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NEONScience / NEON-utilities

Utilities and scripts for working with NEON data. Currently: an R package with functions to join (stack) the month-by-site files in downloaded NEON data, to convert data to geoCSV format, and to download data from the API.
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neonUtilities Install Errors and Warnings #56

Closed keramsey closed 5 years ago

keramsey commented 5 years ago

Function Which of the functions in the neonUtilities package is this bug found in? no package called 'hms'

Describe the bug I receive the following errors when attempting to install neonUtilities: Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called 'hms' ERROR: lazy loading failed for package 'neonUtilities'

The downloaded source packages are in ‘C:\Users\\AppData\Local\Temp\RtmpSGzwFh\downloaded_packages’ Warning messages: 1: running command '"C:/PROGRA~1/R/R-34~1.0/bin/x64/R" CMD INSTALL -l "C:\Users\\Documents\R\win-library\3.4" C:\Users\\AppData\Local\Temp\RtmpSGzwFh/downloaded_packages/hms_0.5.0.tar.gz' had status 1 2: In install.packages("neonUtilities") : installation of package ‘hms’ had non-zero exit status 3: running command '"C:/PROGRA~1/R/R-34~1.0/bin/x64/R" CMD INSTALL -l "C:\Users\\Documents\R\win-library\3.4" C:\Users\\AppData\Local\Temp\RtmpSGzwFh/downloaded_packages/neonUtilities_1.3.1.tar.gz' had status 1 4: In install.packages("neonUtilities") : installation of package ‘neonUtilities’ had non-zero exit status To Reproduce What function inputs revealed the bug? install.packages('neonUtilities') library(neonUtilities) Expected behavior A clear and concise description of what you expected to happen. I expected that neonUtilities would finish installing without errors. System (please complete the following information):

Additional context Add any other context about the problem here.

cklunch commented 5 years ago

It looks to me like this is a problem with the paths on your machine. My best guess is that it's trying to install from a location other than CRAN, and can't find hms there. Try running options()$repos to see where the global option for repositories is pointing, and if it isn't CRAN, redirect it there.

keramsey commented 5 years ago

Hi,

I edited the paths to remove my account name. I picked a CRAN repository in Texas from with R.

I reran the install and picked the 0-cloud CRAN repository and I receive the following output:

install.packages('neonUtilities') Installing package into ‘C:/Users//Documents/R/win-library/3.4’ (as ‘lib’ is unspecified) --- Please select a CRAN mirror for use in this session ---

There is a binary version available but the source version is later: binary source needs_compilation neonUtilities 1.2.1 1.3.1 FALSE

installing the source package ‘neonUtilities’

trying URL 'https://cloud.r-project.org/src/contrib/neonUtilities_1.3.1.tar.gz' Content type 'application/x-gzip' length 125297 bytes (122 KB) downloaded 122 KB

The downloaded source packages are in

‘C:\Users\\AppData\Local\Temp\RtmpsT0MT4\downloaded_packages’ Warning messages: 1: running command '"C:/PROGRA~1/R/R-34~1.0/bin/x64/R" CMD INSTALL -l "C:\Users\\Documents\R\win-library\3.4" C:\Users\\AppData\Local\Temp\RtmpsT0MT4/downloaded_packages/neonUtilities_1.3.1.tar.gz' had status 1 2: In install.packages("neonUtilities") : installation of package ‘neonUtilities’ had non-zero exit status

Here is the output of the options($repos) command on the second attempt: CRAN
CRANextra "https://cloud.r-project.org" "http://www.stats.ox.ac.uk/pub/RWin"

Do I need to update R?

Thanks.

Ken

Claire Lunch notifications@github.com 2019-08-14 12:50 PM >>> It looks to me like this is a problem with the paths on your machine. My best guess is that it's trying to install from a location other than CRAN, and can't find hms there. Try running options()$repos to see where the global option for repositories is pointing, and if it isn't CRAN, redirect it there.

-- You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub: https://github.com/NEONScience/NEON-utilities/issues/56#issuecomment-521371670

cklunch commented 5 years ago

Hmm. You may end up needing to update to R 3.6, but it also might be that the repos you're using arent fully up to date. Try this: install.packages("neonUtilities", repos="https://cran.rstudio.com/")

keramsey commented 5 years ago

I tried installing the hms package and received an error stating that a dependent package, vctrs, needed to be 0.2.0 or higher but the installed version was 0.1.0. I tried installing vctrs using type=source and it failed with errors. Perhaps, I need devtools? I used the cran.rstudio.com repository when installing the packages.

I then updated R from 3.4.0 to 3.6.1 and installed neonUtilities. It seems to load the neonUtilities library without errors. I assume that neonUtilities installed properly.

Is there a way to test the installation?

Feel free to close this ticket.

Claire Lunch notifications@github.com 2019-08-14 02:37 PM >>> Hmm. You may end up needing to update to R 3.6, but it also might be that the repos you're using arent fully up to date. Try this: install.packages("neonUtilities", repos="https://cran.rstudio.com/")

-- You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub: https://github.com/NEONScience/NEON-utilities/issues/56#issuecomment-521409092

keramsey commented 5 years ago

Updating to R 3.6.1 seems to have fixed my installation issues.

cklunch commented 5 years ago

Great, glad to hear it!