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traitecoevo / taxonlookup

A versioned and dynamically updating taxonomic lookup table for land plants
http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12517/abstract
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Skipping 1 packages not available: storr #16

Closed rossmounce closed 8 years ago

rossmounce commented 8 years ago

I'm having trouble installing. Apologies if I misread the install instructions.

R version 3.2.2 (2015-08-14) -- "Fire Safety" Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit)

> devtools::install_github("hadley/httr")
Downloading GitHub repo hadley/httr@master
Installing httr
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore CMD INSTALL  \
  '/tmp/Rtmp4KqYYz/devtools4fc633f6c2aa/hadley-httr-733530e'  \
  --library='/home/ross/R/x86_64-pc-linux-gnu-library/3.2' --install-tests 

* installing *source* package ‘httr’ ...
** R
** demo
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (httr)
> devtools::install_github("richfitz/storr")
Downloading GitHub repo richfitz/storr@master
Installing storr
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore CMD INSTALL  \
  '/tmp/Rtmp4KqYYz/devtools4fc626a56a1b/richfitz-storr-b1f420b'  \
  --library='/home/ross/R/x86_64-pc-linux-gnu-library/3.2' --install-tests 

* installing *source* package ‘storr’ ...
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (storr)
> devtools::install_github("wcornwell/taxonlookup")
Downloading GitHub repo wcornwell/taxonlookup@master
Installing taxonlookup
Skipping 1 packages not available: storr
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore CMD INSTALL  \
  '/tmp/Rtmp4KqYYz/devtools4fc6144f9aab/traitecoevo-taxonlookup-311248c'  \
  --library='/home/ross/R/x86_64-pc-linux-gnu-library/3.2' --install-tests 

* installing *source* package ‘taxonlookup’ ...
** R
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (taxonlookup)
> library(taxonlookup)
> lookup_table(c("Pinus ponderosa","Quercus agrifolia"),by_species=TRUE)
Error in plant_lookup_get(version) : 
  could not find function "github_release_storr_get"
richfitz commented 8 years ago

Hi Ross, sorry you've caught the packages in a bit of a state of flux with some breaking changes I'd hoped to get squared away before anyone would notice.

Short story; install the old version of storr for now:

devtools::install_github("richfitz/storr@f95ee2ef")
devtools::install_github("traitecoevo/taxonlookup")

After that:

> taxonlookup::lookup_table(c("Pinus ponderosa","Quercus agrifolia"),by_species=TRUE)
  |======================================================================| 100%
                    genus   family   order       group
Pinus ponderosa     Pinus Pinaceae Pinales Gymnosperms
Quercus agrifolia Quercus Fagaceae Fagales Angiosperms

I've just tested with your example above and that will work.

Longer version:

I'm spinning the data caching part of this out at the moment (literally working on this right now) in preparation for pushing storr onto CRAN without the support that taxonlookup needs, and putting that into a new package (currently dataverse but soon to be renamed). Then I'll backport to get taxonlook working :sweat:

:deciduous_tree: :evergreen_tree: :tulip:

rossmounce commented 8 years ago

I think I might be stuck in some kind of dependency no man's land, behind with storr but ahead with httr ? Or does my RStudio just need a restart?

devtools::install_github("richfitz/storr@f95ee2ef")
Downloading GitHub repo richfitz/storr@f95ee2ef
Installing storr
Skipping 1 packages ahead of CRAN: httr
Installing 1 packages: rappdirs
Installing package into ‘/home/ross/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
--2015-12-08 16:56:31--  https://cran.rstudio.com/src/contrib/rappdirs_0.3.tar.gz
Resolving cran.rstudio.com (cran.rstudio.com)... 54.230.9.253
Connecting to cran.rstudio.com (cran.rstudio.com)|54.230.9.253|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 12732 (12K) [application/x-gzip]
Saving to: ‘/tmp/RtmpjGMh0G/downloaded_packages/rappdirs_0.3.tar.gz’

     0K .......... ..                                         100% 84.5M=0s

2015-12-08 16:56:31 (84.5 MB/s) - ‘/tmp/RtmpjGMh0G/downloaded_packages/rappdirs_0.3.tar.gz’ saved [12732/12732]

* installing *source* package ‘rappdirs’ ...
** package ‘rappdirs’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c win-path.c -o win-path.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o rappdirs.so win-path.o -L/usr/lib/R/lib -lR
installing to /home/ross/R/x86_64-pc-linux-gnu-library/3.2/rappdirs/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (rappdirs)

The downloaded source packages are in
    ‘/tmp/RtmpjGMh0G/downloaded_packages’
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore CMD INSTALL  \
  '/tmp/RtmpjGMh0G/devtools5315546a497d/richfitz-storr-f95ee2e'  \
  --library='/home/ross/R/x86_64-pc-linux-gnu-library/3.2' --install-tests 

* installing *source* package ‘storr’ ...
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (storr)
> devtools::install_github("traitecoevo/taxonlookup")
Downloading GitHub repo traitecoevo/taxonlookup@master
Installing taxonlookup
Skipping 1 packages not available: storr
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore CMD INSTALL  \
  '/tmp/RtmpjGMh0G/devtools5315aaa5c7e/traitecoevo-taxonlookup-311248c'  \
  --library='/home/ross/R/x86_64-pc-linux-gnu-library/3.2' --install-tests 

* installing *source* package ‘taxonlookup’ ...
** R
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (taxonlookup)
> library(taxonlookup)
> 
> lookup_table(c("Pinus ponderosa","Quercus agrifolia"),by_species=TRUE)
Error in plant_lookup_get(version) : 
  could not find function "github_release_storr_get"
richfitz commented 8 years ago

Probably just an Rstudio restart (once a package is loaded a restart seems the best way of ensuring that newer versions are loaded). The messages:

Skipping 1 packages ahead of CRAN: httr

and

Skipping 1 packages not available: storr

are a new devtools feature I think. Not entirely sure what they're up to, but I think it now tries to upgrade all packages that are depended on.

rossmounce commented 8 years ago

working now! Many thanks :)