Closed ahhurlbert closed 8 years ago
ethanwhite
commented
8 years ago Looks like maybe you both have an old cached version of the gentry script. Try running
retriever reset scriptsfrom the command line and then updating the scripts using either
retriever updatefrom the command line or
get_updates()from R.
henrykironde
commented
8 years ago was wondering if that has anything to do with the Cedral site BLOHMR site data
ethanwhite
commented
8 years ago was wondering if that has anything to do with the Cedral site BLOHMR site data
I suspect it's just residual issues from https://github.com/weecology/retriever/issues/402, but we'll know if it's something trickier once they try the reset.
ahhurlbert
commented
8 years ago Ok, I'm on a different outdated machine at the moment. In R I tried ecoretriever::fetch('BBS50') and it downloaded only the species and routes files. So clearly an old install (I think 1.7.0)
In the command line, I reinstalled using pip, then retriever reset scripts and retriever update. Things seemed to go ok, and I can see the scripts file has all newly downloaded scripts in it.
But in R, I get the same problem as before (and it looks like get_updates() isn't quite working properly):
> get_updates()
Please wait while the retriever updates its scripts, ...
The retriever scripts are up-to-date with the most recent official release!
Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) :
'x' must be atomic
> mcg = ecoretriever::fetch('McGlinn2010')
Failed to load script: gentry (C:/Users/hurlbert/Documents/.retriever/scripts/)I'll note that I closed out of both RStudio and Git Bash and then reopened them before trying this.
ethanwhite
commented
8 years ago OK, thanks.
Can you paste the output of retriever --version here and attach the ~/.retriever/scripts/gentry.py file?
ahhurlbert
commented
8 years ago Ok, back on my original machine--same result as above.
$ retriever --version
v1.8.3gentry.py:
#retriever
"""Retriever script for Alwyn H. Gentry Forest Transect Dataset
"""
import os
import sys
import zipfile
import xlrd
from retriever.lib.templates import Script
from retriever.lib.models import Table
from retriever.lib.excel import Excel
VERSION = '1.0.1'
TAX_GROUPS = 9756 #9819
class main(Script):
def __init__(self, **kwargs):
Script.__init__(self, **kwargs)
self.name = "Alwyn H. Gentry Forest Transect Dataset"
self.shortname = "Gentry"
self.urls = {"stems": "http://www.mobot.org/mobot/gentry/123/all_Excel.zip",
"sites": "http://www.ecologicaldata.org/sites/default/files/gentry_sites_data.txt",
"species": "",
"counts": ""}
self.tags = ["Taxon > Plants", "Spatial Scale > Global",
"Data Type > Observational"]
self.ref = "http://www.wlbcenter.org/gentry_data.htm"
self.addendum = """Researchers who make use of the data in publications are requested to acknowledge Alwyn H. Gentry, the Missouri Botanical Garden, and collectors who assisted Gentry or contributed data for specific sites. It is also requested that a reprint of any publication making use of the Gentry Forest Transect Data be sent to:
Bruce E. Ponman
Missouri Botanical Garden
P.O. Box 299
St. Louis, MO 63166-0299
U.S.A. """
def download(self, engine=None, debug=False):
Script.download(self, engine, debug)
self.engine.auto_create_table(Table("sites"), url=self.urls["sites"])
self.engine.insert_data_from_url(self.urls["sites"])
self.engine.download_file(self.urls["stems"], "all_Excel.zip")
local_zip = zipfile.ZipFile(self.engine.format_filename("all_Excel.zip"))
filelist = local_zip.namelist()
local_zip.close()
self.engine.download_files_from_archive(self.urls["stems"], filelist)
filelist = [os.path.basename(filename) for filename in filelist]
# Currently all_Excel.zip is missing CURUYUQU.xls
# Download it separately and add it to the file list
if not self.engine.find_file('CURUYUQU.xls'):
self.engine.download_file("http://www.mobot.org/mobot/gentry/123/samerica/CURUYUQU.xls", "CURUYUQU.xls", clean_line_endings=False)
filelist.append('CURUYUQU.xls')
lines = []
tax = []
for filename in filelist:
print "Extracting data from " + filename + "..."
book = xlrd.open_workbook(self.engine.format_filename(filename))
sh = book.sheet_by_index(0)
rows = sh.nrows
cn = {'stems': []}
n = 0
for colnum, c in enumerate(sh.row(0)):
if not Excel.empty_cell(c):
cid = Excel.cell_value(c).lower()
# line number column is sometimes named differently
if cid in ["sub", "number"]:
cid = "line"
# the "number of individuals" column is named in various
# different ways; they always at least contain "nd"
if "nd" in cid:
cid = "count"
# in QUIAPACA.xls the "number of individuals" column is
# misnamed "STEMDBH" just like the stems columns, so weep
# for the state of scientific data and then fix manually
if filename == "QUIAPACA.xls" and colnum == 13:
cid = "count"
# if column is a stem, add it to the list of stems;
# otherwise, make note of the column name/number
if "stem" in cid or "dbh" in cid:
cn["stems"].append(n)
else:
cn[cid] = n
n += 1
# sometimes, a data file does not contain a liana or count column
if not "liana" in cn.keys():
cn["liana"] = -1
if not "count" in cn.keys():
cn["count"] = -1
for i in range(1, rows):
row = sh.row(i)
cellcount = len(row)
# make sure the row is real, not just empty cells
if not all(Excel.empty_cell(cell) for cell in row):
try:
this_line = {}
def format_value(s):
s = Excel.cell_value(s)
return str(s).title().replace("\\", "/").replace('"', '')
# get the following information from the appropriate columns
for i in ["line", "family", "genus", "species",
"liana", "count"]:
if cn[i] > -1:
this_line[i] = format_value(row[cn[i]])
if this_line[i] == '`':
this_line[i] = 1
this_line["stems"] = [Excel.cell_value(row[c])
for c in cn["stems"]
if not Excel.empty_cell(row[c])]
this_line["site"] = filename[0:-4]
lines.append(this_line)
# Check how far the species is identified
full_id = 0
if len(this_line["species"]) < 3:
if len(this_line["genus"]) < 3:
id_level = "family"
else:
id_level = "genus"
else:
id_level = "species"
full_id = 1
tax.append((this_line["family"],
this_line["genus"],
this_line["species"].lower().replace('\\', '').replace('"', ''),
id_level,
str(full_id)))
except:
raise
pass
tax = sorted(tax, key=lambda group: group[0] + " " + group[1] + " " + group[2])
unique_tax = []
tax_dict = dict()
tax_count = 0
# Get all unique families/genera/species
for group in tax:
if not (group in unique_tax):
unique_tax.append(group)
tax_count += 1
tax_dict[group[0:3]] = tax_count
if tax_count % 10 == 0:
msg = "Generating taxonomic groups: " + str(tax_count) + " / " + str(TAX_GROUPS)
sys.stdout.write(msg + "\b" * len(msg))
print "Generating taxonomic groups: " + str(TAX_GROUPS) + " / " + str(TAX_GROUPS)
# Create species table
table = Table("species", delimiter=",")
table.columns=[("species_id" , ("pk-int",) ),
("family" , ("char", ) ),
("genus" , ("char", ) ),
("species" , ("char", ) ),
("id_level" , ("char", 10) ),
("full_id" , ("bool",) )]
data = [','.join([str(tax_dict[group[:3]])] + ['"%s"' % g for g in group])
for group in unique_tax]
table.pk = 'species_id'
table.contains_pk = True
self.engine.table = table
self.engine.create_table()
self.engine.add_to_table(data)
# Create stems table
table = Table("stems", delimiter=",", contains_pk=False)
table.columns=[("stem_id" , ("pk-auto",) ),
("line" , ("int",) ),
("species_id" , ("int",) ),
("site_code" , ("char", 12) ),
("liana" , ("char", 10) ),
("stem" , ("double",) )]
stems = []
counts = []
for line in lines:
try:
liana = line["liana"]
except KeyError:
liana = ""
species_info = [line["line"],
tax_dict[(line["family"],
line["genus"],
line["species"].lower())],
line["site"],
liana
]
try:
counts.append([str(value) for value in species_info + [line["count"]]])
except KeyError:
pass
for i in line["stems"]:
stem = species_info + [i]
stems.append([str(value) for value in stem])
data = [','.join(stem) for stem in stems]
self.engine.table = table
self.engine.create_table()
self.engine.add_to_table(data)
# Create counts table
table = Table("counts", delimiter=",", contains_pk=False)
table.columns=[("count_id" , ("pk-auto",) ),
("line" , ("int",) ),
("species_id" , ("int",) ),
("site_code" , ("char", 12) ),
("liana" , ("char", 10) ),
("count" , ("double",) )]
data = [','.join(count) for count in counts]
self.engine.table = table
self.engine.create_table()
self.engine.add_to_table(data)
return self.engine
SCRIPT = main()Thanks @ahhurlbert. Sorry for the delay. We're still working on this but running into some issues along the way. I can't reproduce this on Linux. I've been trying to reproduce it on Windows, but we've been running into issues with #32, which means we can't even get this far.
While we keep working on trying to reproduce can you give the current development version a try by running:
pip install git+https://github.com/weecology/retriever --upgrade
retriever reset allAlso, can you run which retriever from the command line and system('which retriever') from R and report what values they return?
ahhurlbert
commented
8 years ago Error on pip install
$ pip install git+https://github.com/weecology/retriever --upgrade
Collecting git+https://github.com/weecology/retriever
Cloning https://github.com/weecology/retriever to c:\users\hurlbert\appdata\local\temp\pip-xsdwwn-build
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "c:\users\hurlbert\appdata\local\temp\pip-xsdwwn-build\setup.py", line 25, in <module>
from __init__ import VERSION
File "__init__.py", line 8, in <module>
from builtins import str
ImportError: No module named builtins
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in c:\users\hurlbert\appdata\local\temp\pip-xsdwwn-build\so I did not run retriever reset all.
which retriever gives /c/Anaconda2/Scripts/retriever, but in R, system('which retriever') gives
Warning message:
running command 'which retriever' had status 127Agh, sorry about that. We recently broke our dependency free install apparently. We'll fix that today. In the mean time do this instead:
pip install future
pip install git+https://github.com/weecology/retriever --upgrade
retriever reset allAlso, can you report the output of these:
> system('retriever ls')
> system('ls')
> system('dir')If you're available for our regularly meeting this afternoon we can also do more poking around then.
ethanwhite
commented
8 years ago For those following along at home, @ahhurlbert & I looked at this over a screen share & found that he was, at least, having issues with #32
OK, we know have #32 fixed... hopefully. Can you run
library(devtools)
install_github('ropensci/ecoretriever')
ecoretriever::datasets()And see what happens?
ahhurlbert
commented
8 years ago I'm now back on my laptop on which I originally had this problem. I did this
pip install future
pip install git+https://github.com/weecology/retriever --upgrade
retriever reset alland then in R get the same error as before:
>ecoretriever::datasets()
...
[78] "TAXONOMY"
[79] "TIME SERIES"
[80] "Failed to load script: gentry (C:/Users/hurlbert/Documents/.retriever/scripts/)"OK, can you report the output of the following two commands?
which retrievershell('which retriever')henrykironde
commented
8 years ago I am getting the results below after running these commands.
library(devtools)
install_github("ropensci/ecoretriever",force = TRUE)
library(ecoretriever)
ecoretriever::datasets()
session_info().all the datasets are shown upto 69 when they start to fail
.
[69] "Failed to load script: bbs (C:/Users/Administrator/Documents/.retriever/scripts/)Failed to load script: bbs50stop (C:/Users/Administrator/Documents/.retriever/scripts/)Failed to load script: bioclim_2pt5 (C:/Users/Administrator/Documents/.retriever/scripts/)Failed to load script: fia (C:/Users/Administrator/Documents/.retriever/scripts/)Failed to load script: gentry (C:/Users/Administrator/Documents/.retriever/scripts/)Failed to load script: gwdd (C:/Users/Administrator/Documents/.retriever/scripts/)Failed to load script: leda (C:/Users/Administrator/Documents/.retriever/scripts/)Failed to load script: npn (C:/Users/Administrator/Documents/.retriever/scripts/)Failed to load script: prism_4km_monthly_modern (C:/Users/Administrator/Documents/.retriever/scripts/)Failed to load script: vertnet (C:/Users/Administrator/Documents/.retriever/scripts/)"
> session_info()
Session info ------------------------------------------------------------------------------------
setting value
version R version 3.2.0 (2015-04-16)
system x86_64, mingw32
ui RStudio (0.99.902)
language (EN)
collate English_United States.1252
tz America/New_York
date 2016-06-27
Packages ----------------------------------------------------------------------------------------
package * version date source
curl 0.9.7 2016-04-10 CRAN (R 3.2.5)
devtools * 1.12.0 2016-06-24 CRAN (R 3.2.5)
digest 0.6.9 2016-01-08 CRAN (R 3.2.4)
ecoretriever * 0.3.0 2016-06-28 Github (ropensci/ecoretriever@9025e1e)
git2r 0.15.0 2016-05-11 CRAN (R 3.2.5)
httr 1.2.0 2016-06-15 CRAN (R 3.2.0)
knitr 1.13 2016-05-09 CRAN (R 3.2.0)
memoise 1.0.0 2016-01-29 CRAN (R 3.2.5)
R6 2.1.2 2016-01-26 CRAN (R 3.2.5)
withr 1.0.1 2016-02-04 CRAN (R 3.2.5)
yaml 2.1.13 2014-06-12 CRAN (R 3.2.5) shell('which retriever')
/cygdrive/c/Python27/Scripts/retriever
ethanwhite
commented
8 years ago @henrykironde can you explain what you just posted a little bit? Is this the output and session info you have on your Windows machine?
henrykironde
commented
8 years ago Update: After retriever reset all the retriever on the same machine no scripts fail
henrykironde
commented
8 years ago library(ecoretriever)
ecoretriever::datasets() [1] "Available datasets : 47" "" "Adler2007"
[4] "AmnioteDB" "Anderson2011" "ArcticBreedBird"
[7] "AvianBodySize" "BAAD" "BBS"
[10] "BBS50" "Bioclim" "CForBioData"
[13] "Clark2006" "DelMoral2010" "eBirdOD"
[16] "EltonTraits" "FIA" "FishParasiteHosts"
[19] "FrayJorge" "Gentry" "GWDD"
[22] "HomeRanges" "leaf_herbivory" "leda"
[25] "MammalDIET" "MammalLH" "MammalMR2010"
[28] "mammsupertree" "MarineSize" "Matter2014"
[31] "MCDB" "McGlinn2010" "MiscAbundanceDB"
[34] "MoM2003" "NPN" "Palmer2007"
[37] "Pantheria" "Petraitis2008" "PhytoplankonBiovolume"
[40] "PlantTaxonomy" "PortalMammals" "PRISM"
[43] "Ramesh2010" "SonoranPerennials" "Steppe_plants_2013"
[46] "TreeWesternGhats" "vertnet" "Woods2009"
[49] "Zachmann2010" Ok, I'm now back on my work machine and still doesn't work, but slightly different:
> ecoretriever::datasets()
[1] "Available datasets : 45"
[2] ""
[3] "Adler2007"
[4] "AmnioteDB"
[5] "Anderson2011"
[6] "ArcticBreedBird"
[7] "AvianBodySize"
[8] "BAAD"
[9] "BBS"
[10] "BBS50"
[11] "Bioclim"
[12] "CForBioData"
[13] "Clark2006"
[14] "DelMoral2010"
[15] "eBirdOD"
[16] "EltonTraits"
[17] "FIA"
[18] "FishParasiteHosts"
[19] "FrayJorge"
[20] "GWDD"
[21] "HomeRanges"
[22] "leaf_herbivory"
[23] "MammalDIET"
[24] "MammalLH"
[25] "MammalMR2010"
[26] "mammsupertree"
[27] "MarineSize"
[28] "Matter2014"
[29] "MCDB"
[30] "McGlinn2010"
[31] "MiscAbundanceDB"
[32] "MoM2003"
[33] "NPN"
[34] "Palmer2007"
[35] "Pantheria"
[36] "Petraitis2008"
[37] "PhytoplankonBiovolume"
[38] "PlantTaxonomy"
[39] "PortalMammals"
[40] "PRISM"
[41] "Ramesh2010"
[42] "SonoranPerennials"
[43] "Steppe_plants_2013"
[44] "TreeWesternGhats"
[45] "vertnet"
[46] "Woods2009"
[47] "Zachmann2010"
[48] "Failed to load script: gentry (C:/Users/hurlbert/Documents/.retriever/scripts/)"
[49] "Exception: cannot import name ScriptTest " In both cases when I type retriever reset all and it asks if I want to proceed I type 'y' and nothing happens. I seem to recall in the past that I would see progress of redownloading scripts, or is that a faulty memory.
BTW,
$ which retriever
/c/Anaconda2/Scripts/retrieverand
> shell("which retriever")
'which' is not recognized as an internal or external command,
operable program or batch file.
Warning messages:
1: running command 'C:\Windows\system32\cmd.exe /c which retriever' had status 1
2: In shell("which retriever") :
'which retriever' execution failed with error code 1
> system("which retriever")
Warning message:
running command 'which retriever' had status 127 We can troubleshoot further over our 2pm chat...
henrykironde
commented
8 years ago you can do a reset manually by deleting the entire C:/Users/hurlbert/Documents/.retriever
ahhurlbert
commented
8 years ago Had to manually delete the Ecoretriever folder in Program Files as well as the .retriever folder mentioned above. Now, all is well!
ethanwhite
commented
8 years ago Adding a little more information in case anyone else encounters this. There were two installations of the retriever, one using the Windows installer and one using pip. The command line was finding the pip install, but the R package was finding the older Windows installer version. Once we removed the older version (having already fixed #32) everything works as expected.
dmcglinn
commented
8 years ago Big thanks to @ethanwhite for following this up and also to @ahhurlbert for reporting! I'll try to whip up #69 before CRAN submission stay tuned for future PR
ahhurlbert
commented
8 years ago I'm having a similar problem to before with reading datasets using ecoretriever in R. As suggested above I have
1) deleted all existing versions of EcoDataRetriever that I know of including folders in Program Files, Program Files (x86), /c/users/hurlbert/.retriever, /c/users/hurlbert/appdata/local/continuum/anaconda/scripts/retriever, and /c/users/hurlbert/documents/R/win-library/ecoretriever
2) reinstalled ecoretriever from scratch
pip install future
pip install git+https://github.com/weecology/retriever --upgradeafter which I get
$ pip install git+https://github.com/weecology/retriever --upgrade
Downloading/unpacking git+https://github.com/weecology/retriever
Cloning https://github.com/weecology/retriever to c:\users\hurlbert\appdata\lo
cal\temp\pip-zjnivb-build
Running setup.py (path:c:\users\hurlbert\appdata\local\temp\pip-zjnivb-build\s
etup.py) egg_info for package from git+https://github.com/weecology/retriever
C:\Users\hurlbert\AppData\Local\Continuum\Anaconda\lib\distutils\dist.py:267
: UserWarning: Unknown distribution option: 'console'
warnings.warn(msg)
C:\Users\hurlbert\AppData\Local\Continuum\Anaconda\lib\distutils\dist.py:267
: UserWarning: Unknown distribution option: 'app'
warnings.warn(msg)
C:\Users\hurlbert\AppData\Local\Continuum\Anaconda\lib\distutils\dist.py:267
: UserWarning: Unknown distribution option: 'zipfile'
warnings.warn(msg)
Compiling retriever scripts...
Adler2007 is supported by Retriever version 2.0.0-dev
Current version is v2.0.0-dev
...<all the scripts load>...
Zachmann2010 is supported by Retriever version 2.0.0-dev
Current version is v2.0.0-dev
done.
Requirement already up-to-date: xlrd in c:\users\hurlbert\appdata\local\continuu
m\anaconda\lib\site-packages (from retriever==2.0.0-de)
Requirement already up-to-date: future in c:\users\hurlbert\appdata\local\contin
uum\anaconda\lib\site-packages (from retriever==2.0.0-de)
Installing collected packages: retriever
Found existing installation: retriever 2.0.0-de
Uninstalling retriever:
Successfully uninstalled retriever
Running setup.py install for retriever
C:\Users\hurlbert\AppData\Local\Continuum\Anaconda\lib\distutils\dist.py:267
: UserWarning: Unknown distribution option: 'console'
warnings.warn(msg)
C:\Users\hurlbert\AppData\Local\Continuum\Anaconda\lib\distutils\dist.py:267
: UserWarning: Unknown distribution option: 'app'
warnings.warn(msg)
C:\Users\hurlbert\AppData\Local\Continuum\Anaconda\lib\distutils\dist.py:267
: UserWarning: Unknown distribution option: 'zipfile'
warnings.warn(msg)
Installing retriever-script.py script to C:\Users\hurlbert\AppData\Local\Con
tinuum\Anaconda\Scripts
Installing retriever.exe script to C:\Users\hurlbert\AppData\Local\Continuum
\Anaconda\Scripts
Compiling retriever scripts...
Adler2007 is supported by Retriever version 2.0.0-dev
...<all the scripts load AGAIN>...
Zachmann2010 is supported by Retriever version 2.0.0-dev
Current version is v2.0.0-dev
done.
Successfully installed retriever
Cleaning up...So it looks like it's not a clean install, or it installs, uninstalls, and then reinstalls.
In any case, which and version are:
$ which retriever
/c/Users/hurlbert/AppData/Local/Continuum/Anaconda/Scripts/retriever
$ retriever --version
v2.0.0-devI ran retriever reset all and said yes, with no complaints.
Finally, in RStudio (running R 3.3.1) I get:
> library(devtools)
Attaching package: ‘devtools’
The following object is masked from ‘package:ecoretriever’:
install
> install_github("ropensci/ecoretriever",force = TRUE)
Downloading GitHub repo ropensci/ecoretriever@master
from URL https://api.github.com/repos/ropensci/ecoretriever/zipball/master
Installing ecoretriever
"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL \
"C:/Users/hurlbert/AppData/Local/Temp/RtmpQnXoNK/devtools111441a842c5/ropensci-ecoretriever-9025e1e" \
--library="C:/Users/hurlbert/Documents/R/win-library/3.3" --install-tests
* installing *source* package 'ecoretriever' ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (ecoretriever)
Reloading installed ecoretriever
Use get_updates() to download the most recent release of download scripts
New to ecoretriever? Examples at
https://github.com/ropensci/ecoretriever/
Use citation(package='ecoretriever') for the package citation
Use suppressPackageStartupMessages() to suppress these messages in the future
Attaching package: ‘ecoretriever’
The following object is masked from ‘package:devtools’:
install
> library(ecoretriever)
> ecoretriever::datasets()
[1] "No scripts are currently available. Updating scripts now..."
[2] "Traceback (most recent call last):"
[3] " File \"C:\\Users\\hurlbert\\AppData\\Local\\Continuum\\Anaconda\\Scripts\\retriever-script.py\", line 9, in <module>"
[4] " load_entry_point('retriever==2.0.0-de', 'console_scripts', 'retriever')()"
[5] " File \"C:\\Users\\hurlbert\\AppData\\Local\\Continuum\\Anaconda\\lib\\site-packages\\retriever\\__main__.py\", line 122, in main"
[6] " check_for_updates()"
[7] " File \"C:\\Users\\hurlbert\\AppData\\Local\\Continuum\\Anaconda\\lib\\site-packages\\retriever\\lib\\repository.py\", line 51, in check_for_updates"
[8] " init.run()"
[9] " File \"C:\\Users\\hurlbert\\AppData\\Local\\Continuum\\Anaconda\\lib\\site-packages\\retriever\\lib\\repository.py\", line 96, in run"
[10] " version_file = urllib.request.urlopen(REPOSITORY + \"version.txt\")"
[11] " File \"C:\\Users\\hurlbert\\AppData\\Local\\Continuum\\Anaconda\\lib\\site-packages\\future\\backports\\urllib\\request.py\", line 171, in urlopen"
[12] " return opener.open(url, data, timeout)"
[13] " File \"C:\\Users\\hurlbert\\AppData\\Local\\Continuum\\Anaconda\\lib\\site-packages\\future\\backports\\urllib\\request.py\", line 494, in open"
[14] " response = self._open(req, data)"
[15] " File \"C:\\Users\\hurlbert\\AppData\\Local\\Continuum\\Anaconda\\lib\\site-packages\\future\\backports\\urllib\\request.py\", line 517, in _open"
[16] " 'unknown_open', req)"
[17] " File \"C:\\Users\\hurlbert\\AppData\\Local\\Continuum\\Anaconda\\lib\\site-packages\\future\\backports\\urllib\\request.py\", line 466, in _call_chain"
[18] " result = func(*args)"
[19] " File \"C:\\Users\\hurlbert\\AppData\\Local\\Continuum\\Anaconda\\lib\\site-packages\\future\\backports\\urllib\\request.py\", line 1353, in unknown_open"
[20] " raise URLError('unknown url type: %s' % type)"
[21] "future.backports.urllib.error.URLError: <urlopen error unknown url type: https>"
attr(,"status")
[1] 1
Warning message:
running command 'C:\Windows\system32\cmd.exe /c retriever ls' had status 1 Do I still have ecoretriever files from a previous install hiding out somewhere on my machine (Windows 8) that are messing things up?
ethanwhite
commented
8 years ago This is a separate issue from the previous one. Let's do the following:
retriever update from the command line. If that errors then this is an issue with the retriever itself. Open a new issue in the retriever repository.> system("retriever --version") in both R and RStudio and report what it returns.From the looks of things I suspect it's going to be a core retriever issue.
ethanwhite
commented
8 years ago Closing this issue again since this is a new problem.
ahhurlbert
commented
8 years ago Unfortunately, the problem is on my laptop at home, so I won't be able to test until tonight. However, I did run retriever update when messing around before and definitely got some kind of unhappy error message.
Will follow up and post a separate issue tonight.
ethanwhite
commented
8 years ago Thanks Allen.
I just reinstalled retriever, and reinstalled the ecoretriever R package. Here is what I get when I try to fetch any data package:
However, I WAS successfully able to install a dataset from the command line.
Note that my student gets basically the same message at the command line when typing
retriever --version:Failed to load script: gentry (C:/Users/hurlbert/Documents/.retriever/scripts/)v1.8.3