Resolving "non-zero exit status"

[DWArren314]

I am trying to install the "spocc" package to conduct some GIS-based analysis using species occurrence data. I have tried to follow the installation guides provided online, but continue to fail to install the package. Whenever I try to install the package, a number of the dependencies, including "rvertnet", "rbison" and "rgbif" are flagged as having a "non-zero exit status".... Having spoken to other R-users, they too appear to have the same issues. Could you please recommend a workaround for this issue? Thank you.

remotes::install_github('ropensci/spocc') # alternative pathway # Can't get to install, try to install independent packages, then reload Downloading GitHub repo ropensci/spocc@HEAD These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: wellknown (0.6.0 -> 0.7.4) [CRAN]

Enter one or more numbers, or an empty line to skip updates: Installing 3 packages: rvertnet, rbison, rgbif Installing packages into ‘C:/Users/User/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) also installing the dependency ‘wellknown’

There are binary versions available but the source versions are later: binary source needs_compilation wellknown 0.6.0 0.7.4 TRUE rvertnet 0.8.0 0.8.2 FALSE rbison 0.8.0 1.0.0 FALSE rgbif 2.2.0 3.6.0 FALSE

Binaries will be installed trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/wellknown_0.6.0.zip' Content type 'application/zip' length 582990 bytes (569 KB) downloaded 569 KB

package ‘wellknown’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\User\AppData\Local\Temp\RtmpAvT46Q\downloaded_packages installing the source packages ‘rvertnet’, ‘rbison’, ‘rgbif’

trying URL 'https://cran.rstudio.com/src/contrib/rvertnet_0.8.2.tar.gz' Content type 'application/x-gzip' length 768107 bytes (750 KB) downloaded 750 KB

trying URL 'https://cran.rstudio.com/src/contrib/rbison_1.0.0.tar.gz' Content type 'application/x-gzip' length 1726473 bytes (1.6 MB) downloaded 1.6 MB

trying URL 'https://cran.rstudio.com/src/contrib/rgbif_3.6.0.tar.gz' Content type 'application/x-gzip' length 3612058 bytes (3.4 MB) downloaded 3.4 MB

• installing source package 'rvertnet' ... ** package 'rvertnet' successfully unpacked and MD5 sums checked ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'rvertnet' finding HTML links ... done bigsearch html
  dump-defunct html
  rvertnet-defunct html
  rvertnet-package html
  searchbyterm html
  spatialsearch html
  traitsearch html
  vert_id html
  vertavailablemaps-defunct html
  vertlocations-defunct html
  vertmap html
  vertoccurrence-defunct html
  vertoccurrencecount-defunct html
  vertproviders-defunct html
  vertsearch html
  vertsummary html
  verttaxa-defunct html
  *** copying figures ** building package indices ** testing if installed package can be loaded *** arch - i386 Error: package or namespace load failed for 'rvertnet' in library.dynam(lib, package, package.lib): DLL 'maps' not found: maybe not installed for this architecture? Error: loading failed Execution halted *** arch - x64 ERROR: loading failed for 'i386'
• removing 'C:/Users/User/Documents/R/win-library/3.5/rvertnet' In R CMD INSTALL
• installing source package 'rbison' ... ** package 'rbison' successfully unpacked and MD5 sums checked ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'rbison' finding HTML links ... done all_states html
  bison html
  bison_datause html
  bison_providers html
  bison_solr html
  bison_stats html
  bison_tax html
  bisonmap html
  fips html
  is.bison html
  is.bison_solr html
  rbison-package html
  *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded *** arch - i386 Error: package or namespace load failed for 'rbison' in library.dynam(lib, package, package.lib): DLL 'maps' not found: maybe not installed for this architecture? Error: loading failed Execution halted *** arch - x64 ERROR: loading failed for 'i386'
• removing 'C:/Users/User/Documents/R/win-library/3.5/rbison' In R CMD INSTALL
• installing source package 'rgbif' ... ** package 'rgbif' successfully unpacked and MD5 sums checked ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace 'wellknown' 0.6.0 is being loaded, but >= 0.7.2 is required ERROR: lazy loading failed for package 'rgbif'
• removing 'C:/Users/User/Documents/R/win-library/3.5/rgbif' In R CMD INSTALL

The downloaded source packages are in ‘C:\Users\User\AppData\Local\Temp\RtmpAvT46Q\downloaded_packages’ √ checking for file 'C:\Users\User\AppData\Local\Temp\RtmpAvT46Q\remotesf84332b17b3\ropensci-spocc-ae4f55f/DESCRIPTION'

• preparing 'spocc': (515ms) √ checking DESCRIPTION meta-information ...
• checking for LF line-endings in source and make files and shell scripts
• checking for empty or unneeded directories Removed empty directory 'spocc/inst' Removed empty directory 'spocc/vignettes'
• building 'spocc_1.2.0.91.tar.gz'

Installing package into ‘C:/Users/User/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) ERROR: dependencies 'rgbif', 'rbison', 'rvertnet' are not available for package 'spocc'

• removing 'C:/Users/User/Documents/R/win-library/3.5/spocc' In R CMD INSTALL Warning messages: 1: In i.p(...) : installation of package ‘rvertnet’ had non-zero exit status 2: In i.p(...) : installation of package ‘rbison’ had non-zero exit status 3: In i.p(...) : installation of package ‘rgbif’ had non-zero exit status 4: In i.p(...) : installation of package ‘C:/Users/User/AppData/Local/Temp/RtmpAvT46Q/filef8450765237/spocc_1.2.0.91.tar.gz’ had non-zero exit status

[hannahlowens]

Hi, It looks like there is another package, "wellknown", that needs to be updated as well. Could you try that and let me know if it works?

Thanks, Hannah