def.format.sdg function

[jbeaulie]

This function calls a function from the neonDataStackR package, which isn't available on CRAN. This package needs to be made available to user.

[kcawley]

I fixed up the importing so that you shouldn't need to install neonDataStackR separately if you install this package using the following procedure. If it still doesn't work I'll have to look into how to better set up the dependencies.
install.packages("devtools")
library(devtools)
install_github("NEONScience/neonDissGas")

[jbeaulie]

This failed for me:

install.packages("devtools")
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/devtools_1.13.3.zip'
Content type 'application/zip' length 440079 bytes (429 KB)
downloaded 429 KB

package ‘devtools’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\JBEAULIE\AppData\Local\Temp\RtmpYX2B1u\downloaded_packages

library(devtools)
Warning message:
package ‘devtools’ was built under R version 3.3.3
install_github("NEONScience/neonDissGas")
Downloading GitHub repo NEONScience/neonDissGas@master
from URL https://api.github.com/repos/NEONScience/neonDissGas/zipball/master
Installation failed: Not Found (404)

sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] devtools_1.13.3

loaded via a namespace (and not attached):
[1] httr_1.2.1 R6_2.1.3 tools_3.3.0 withr_1.0.2 curl_2.4 memoise_1.0.0
[7] git2r_0.18.0 jsonlite_1.4 digest_0.6.12

[kcawley]

@jbeaulie
try the following, I think I forgot to include the "NEON-dissolved-gas" part!
install_github("NEONScience/NEON-dissolved-gas/neonDissGas")

[jbeaulie]

It seems we are still missing something.

install_github("NEONScience/NEON-dissolved-gas/neonDissGas")
Downloading GitHub repo NEONScience/NEON-dissolved-gas@master
from URL https://api.github.com/repos/NEONScience/NEON-dissolved-gas/zipball/master
Installing neonDissGas
"C:/PROGRA1/R/R-341.0/bin/x64/R" --no-site-file --no-environ --no-save --no-restore
--quiet CMD INSTALL
"C:/Users/JBEAULIE/AppData/Local/Temp/Rtmp8wTXzv/devtools56c4e6e1eb0/NEONScience-NEON-dissolved-gas-253fab7/neonDissGas"
--library="C:/Program Files/R/R-3.4.0/library" --install-tests

ERROR: dependency 'neonDataStackR' is not available for package 'neonDissGas'

• removing 'C:/Program Files/R/R-3.4.0/library/neonDissGas'
  Installation failed: Command failed (1)

session_info()
Session info --------------------------------------------------------------------------------
setting value
version R version 3.4.0 (2017-04-21)
system x86_64, mingw32
ui RStudio (1.0.143)
language (EN)
collate English_United States.1252
tz America/New_York
date 2017-09-29

Packages ------------------------------------------------------------------------------------
package * version date source
base * 3.4.0 2017-04-21 local
compiler 3.4.0 2017-04-21 local
curl 2.8.1 2017-07-21 CRAN (R 3.4.1)
datasets * 3.4.0 2017-04-21 local
devtools * 1.13.3 2017-08-02 CRAN (R 3.4.1)
digest 0.6.12 2017-01-27 CRAN (R 3.4.1)
git2r 0.19.0 2017-07-19 CRAN (R 3.4.1)
graphics * 3.4.0 2017-04-21 local
grDevices * 3.4.0 2017-04-21 local
httr 1.3.1 2017-08-20 CRAN (R 3.4.1)
memoise 1.1.0 2017-04-21 CRAN (R 3.4.1)
methods * 3.4.0 2017-04-21 local
R6 2.2.2 2017-06-17 CRAN (R 3.4.1)
stats * 3.4.0 2017-04-21 local
tools 3.4.0 2017-04-21 local
utils * 3.4.0 2017-04-21 local
withr 2.0.0 2017-07-28 CRAN (R 3.4.1)

[cklunch]

I'm looking into it. Thanks for trying out this code!

[jbeaulie]

@kcawley @cklunch

OK, your update to the DESCRIPTION files seems to have done the trick. Now I can install the package and access the functions, but I"m still having trouble with the def.format.sdg function. Should I apply this function to the NEON-dissolved-gas/neonDissGas/inst/extdata directory? I assume this directory contains example datasets pulled from NEON data portal. Do all the files need to be unzipped first?

[kcawley]

@jbeaulie You shouldn't need to unzip the files first. The input for def.format.sdg should be in the form of the path to the zipped folder plus the zipped folder, e.g. "~/Downloads/NEON_dissolved-gases-surfacewater.zip"

[jbeaulie]

@kcawley @cklunch

Ok, getting closer. Here is the most recent error:

library(neonDissGas)
def.format.sdg("C:/Users/JBEAULIE/GitRepository/NEON-dissolved-gas/neonDissGas/inst/extdata/NEON_dissolved-gases-surfacewater.zip")
Unpacked NEON.D01.HOPB.DP1.20097.001.2016-09.expanded.20170705T171439Z.zip
Unpacked NEON.D01.HOPB.DP1.20097.001.2016-10.expanded.20170705T171457Z.zip
Unpacked NEON.D01.HOPB.DP1.20097.001.2016-11.expanded.20170705T170913Z.zip
Unpacked NEON.D01.HOPB.DP1.20097.001.2016-12.expanded.20170705T170516Z.zip
Unpacked NEON.D03.BARC.DP1.20097.001.2016-07.expanded.20170705T170424Z.zip
Unpacked NEON.D03.BARC.DP1.20097.001.2016-08.expanded.20170705T170807Z.zip
Unpacked NEON.D03.BARC.DP1.20097.001.2016-09.expanded.20170705T170617Z.zip
Unpacked NEON.D03.BARC.DP1.20097.001.2016-10.expanded.20170705T171631Z.zip
Unpacked NEON.D03.BARC.DP1.20097.001.2016-11.expanded.20170705T171645Z.zip
Unpacked NEON.D03.BARC.DP1.20097.001.2016-12.expanded.20170705T171518Z.zip
Error in stackDataFiles(location.data) : object 'table_types' not found

[cklunch]

@jbeaulie
I got that error a couple of days ago and had to re-install neonDataStackR. If you re-install neonDissGas, I think it will also grab the newest version of neonDataStackR. If not, we'll need to look into it.

Sorry, this is the nature of NEON code at this stage, we're constantly updating and revising these packages!

[jbeaulie]

@cklunch
Same result on 2/7/2018.

[kcawley]

@jbeaulie Try adding the following line before you fun the package. Sometimes it won't re-install even though there are changes if I don't set force = T.
install_github("NEONScience/NEON-utilities/neonDataStackR", force = T)

[kcawley]

@jbeaulie Try running the code in "installingPackages.R" to install the required packages to run the code here. The neonDataStackR has been replaces by the neonUtilities package.