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rosemckeon / ploidy

How does disturbance on a landscape affect the establishment of new polyploid plant species?
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Make package install without errors #77

Closed rosemckeon closed 5 years ago

rosemckeon commented 5 years ago 
Downloading GitHub repo rozeykex/ploidy@rose
Error in get0(oNam, envir = ns) : 
  lazy-load database '/home/rose/R/x86_64-pc-linux-gnu-library/3.4/callr/R/callr.rdb' is corrupt
In addition: Warning messages:
1: In is.na(remote_deps$package) :
  is.na() applied to non-(list or vector) of type 'NULL'
2: In get0(oNam, envir = ns) : restarting interrupted promise evaluation
3: In get0(oNam, envir = ns) : internal error -3 in R_decompress1
bradduthie commented 5 years ago

@rozeykex Tried to install from GitHub with devtools. This was the error for me:

> library(devtools)
> install_github("rozykex/ploidy@rose")
Downloading GitHub repo rozykex/ploidy@rose
from URL https://api.github.com/repos/rozykex/ploidy/zipball/rose
Installation failed: Not Found (404)

Might need to be in Master? Should I approve the merge?

rosemckeon commented 5 years ago

@bradduthie I tried with this command:

install_github("rozeykex/ploidy", ref = "rose", auth_token = "a special pat token I set up on my account to access private repositories")

If you run it without the token you should get an error that links to where to set one up.

I might not have given the token the right permissions?

All that said, yes - approve the merge! (I should have done the anlaysis on a separate branch - d'oh).

rosemckeon commented 5 years ago

Installs now, just with warnings:

─  preparing ‘disturploidy’:
✔  checking DESCRIPTION meta-information
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘disturploidy_0.0.0005.tar.gz’

Installing package into ‘/home/rose/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
* installing *source* package ‘disturploidy’ ...
** R
** preparing package for lazy loading
** help
Warning: /tmp/Rtmpq0vkJH/R.INSTALL1e5621ec7316/disturploidy/man/hard_select.Rd:18: unexpected section header '\value'
Warning: /tmp/Rtmpq0vkJH/R.INSTALL1e5621ec7316/disturploidy/man/hard_select.Rd:21: unexpected section header '\description'
Warning: /tmp/Rtmpq0vkJH/R.INSTALL1e5621ec7316/disturploidy/man/hard_select.Rd:24: unexpected section header '\author'
Warning: /tmp/Rtmpq0vkJH/R.INSTALL1e5621ec7316/disturploidy/man/hard_select.Rd:27: unexpected END_OF_INPUT '
'
Warning: /tmp/Rtmpq0vkJH/R.INSTALL1e5621ec7316/disturploidy/man/survive.Rd:16: unexpected section header '\value'
Warning: /tmp/Rtmpq0vkJH/R.INSTALL1e5621ec7316/disturploidy/man/survive.Rd:19: unexpected section header '\description'
Warning: /tmp/Rtmpq0vkJH/R.INSTALL1e5621ec7316/disturploidy/man/survive.Rd:22: unexpected section header '\author'
Warning: /tmp/Rtmpq0vkJH/R.INSTALL1e5621ec7316/disturploidy/man/survive.Rd:25: unexpected END_OF_INPUT '
'
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (disturploidy)
Warning message:
In is.na(remote_deps$package) :
  is.na() applied to non-(list or vector) of type 'NULL'
bradduthie commented 5 years ago

Doesn't seem to like the roxygen headings? See here for an example @rozeykex -- author might not be recognised, and description might take a slightly different format?

rosemckeon commented 5 years ago

@bradduthie It's the % symbols in the parameter explanations! I must need to escape them - just removed for now.

rosemckeon commented 5 years ago

not sure about that last part though 

Warning message:
In is.na(remote_deps$package) :
  is.na() applied to non-(list or vector) of type 'NULL'