHub repo emanuelhuber/RGPR@HEAD
Installing 12 packages: robustbase, spam, terra, hdf5r, robfilter, sf, fields, raster, adimpro, Cairo, rgeos, rgdal
Installing packages into ‘/home/changwan/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/robustbase_0.99-0.tar.gz'
Content type 'application/x-gzip' length 2291216 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

trying URL 'https://cloud.r-project.org/src/contrib/spam_2.9-1.tar.gz'
Content type 'application/x-gzip' length 1815928 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

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* installing *source* package ‘robustbase’ ...
** package ‘robustbase’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
using Fortran compiler: ‘GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c R-rng4ftn.c -o R-rng4ftn.o
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c eigen.f -o eigen.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c init.c -o init.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c lmrob.c -o lmrob.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c mc.c -o mc.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c monitor.c -o monitor.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c qn_sn.c -o qn_sn.o
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c rf-common.f -o rf-common.o
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c rffastmcd.f -o rffastmcd.o
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c rfltsreg.f -o rfltsreg.o
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c rllarsbi.f -o rllarsbi.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c rob-utils.c -o rob-utils.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c rowMedians.c -o rowMedians.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c wgt_himed.c -o wgt_himed.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o robustbase.so R-rng4ftn.o eigen.o init.o lmrob.o mc.o monitor.o qn_sn.o rf-common.o rffastmcd.o rfltsreg.o rllarsbi.o rob-utils.o rowMedians.o wgt_himed.o -llapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack: No such file or directory
/usr/bin/ld: cannot find -lblas: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:10: robustbase.so] Error 1
ERROR: compilation failed for package ‘robustbase’
* removing ‘/home/changwan/R/x86_64-pc-linux-gnu-library/4.3/robustbase’
* installing *source* package ‘spam’ ...
** package ‘spam’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
using Fortran compiler: ‘GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c bckslvmodified.f -o bckslvmodified.o
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c cholmodified.f -o cholmodified.o
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c dgetv0.f -o dgetv0.o
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c dist.f -o dist.o
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c dn_ARPACK.f -o dn_ARPACK.o
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c dn_eigen.f -o dn_eigen.o
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c ds_ARPACK.f -o ds_ARPACK.o
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c ds_eigen.f -o ds_eigen.o
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c fromsparsekit.f -o fromsparsekit.o
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c gmult.f -o gmult.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c init.c -o init.o
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c kronecker.f -o kronecker.o
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c permutation.f -o permutation.o
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c rowcolstats.f -o rowcolstats.o
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c spamown.f -o spamown.o
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c spamown2.f -o spamown2.o
gfortran  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c xybind.f -o xybind.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o spam.so bckslvmodified.o cholmodified.o dgetv0.o dist.o dn_ARPACK.o dn_eigen.o ds_ARPACK.o ds_eigen.o fromsparsekit.o gmult.o init.o kronecker.o permutation.o rowcolstats.o spamown.o spamown2.o xybind.o -llapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack: No such file or directory
/usr/bin/ld: cannot find -lblas: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:10: spam.so] Error 1
ERROR: compilation failed for package ‘spam’
* removing ‘/home/changwan/R/x86_64-pc-linux-gnu-library/4.3/spam’
* installing *source* package ‘terra’ ...
** package ‘terra’ successfully unpacked and MD5 sums checked
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++17
checking for gdal-config... no
no
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘terra’
* removing ‘/home/changwan/R/x86_64-pc-linux-gnu-library/4.3/terra’
* installing *source* package ‘hdf5r’ ...
** package ‘hdf5r’ successfully unpacked and MD5 sums checked
** using staged installation
checking for a sed that does not truncate output... /bin/sed
checking for gawk... no
checking for mawk... mawk
checking for grep that handles long lines and -e... /usr/bin/grep
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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for h5cc... /home/changwan/anaconda3/bin/h5cc
checking for HDF5 libraries... yes (version 1.10.6)
checking for hdf5.h... no
checking for H5Fcreate in -lhdf5... no
configure: WARNING: Unable to compile HDF5 test program
checking for hdf5_hl.h... no
checking for H5LTpath_valid in -lhdf5_hl... no
configure: WARNING: Unable to compile HDF5_HL test program
checking for main in -lhdf5_hl... no
checking for matching HDF5 Fortran wrapper... /home/changwan/anaconda3/bin/h5fc
Found hdf5 with version: 1.10.6
checking for ggrep... /usr/bin/grep
checking whether /usr/bin/grep accepts -o... yes
checking for ggrep... (cached) /usr/bin/grep
checking whether /usr/bin/grep accepts -o... yes
Using variables:
HDF5_LIBS= -L/home/changwan/anaconda3/lib  -L/home/changwan/anaconda3/lib  -L/home/changwan/anaconda3/lib  -lpthread  -lz  -ldl  -lm  -L. -lhdf5_hl -lhdf5 -lz -lm
HDF5_CFLAGS=
HDF5_CPPFLAGS=-I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include 
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
cp 1_10_3/*.c 1_10_3/*.h .
if [ "1.10.6" != "" ]; then patch -p2 < patch_1.10.6; fi
patching file datatype_export.c
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c const_export.c -o const_export.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c datatype_export.c -o datatype_export.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5A.c -o Wrapper_auto_H5A.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5.c -o Wrapper_auto_H5.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5D.c -o Wrapper_auto_H5D.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5DS.c -o Wrapper_auto_H5DS.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5E.c -o Wrapper_auto_H5E.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5F.c -o Wrapper_auto_H5F.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5G.c -o Wrapper_auto_H5G.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5I.c -o Wrapper_auto_H5I.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5IM.c -o Wrapper_auto_H5IM.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5L.c -o Wrapper_auto_H5L.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5LT.c -o Wrapper_auto_H5LT.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5O.c -o Wrapper_auto_H5O.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5P.c -o Wrapper_auto_H5P.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5R.c -o Wrapper_auto_H5R.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5S.c -o Wrapper_auto_H5S.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5TB.c -o Wrapper_auto_H5TB.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5T.c -o Wrapper_auto_H5T.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5Z.c -o Wrapper_auto_H5Z.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5FDcore.c -o Wrapper_auto_H5FDcore.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5FDfamily.c -o Wrapper_auto_H5FDfamily.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5FDlog.c -o Wrapper_auto_H5FDlog.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5FDsec2.c -o Wrapper_auto_H5FDsec2.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_auto_H5FDstdio.c -o Wrapper_auto_H5FDstdio.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c convert.c -o convert.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c hdf5r_init.c -o hdf5r_init.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c H5Error.c -o H5Error.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c H5ls.c -o H5ls.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/home/changwan/anaconda3/include -I/home/changwan/anaconda3/include      -D__USE_MINGW_ANSI_STDIO  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Wrapper_manual_H5T.c -o Wrapper_manual_H5T.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o hdf5r.so const_export.o datatype_export.o Wrapper_auto_H5A.o Wrapper_auto_H5.o Wrapper_auto_H5D.o Wrapper_auto_H5DS.o Wrapper_auto_H5E.o Wrapper_auto_H5F.o Wrapper_auto_H5G.o Wrapper_auto_H5I.o Wrapper_auto_H5IM.o Wrapper_auto_H5L.o Wrapper_auto_H5LT.o Wrapper_auto_H5O.o Wrapper_auto_H5P.o Wrapper_auto_H5R.o Wrapper_auto_H5S.o Wrapper_auto_H5TB.o Wrapper_auto_H5T.o Wrapper_auto_H5Z.o Wrapper_auto_H5FDcore.o Wrapper_auto_H5FDfamily.o Wrapper_auto_H5FDlog.o Wrapper_auto_H5FDsec2.o Wrapper_auto_H5FDstdio.o convert.o hdf5r_init.o H5Error.o H5ls.o Wrapper_manual_H5T.o -L/home/changwan/anaconda3/lib -L/home/changwan/anaconda3/lib -L/home/changwan/anaconda3/lib -lpthread -lz -ldl -lm -L. -lhdf5_hl -lhdf5 -lz -lm -L/usr/lib/R/lib -lR
installing to /home/changwan/R/x86_64-pc-linux-gnu-library/4.3/00LOCK-hdf5r/00new/hdf5r/libs
** 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
Error: package or namespace load failed for ‘hdf5r’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/changwan/R/x86_64-pc-linux-gnu-library/4.3/00LOCK-hdf5r/00new/hdf5r/libs/hdf5r.so':
  libhdf5_hl.so.100: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/changwan/R/x86_64-pc-linux-gnu-library/4.3/hdf5r’
* installing *source* package ‘sf’ ...
** package ‘sf’ successfully unpacked and MD5 sums checked
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++17
checking for gdal-config... no
no
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘sf’
* removing ‘/home/changwan/R/x86_64-pc-linux-gnu-library/4.3/sf’
* installing *source* package ‘adimpro’ ...
** package ‘adimpro’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
using Fortran compiler: ‘GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Rentries.c -o Rentries.o
gfortran -fopenmp -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c aniso.f -o aniso.o
gfortran -fopenmp -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c awsimage.f -o awsimage.o
gfortran -fopenmp -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c awspimage.f -o awspimage.o
gfortran -fopenmp -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c demosaic.f -o demosaic.o
gfortran -fopenmp -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c edges.f -o edges.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c init.c -o init.o
gfortran -fopenmp -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c misc.f -o misc.o
gfortran -fopenmp -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c segment.f -o segment.o
gfortran -fopenmp -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c shrink.f -o shrink.o
gfortran -fopenmp -fpic  -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong  -c smsensor.f -o smsensor.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o adimpro.so Rentries.o aniso.o awsimage.o awspimage.o demosaic.o edges.o init.o misc.o segment.o shrink.o smsensor.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack: No such file or directory
/usr/bin/ld: cannot find -lblas: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:10: adimpro.so] Error 1
ERROR: compilation failed for package ‘adimpro’
* removing ‘/home/changwan/R/x86_64-pc-linux-gnu-library/4.3/adimpro’
* installing *source* package ‘Cairo’ ...
** package ‘Cairo’ successfully unpacked and MD5 sums checked
** using staged installation
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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for pkg-config... /usr/bin/pkg-config
checking whether pkg-config knows about cairo... no
configure: CAIRO_LIBS is unset, attempting to guess it.
configure: CAIRO_CFLAGS=
checking if R was compiled with the RConn patch... no
checking for cairo.h... no
configure: error: Cannot find cairo.h! Please install cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly.
ERROR: configuration failed for package ‘Cairo’
* removing ‘/home/changwan/R/x86_64-pc-linux-gnu-library/4.3/Cairo’
* installing *source* package ‘rgeos’ ...
** package ‘rgeos’ successfully unpacked and MD5 sums checked
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++17
configure: rgeos: 0.6-3
checking for /usr/bin/svnversion... no
configure: svn revision: 696
checking for geos-config... no
no
configure: error: geos-config not found or not executable.
ERROR: configuration failed for package ‘rgeos’
* removing ‘/home/changwan/R/x86_64-pc-linux-gnu-library/4.3/rgeos’
* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
** using staged installation
configure: R_HOME: /usr/lib/R
configure: CC: gcc
configure: CXX: g++ -std=gnu++17
configure: CFLAGS: -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2
configure: CPPFLAGS: 
configure: CXXFLAGS: -g -O2 -ffile-prefix-map=/build/r-base-JhpCKt/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2
configure: LDFLAGS: -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro
configure: LDFLAGS: -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro
configure: CXX17 is: g++, CXX17STD is: -std=gnu++17
configure: CXX is: g++ -std=gnu++17
configure: C++17 support available
configure: rgdal: 1.6-7
checking for /usr/bin/svnversion... no
configure: svn revision: 1203
checking for gdal-config... no
no
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘rgdal’
* removing ‘/home/changwan/R/x86_64-pc-linux-gnu-library/4.3/rgdal’
ERROR: dependency ‘robustbase’ is not available for package ‘robfilter’
* removing ‘/home/changwan/R/x86_64-pc-linux-gnu-library/4.3/robfilter’
ERROR: dependency ‘spam’ is not available for package ‘fields’
* removing ‘/home/changwan/R/x86_64-pc-linux-gnu-library/4.3/fields’
ERROR: dependency ‘terra’ is not available for package ‘raster’
* removing ‘/home/changwan/R/x86_64-pc-linux-gnu-library/4.3/raster’

The downloaded source packages are in
	‘/tmp/RtmpgdqIL1/downloaded_packages’
── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/tmp/RtmpgdqIL1/remotes1ed9074a3b3db/emanuelhuber-RGPR-9568bdf/DESCRIPTION’ ...
─  preparing ‘RGPR’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
     NB: this package now depends on R (>= 3.5.0)
     WARNING: Added dependency on R >= 3.5.0 because serialized objects in
     serialize/load version 3 cannot be read in older versions of R.
     File(s) containing such objects:
       ‘RGPR/test.rds’
─  building ‘RGPR_0.0.7.tar.gz’
   
Installing package into ‘/home/changwan/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
ERROR: dependencies ‘rgdal’, ‘rgeos’, ‘Cairo’, ‘adimpro’, ‘raster’, ‘fields’, ‘sf’, ‘robfilter’, ‘hdf5r’ are not available for package ‘RGPR’
* removing ‘/home/changwan/R/x86_64-pc-linux-gnu-library/4.3/RGPR’
There were 13 warnings (use warnings() to see them)

Best regards,

Changwan

emanuelhuber · 2023-06-18T20:38:58Z

emanuelhuber
Jun 18, 2023
Maintainer

Hello Changwan

The error messages indicate that you need to install some libraries before installing the package. I think that the followin libraries have to be installed:

llapack
lblas
gdal (or maybe gdal-lib, check on internet)
libhdf5
cairo
geos

Check google for the correct name (e.g. gdal or gdal-lib).

Be patient, it is a pain with ubuntu at the begining but then it works smoothly (I am using ubuntu).

Best,

Emanuel

0 replies

Changwan-planet · 2023-06-19T08:39:46Z

Changwan-planet
Jun 19, 2023
Author

Ok. Great.

I leave some my experiences about issues when installing RGPR.

Those sites help you address your installing issues.

cairo
--> https://www.cairographics.org/download/
--> https://github.com/s-u/Cairo

gdal
-->https://mothergeo-py.readthedocs.io/en/latest/development/how-to/gdal-ubuntu-pkg.html

When you finished to install the above libraries, you would face the last enemy, hdf5r.
I noticed that It is infamous for its install in R.

sudo apt-get install libhdf5-dev

devtools::install_github("hhoeflin/hdf5r")

(https://github.com/hhoeflin/hdf5r)

Those were bad solutions for me.

This command help me a lot to install hdf5r.

conda install -c conda-forge r-hdf5r

(https://anaconda.org/conda-forge/r-hdf5r)

After the above steps, I got this message!

** help
*** installing help indices
** building package indices
** 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 (RGPR)
> library(RGPR)
The legacy packages maptools, rgdal, and rgeos, underpinning this package
will retire shortly. Please refer to R-spatial evolution reports on
https://r-spatial.org/r/2023/05/15/evolution4.html for details.
This package is now running under evolution status 0 
Don't hesitate to contact me if you have any question:
emanuel.huber@pm.me

Attaching package: ‘RGPR’

The following object is masked from ‘package:graphics’:

    clip

I hope this post help someone install RGPR in the future.

I really appreciate your warm help, Dr. huber!!

Changwan

0 replies

emanuelhuber · 2023-06-24T14:13:00Z

emanuelhuber
Jun 24, 2023
Maintainer

Thank you for your feedback Changwan. I think I will write a short tutorial for RGPR installation in ubuntu/linux.

Best,

Emanuel

0 replies

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