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mcglinnlab / soar

SOAR: species occurrence aggregator in R
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install errors #19

Open dmcglinn opened 5 years ago

dmcglinn commented 5 years ago

Hey @AshleyWoods I'm getting some install errors:

library(devtools)
install_github('mcglinnlab/soar')
** byte-compile and prepare package for lazy loading
Error : 401 - Unauthorized
Error : unable to load R code in package ‘soar’
ERROR: lazy loading failed for package ‘soar’
* removing ‘/home/mcglinnd/R/x86_64-pc-linux-gnu-library/3.5/soar’
Error in i.p(...) : 
  (converted from warning) installation of package ‘/tmp/RtmpRsFxZD/file950a6903677a/soar_0.0.0.1.tar.gz’ had non-zero exit status

Can you please see if you get the same errors, thanks!

AshleyWoods commented 5 years ago

My problem seems to be coming from the package "digest" Are all your packages updated? Because I can't get any of mine to update.

dmcglinn commented 5 years ago

ahh ok I think maybe the problem is that the required packages are not listed in the DESCRIPTION file under a section called imports: http://r-pkgs.had.co.nz/description.html

So in our DESCRIPTION file we should rename the field depends to imports and add the missing packages.

AshleyWoods commented 5 years ago

Maybe, but it tried to update my packages as it was installed, but the digest package won't update correctly.

AshleyWoods commented 5 years ago

It could also be due to an old version of R studio or R. That's what the internet says at least.

AshleyWoods commented 5 years ago

I just tried on the Uniola server and mine is mentioning this:

Downloading GitHub repo mcglinnlab/soar@master
✔  checking for file ‘/tmp/Rtmpyn6PiE/remotes68c072e067df/mcglinnlab-soar-64a218e/DESCRIPTION’ ...
─  preparing ‘soar’:
✔  checking DESCRIPTION meta-information ...
─  excluding invalid files
   Subdirectory 'R' contains invalid file names:
     ‘0019554-181003121212138.zip’ ‘0019660-190415153152247.zip’
     ‘full_GBIF_mapfetch.grd’ ‘full_GBIF_mapfetch.gri’
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘soar_0.0.0.1.tar.gz’

Installing package into ‘/home/woodsae/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
* installing *source* package ‘soar’ ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Error : 401 - Unauthorized
Error : unable to load R code in package ‘soar’
ERROR: lazy loading failed for package ‘soar’
* removing ‘/home/woodsae/R/x86_64-pc-linux-gnu-library/3.5/soar’
Error in i.p(...) : 
  (converted from warning) installation of package ‘/tmp/Rtmpyn6PiE/file68c06d8bcac5/soar_0.0.0.1.tar.gz’ had non-zero exit stat

I think the biggest thing here is: ─ excluding invalid files Subdirectory 'R' contains invalid file names: ‘0019554-181003121212138.zip’ ‘0019660-190415153152247.zip’ ‘full_GBIF_mapfetch.grd’ ‘full_GBIF_mapfetch.gri’

These are necessary files in some cases, though it shouldn't be a problem until the line mentioning them is run. Do you think this might be causing the errors? I googled the 401 error as well and it usually brings up a Twitter R package where people have either not installed the right packages or have entered the wrong username/password. Is this relevant?

AshleyWoods commented 5 years ago

It is possible that only R files can be in the R folder? If so, it's going to be trickier to use these files.

dmcglinn commented 5 years ago

I think that is the reason it won't install. I believe there is a work around here where you tell the R installer to ignore specific files. I can look into this. For the time being though it seems like all the code is working when I clone the repo.

The 401 error sounds like maybe its trying to ping off a website that is firewalled. I'm not too sure about that.