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lifewatch / eurobis

Loads data from EurOBIS into R and query on taxon, location and more
https://lifewatch.github.io/eurobis/
MIT License
1 stars 0 forks source link

Failing installation eurobis package (R 4.0.2) #11

Closed salvafern closed 2 years ago

salvafern commented 3 years ago

Installing the package gives issues due to its several downstream dependencies. This might be caused partially due to https://github.com/vlizBE/imis/issues/3

See the reprex below run in a clean virtual env.

# Start a virtual environment
# install.packages("renv")
renv::activate()

# install reprex for reproducibility
install.packages("reprex")
#> Retrieving 'https://cran.rstudio.com/bin/windows/contrib/4.0/reprex_1.0.0.zip' ...
#>  OK [downloaded 476.8 Kb in 0.3 secs]
#> Retrieving 'https://cran.rstudio.com/bin/windows/contrib/4.0/callr_3.5.1.zip' ...
#>  OK [downloaded 377.8 Kb in 0.3 secs]
#> Retrieving 'https://cran.rstudio.com/bin/windows/contrib/4.0/processx_3.4.5.zip' ...
#>  OK [downloaded 1.3 Mb in 0.5 secs]
#> Retrieving 'https://cran.rstudio.com/src/contrib/ps_1.6.0.tar.gz' ...
#>  OK [downloaded 116.9 Kb in 0.2 secs]
#> Retrieving 'https://cran.rstudio.com/src/contrib/cli_2.3.1.tar.gz' ...
#>  OK [downloaded 131 Kb in 0.2 secs]
#> Retrieving 'https://cran.rstudio.com/bin/windows/contrib/4.0/clipr_0.7.1.zip' ...
#>  OK [downloaded 50.9 Kb in 0.2 secs]
#> Retrieving 'https://cran.rstudio.com/bin/windows/contrib/4.0/knitr_1.31.zip' ...
#>  OK [downloaded 1.4 Mb in 0.4 secs]
#> Retrieving 'https://cran.rstudio.com/bin/windows/contrib/4.0/xfun_0.21.zip' ...
#>  OK [downloaded 311.9 Kb in 0.3 secs]
#> Retrieving 'https://cran.rstudio.com/bin/windows/contrib/4.0/mime_0.10.zip' ...
#>  OK [downloaded 47.3 Kb in 0.2 secs]
#> Retrieving 'https://cran.rstudio.com/bin/windows/contrib/4.0/stringi_1.5.3.zip' ...
#>  OK [downloaded 14.5 Mb in 3.1 secs]
#> Retrieving 'https://cran.rstudio.com/src/contrib/rmarkdown_2.7.tar.gz' ...
#>  OK [downloaded 3.1 Mb in 0.9 secs]
#> Retrieving 'https://cran.rstudio.com/bin/windows/contrib/4.0/htmltools_0.5.1.1.zip' ...
#>  OK [downloaded 238.1 Kb in 0.2 secs]
#> Retrieving 'https://cran.rstudio.com/bin/windows/contrib/4.0/jsonlite_1.7.2.zip' ...
#>  OK [downloaded 531.1 Kb in 0.2 secs]
#> Retrieving 'https://cran.rstudio.com/bin/windows/contrib/4.0/tinytex_0.29.zip' ...
#>  OK [downloaded 114 Kb in 0.2 secs]
#> Retrieving 'https://cran.rstudio.com/bin/windows/contrib/4.0/withr_2.4.1.zip' ...
#>  OK [downloaded 201.2 Kb in 0.2 secs]
#> Installing ps [1.6.0] ...
#>  OK [built from source]
#> Installing R6 [2.5.0] ...
#>  OK [linked cache]
#> Installing processx [3.4.5] ...
#>  OK [installed binary]
#> Installing callr [3.5.1] ...
#>  OK [installed binary]
#> Installing assertthat [0.2.1] ...
#>  OK [linked cache]
#> Installing glue [1.4.2] ...
#>  OK [linked cache]
#> Installing cli [2.3.1] ...
#>  OK [built from source]
#> Installing clipr [0.7.1] ...
#>  OK [installed binary]
#> Installing fs [1.5.0] ...
#>  OK [linked cache]
#> Installing evaluate [0.14] ...
#>  OK [linked cache]
#> Installing highr [0.8] ...
#>  OK [linked cache]
#> Installing xfun [0.21] ...
#>  OK [installed binary]
#> Installing mime [0.10] ...
#>  OK [installed binary]
#> Installing markdown [1.1] ...
#>  OK [linked cache]
#> Installing magrittr [2.0.1] ...
#>  OK [linked cache]
#> Installing stringi [1.5.3] ...
#>  OK [installed binary]
#> Installing stringr [1.4.0] ...
#>  OK [linked cache]
#> Installing yaml [2.2.1] ...
#>  OK [linked cache]
#> Installing knitr [1.31] ...
#>  OK [installed binary]
#> Installing rlang [0.4.10] ...
#>  OK [linked cache]
#> Installing digest [0.6.27] ...
#>  OK [linked cache]
#> Installing base64enc [0.1-3] ...
#>  OK [linked cache]
#> Installing htmltools [0.5.1.1] ...
#>  OK [installed binary]
#> Installing jsonlite [1.7.2] ...
#>  OK [installed binary]
#> Installing tinytex [0.29] ...
#>  OK [installed binary]
#> Installing rmarkdown [2.7] ...
#>  OK [built from source]
#> Installing withr [2.4.1] ...
#>  OK [installed binary]
#> Installing reprex [1.0.0] ...
#>  OK [installed binary]
#> The following package(s) have been updated:
#> 
#>  xfun      [installed version 0.21    != loaded version 0.16 ]
#>  stringi   [installed version 1.5.3   != loaded version 1.4.6]
#>  knitr     [installed version 1.31    != loaded version 1.29 ]
#>  htmltools [installed version 0.5.1.1 != loaded version 0.5.0]
#>  rmarkdown [installed version 2.7     != loaded version 2.5  ]
#> 
#> Consider restarting the R session and loading the newly-installed packages.

# Install package
install.packages("remotes")
#> Installing remotes [2.2.0] ...
#>  OK [linked cache]

remotes::install_github("lifewatch/eurobis")
#> Downloading GitHub repo lifewatch/eurobis@HEAD
#> Warning in untar2(tarfile, files, list, exdir, restore_times): skipping pax
#> global extended headers

#> Warning in untar2(tarfile, files, list, exdir, restore_times): skipping pax
#> global extended headers
#> Rcpp       (NA -> 1.0.6 ) [CRAN]
#> e1071      (NA -> 1.7-4 ) [CRAN]
#> rappdirs   (NA -> 0.3.3 ) [CRAN]
#> utf8       (NA -> 1.1.4 ) [CRAN]
#> crayon     (NA -> 1.4.1 ) [CRAN]
#> purrr      (NA -> 0.3.4 ) [CRAN]
#> pkgconfig  (NA -> 2.0.3 ) [CRAN]
#> pillar     (NA -> 1.5.0 ) [CRAN]
#> fansi      (NA -> 0.4.2 ) [CRAN]
#> curl       (NA -> 4.3   ) [CRAN]
#> V8         (NA -> 3.4.0 ) [CRAN]
#> lazyeval   (NA -> 0.2.2 ) [CRAN]
#> jsonld     (NA -> 2.2   ) [CRAN]
#> vctrs      (NA -> 0.3.6 ) [CRAN]
#> tidyselect (NA -> 1.1.0 ) [CRAN]
#> tibble     (NA -> 3.1.0 ) [CRAN]
#> lifecycle  (NA -> 1.0.0 ) [CRAN]
#> generics   (NA -> 0.1.0 ) [CRAN]
#> ellipsis   (NA -> 0.3.1 ) [CRAN]
#> dplyr      (NA -> 1.0.4 ) [CRAN]
#> uuid       (NA -> 0.1-4 ) [CRAN]
#> jqr        (NA -> 1.2.0 ) [CRAN]
#> emld       (NA -> 0.5.1 ) [CRAN]
#> xml2       (NA -> 1.3.2 ) [CRAN]
#> units      (NA -> 0.7-0 ) [CRAN]
#> DBI        (NA -> 1.1.1 ) [CRAN]
#> classInt   (NA -> 0.4-3 ) [CRAN]
#> hoardr     (NA -> 0.5.2 ) [CRAN]
#> data.table (NA -> 1.14.0) [CRAN]
#> EML        (NA -> 2.0.5 ) [CRAN]
#> plyr       (NA -> 1.8.6 ) [CRAN]
#> sf         (NA -> 0.9-7 ) [CRAN]
#> finch      (NA -> 0.4.0 ) [CRAN]
#> reshape2   (NA -> 1.4.4 ) [CRAN]
#> Installing 34 packages: Rcpp, e1071, rappdirs, utf8, crayon, purrr, pkgconfig, pillar, fansi, curl, V8, lazyeval, jsonld, vctrs, tidyselect, tibble, lifecycle, generics, ellipsis, dplyr, uuid, jqr, emld, xml2, units, DBI, classInt, hoardr, data.table, EML, plyr, sf, finch, reshape2
#> Installing packages into 'C:/Users/salvadorf/AppData/Local/Temp/RtmpyQPd6y/reprex44b06ebe3f0e/renv/library/R-4.0/x86_64-w64-mingw32'
#> (as 'lib' is unspecified)
#> 
#>   There are binary versions available but the source versions are later:
#>            binary source needs_compilation
#> pillar      1.4.7  1.5.0             FALSE
#> tibble      3.0.6  3.1.0              TRUE
#> units       0.6-7  0.7-0              TRUE
#> data.table 1.13.6 1.14.0              TRUE
#> EML         2.0.4  2.0.5             FALSE
#> 
#>   Binaries will be installed
#> package 'Rcpp' successfully unpacked and MD5 sums checked
#> package 'e1071' successfully unpacked and MD5 sums checked
#> package 'rappdirs' successfully unpacked and MD5 sums checked
#> package 'utf8' successfully unpacked and MD5 sums checked
#> package 'crayon' successfully unpacked and MD5 sums checked
#> package 'purrr' successfully unpacked and MD5 sums checked
#> package 'pkgconfig' successfully unpacked and MD5 sums checked
#> package 'fansi' successfully unpacked and MD5 sums checked
#> package 'curl' successfully unpacked and MD5 sums checked
#> package 'V8' successfully unpacked and MD5 sums checked
#> package 'lazyeval' successfully unpacked and MD5 sums checked
#> package 'jsonld' successfully unpacked and MD5 sums checked
#> package 'vctrs' successfully unpacked and MD5 sums checked
#> package 'tidyselect' successfully unpacked and MD5 sums checked
#> package 'tibble' successfully unpacked and MD5 sums checked
#> package 'lifecycle' successfully unpacked and MD5 sums checked
#> package 'generics' successfully unpacked and MD5 sums checked
#> package 'ellipsis' successfully unpacked and MD5 sums checked
#> package 'dplyr' successfully unpacked and MD5 sums checked
#> package 'uuid' successfully unpacked and MD5 sums checked
#> package 'jqr' successfully unpacked and MD5 sums checked
#> package 'emld' successfully unpacked and MD5 sums checked
#> package 'xml2' successfully unpacked and MD5 sums checked
#> package 'units' successfully unpacked and MD5 sums checked
#> package 'DBI' successfully unpacked and MD5 sums checked
#> package 'classInt' successfully unpacked and MD5 sums checked
#> package 'hoardr' successfully unpacked and MD5 sums checked
#> package 'data.table' successfully unpacked and MD5 sums checked
#> package 'plyr' successfully unpacked and MD5 sums checked
#> package 'sf' successfully unpacked and MD5 sums checked
#> package 'finch' successfully unpacked and MD5 sums checked
#> package 'reshape2' successfully unpacked and MD5 sums checked
#> 
#> The downloaded binary packages are in
#>  C:\Users\salvadorf\AppData\Local\Temp\RtmpQR2G5D\downloaded_packages
#> installing the source packages 'pillar', 'EML'
#> Running `R CMD build`...
#> * checking for file 'C:\Users\salvadorf\AppData\Local\Temp\RtmpQR2G5D\remotes415c3b2eb85\lifewatch-eurobis-3ae735c/DESCRIPTION' ... OK
#> * preparing 'eurobis':
#> * checking DESCRIPTION meta-information ... OK
#> * checking for LF line-endings in source and make files and shell scripts
#> * checking for empty or unneeded directories
#> * building 'eurobis_0.0.0.9000.tar.gz'
#> Installing package into 'C:/Users/salvadorf/AppData/Local/Temp/RtmpyQPd6y/reprex44b06ebe3f0e/renv/library/R-4.0/x86_64-w64-mingw32'
#> (as 'lib' is unspecified)

library(eurobis)
#> Error: package or namespace load failed for 'eurobis' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
#>  there is no package called 'RCurl'

# Install missing package 1
install.packages('RCurl')
#> Installing bitops [1.0-6] ...
#>  OK [linked cache]
#> Installing RCurl [1.98-1.2] ...
#>  OK [linked cache]

library(eurobis)
#> Registered S3 method overwritten by 'finch':
#>   method         from 
#>   print.location dplyr
#> Error: package or namespace load failed for 'eurobis' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
#>  there is no package called 'imis'

# Install missing package 2

remotes::install_github("vlizBE/imis") 
#> Downloading GitHub repo vlizBE/imis@HEAD
#> Warning in untar2(tarfile, files, list, exdir, restore_times): skipping pax
#> global extended headers

#> Warning in untar2(tarfile, files, list, exdir, restore_times): skipping pax
#> global extended headers
#> sys     (NA    -> 3.4  ) [CRAN]
#> askpass (NA    -> 1.1  ) [CRAN]
#> tibble  (3.0.6 -> 3.1.0) [CRAN]
#> openssl (NA    -> 1.4.3) [CRAN]
#> httr    (NA    -> 1.4.2) [CRAN]
#> Installing 5 packages: sys, askpass, tibble, openssl, httr
#> Installing packages into 'C:/Users/salvadorf/AppData/Local/Temp/RtmpyQPd6y/reprex44b06ebe3f0e/renv/library/R-4.0/x86_64-w64-mingw32'
#> (as 'lib' is unspecified)
#> 
#>   There is a binary version available but the source version is later:
#>        binary source needs_compilation
#> tibble  3.0.6  3.1.0              TRUE
#> 
#>   Binaries will be installed
#> package 'sys' successfully unpacked and MD5 sums checked
#> package 'askpass' successfully unpacked and MD5 sums checked
#> package 'tibble' successfully unpacked and MD5 sums checked
#> Error: Failed to install 'imis' from GitHub:
#>   (converted from warning) cannot remove prior installation of package 'tibble'

library(eurobis)
#> Error: package or namespace load failed for 'eurobis' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
#>  there is no package called 'imis'

# And continue...

# Session info for reproducibility
sessionInfo()
#> Warning in FUN(X[[i]], ...): DESCRIPTION file of package 'tibble' is missing or
#> broken
#> R version 4.0.2 (2020-06-22)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows 10 x64 (build 18363)
#> 
#> Matrix products: default
#> 
#> locale:
#> [1] LC_COLLATE=English_United States.1252 
#> [2] LC_CTYPE=English_United States.1252   
#> [3] LC_MONETARY=English_United States.1252
#> [4] LC_NUMERIC=C                          
#> [5] LC_TIME=English_United States.1252    
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#> Error in x[["Version"]]: subscript out of bounds

Created on 2021-03-01 by the reprex package (v1.0.0)

salvafern commented 2 years ago

imis dependency removed since f2131f30c35cebd5ae5757a9e877ca7cc59bcefe. As we say in Spanish: Muerto el perro, se acabó la rabia 😄