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ropensci / taxize

A taxonomic toolbelt for R
https://docs.ropensci.org/taxize
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itis_downstream() broken R-3.0.0 #130

Closed philippi closed 11 years ago

philippi commented 11 years ago

in both x64 and i386 R-3.0.0, itis_downstream gives an "Error in data.frame(parentName = parentName, parentTsn = parentTsn, rankName = rankName, : arguments imply differing number of rows:"

I've tried with both the stable cran version taxize_0.0.5 and the github version taxize_0.0.6, using the example from the man page: itis_downstream(tsns=846509, downto="Genus") I only append 1 of the 4 results and sessionInfos.

itis_downstream(tsns=846509, downto="Genus") http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=846509 http://www.itis.gov/ITISWebService/services/ITISService/getHierarchyDownFromTSN?tsn=846509 http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=11490 http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=11490 http://www.itis.gov/ITISWebService/services/ITISService/getHierarchyDownFromTSN?tsn=11490 http://www.itis.gov/ITISWebService/services/ITISService/getHierarchyDownFromTSN?tsn=11490 http://www.itis.gov/ITISWebService/services/ITISService/getHierarchyDownFromTSN?tsn=11490 http://www.itis.gov/ITISWebService/services/ITISService/getHierarchyDownFromTSN?tsn=11490 http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=11530 http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=11530 http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=11530 http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=11530 http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=11530 http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=11530 http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=11530 http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=11530 http://www.itis.gov/ITISWebService/services/ITISService/getHierarchyDownFromTSN?tsn=11530 Error in data.frame(parentName = parentName, parentTsn = parentTsn, rankName = rankName, : arguments imply differing number of rows: 4, 5 sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-w64-mingw32/x64 (64-bit)

locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 [4] 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] taxize_0.0.5

loaded via a namespace (and not attached): [1] ape_3.0-8 codetools_0.2-8 digest_0.6.3 foreach_1.4.0
[5] fortunes_1.5-0 grid_3.0.0 httr_0.2 iterators_1.0.6 [9] lattice_0.20-15 NCBI2R_1.4.4 nlme_3.1-109 plyr_1.8
[13] RCurl_1.95-4.1 RJSONIO_1.0-3 stringr_0.6.2 Taxonstand_1.0 [17] tools_3.0.0 XML_3.96-1.1

sckott commented 11 years ago

Thanks for the bug report! I will take a look. We haven't tested it in v3 yet - sorry about that.

sckott commented 11 years ago

It works now, sorry for the trouble. It was an error in the function gethierarchydownfromtsn() that is now fixed

philippi commented 11 years ago

Scott-- Thanks. I have trouble with NPS web services changing out from under my own code (without informing me when they change something); I can imagine how hard it is to keep up with changes for so many different APIs. In the next year or less, I expect NPS to put their certified species lists, vegetation plot data, and perhaps a block of species occurrence records on the public-facing IRMA site. When they do that, I'll contact you about me perhaps revising my code to match the structure of the rest of taxize, and then submitting a few functions to you.

Thanks for your work on taxize!

Tom 2

On Wed, May 8, 2013 at 11:46 PM, Scott Chamberlain <notifications@github.com

wrote:

It works now, sorry for the trouble. It was an error in the function gethierarchydownfromtsn() that is now fixed

— Reply to this email directly or view it on GitHubhttps://github.com/ropensci/taxize_/issues/130#issuecomment-17651906 .

sckott commented 11 years ago

Tom, Awesome, I look forward to your pull requests! I want to try to keep taxize mostly about taxonomic data, so if its occurrence records that may fit better in a different package. -Scott