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Resolving "non-zero exit status" #248

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DWArren314 opened this issue Dec 9, 2021 · 1 comment
Open

Resolving "non-zero exit status" #248

DWArren314 opened this issue Dec 9, 2021 · 1 comment

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@DWArren314
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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
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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

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