According to the Rfigshare readme:,
The first time you use an rfigshare function, it will ask you to authenticate online. Just log in and click okay to authenticate rfigshare. R will allow you to cache your login credentials so that you won't be asked to authenticate again (even between R sessions), as long as you are using the same working directory in future.
After installing rfigshare on a fresh machine (without an existing .httr-oauth)
library(devtools)
install_github('ropensci/rfigshare')
library(rfigshare)
id = 3761562
fs_browse(id)
Error in value[[3L]](cond) : Requires authentication.
Are your credentials stored in options?
See fs_auth function for details.
Thus, in spite of what the readme says, I am not asked to authenticate.
Directly calling fs_auth does not work either:
> fs_auth()
Error in init_oauth1.0(self$endpoint, self$app, permission = self$params$permission, :
Bad Request (HTTP 400).
My sessionInfo is as follows:
sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rfigshare_0.3.7.100
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 magrittr_2.0.1 tidyselect_1.1.0 munsell_0.5.0
[5] colorspace_2.0-1 R6_2.5.0 rlang_0.4.11 fansi_0.5.0
[9] httr_1.4.2 dplyr_1.0.5 grid_4.0.5 gtable_0.3.0
[13] utf8_1.2.1 DBI_1.1.1 ellipsis_0.3.2 assertthat_0.2.1
[17] yaml_2.2.1 tibble_3.1.2 lifecycle_1.0.0 crayon_1.4.1
[21] RJSONIO_1.3-1.4 purrr_0.3.4 ggplot2_3.3.3 later_1.2.0
[25] vctrs_0.3.8 promises_1.2.0.1 glue_1.4.2 compiler_4.0.5
[29] pillar_1.6.1 generics_0.1.0 scales_1.1.1 XML_3.99-0.6
[33] httpuv_1.6.1 pkgconfig_2.0.3
Does anyone have any tips or workarounds? This definitely did work maybe 6 months ago when I last tried. I also have an open thread about this issue with Figshare support, but their knowledge of the R library seems limited.
(cross-posted from Github)
The master branch of rfigshare seems to be out of sink with what figshare now offers in that the master branch seems to use v1 of the api along with oauth v1 authentication whereas figshare has moved on with v2 of the api and now promotes the use of oauth v2.
While I am unsure whether figshare has shutdown v1 of the api and/or has disallowed oauth v1, it seems like you might still be able to use the package if you install from the sckott branch and use a personal access token (PAT).
To generate a PAT, navigate to https://figshare.com/account/applications in a web browser. At the bottom of this page, you can generate a PAT. When the token is presented, copy it as you will not be able to view it again (although you can easily generate a new one at any time).
You will want to store this token in your .Renviron file. The usethis package has a nifty edit_r_environ() function to make this a little easier:
usethis::edit_r_environ()
Running the above in R should find your .Renviron file and open it for editing. Store your PAT on a new line.
RFIGSHARE_PAT="the-really-long-pat-you-should-have-on-your-clipbord"
Save and close the file. Make sure to restart your R session for this change to take effect.
You might then test to see if the above worked by running:
Sys.getenv("RFIGSHARE_PAT")
To see if your PAT is found.
Then install rfigshare from the sckott branch.
remotes::install_github("https://github.com/ropensci/rfigshare/tree/sckott")
Now you should be able to
library(rfigshare)
fs_browse()
You might also consider leveraging the fact that the current figshare api is Open API compatible and build your own client on the fly with the swagger specification.
Generate and store a personal access token as I described in my other answer. Then you could do
library(rapiclient)
library(httr)
fs_api <- get_api("https://docs.figshare.com/swagger.json")
header <- c(Authorization = sprintf("token %s", Sys.getenv("RFIGSHARE_PAT")))
fs_api <- list(operations = get_operations(fs_api, header),
schemas = get_schemas(fs_api))
my_articles <- fs_api$operations$private_articles_list()
content(my_articles)
I think one of the issues is that you're passing an article_id to fs_browse, which the first argument is not that. If you're looking to browse a public set, you can set mine = FALSE and session = NULL, like:
out = fs_details(article_id = 3761562, mine = FALSE, session = NULL)
Figshare support informed me that they have blocked requests done using http://. Switching the requests to https:// seemed to fix some of the issues on rfigshare. In particular, fs_details(), and fs_delete() works after switching to https://.
fs_upload() is broken even after switching to https.
Related
Context:
I have a website that I've made using blogdown and Hugo, deployed on Netlify. I'm currently working on some posts (.Rmd files) (in RStudio) that are still drafts (draft: true in the YAML header). As I work on a draft, I like to save things as I go.
Problem:
If I've already used the command blogdown::serve_site() at least once during my R session, then every time I save a .Rmd draft post, it 'renders' the document (i.e. hitting the 'save' icon leads to Rendering content/post/Post 1.Rmd appearing in the console, and -if it works- eventually the post is updated in the viewer).
This always takes a long time (at least 5 minutes), and if there are any mistakes in a code block (typo, missing argument, etc) then it goes into a loop wherein it continuously tries to render the document and continuously fails. Sometimes, I can fix the code mistake while this is happening and then the next render attempt will be successful.
More often, however, although I fix the mistake in the code, my session totally freezes; either nothing happens (no error but no more activity in the console) but I can't use anything in RStudio anymore, or I get an error from RStudio (a dropdown message box from the application, not a code error in the console) that says "Save File: Unable to establish connection with R session." In both cases, my only option is to Force Quit RStudio, and I lose any unsaved changes in my .Rmd file.
This endless error loop looks like this (in this case, there is a mistake in an argument in the legend() function):
Quitting from lines 317-357 (Post 1.Rmd)
Error in legend("topleft", lables = unique(df.vis$PtType), pch = unique(df.vis$PtSym), :
unused argument (lables = unique(df.vis$PtType))
Calls: local ... handle -> withCallingHandlers -> withVisible -> eval -> eval
Execution halted
<simpleError in render_page(f): Failed to render 'content/post/Post 1.Rmd'>
* Retrying in 2 seconds...
Rendering content/post/Post 1.Rmd
....and the "2" seconds becomes 8 seconds, etc up to 32 seconds, and then it loops at 32 over and over again, until it recognizes my fixes or (way more often) it freezes.
I never have such problems when I call blogdown::serve_site() which just throws an error and stops trying if there is a mistake in a code chunk.
Question:
How can I prevent blogdown from rendering my .Rmd post documents every time I save them?
OR
How can I make it so that if rendering on save throws an error, it just stops trying to render it (but, if possible, still saves my .Rmd file)?
I have read the blogdown book start to finish, and I think that this probably has something to do with LiveReload, but I'm not entirely sure how to apply these instructions to my specific issue...
Any help would be appreciated! Thanks!
Update - Session info
> xfun::session_info('blogdown')
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.14, RStudio 1.2.1114
Locale: en_CA.UTF-8 / en_CA.UTF-8 / en_CA.UTF-8 / C / en_CA.UTF-8 / en_CA.UTF-8
Package version:
backports_1.1.2
base64enc_0.1.3
BH_1.66.0.1
blogdown_0.9
bookdown_0.7
digest_0.6.18
evaluate_0.12
glue_1.3.0
graphics_3.5.1
grDevices_3.5.1
highr_0.7
htmltools_0.3.6
httpuv_1.4.5
jsonlite_1.5
knitr_1.20
later_0.7.5
magrittr_1.5
markdown_0.8
methods_3.5.1
mime_0.6
promises_1.0.1
R6_2.3.0
Rcpp_1.0.0
rlang_0.3.0.1
rmarkdown_1.10
rprojroot_1.3.2
servr_0.11
stats_3.5.1
stringi_1.2.4
stringr_1.3.1
tinytex_0.9
tools_3.5.1
utils_3.5.1
xfun_0.4
yaml_2.2.0
When I run a Shiny App either an example or my own it starts a new window, freezes and then aborts. It tries to listening to a local port then starts a new session.
Details of my system:
My R version: 3.1.3 on MacOS Maverick
other attached packages:
[1] shiny_0.12.0 Rcpp_0.11.6
loaded via a namespace (and not attached):
[1] digest_0.6.8 htmltools_0.2.6 httpuv_1.3.2 mime_0.3 R6_2.0.1
[6] tools_3.1.3 xtable_1.7-4
What I tried so far:
From different internet forums I found a lot of suggestions:
I reinstalled Rstudio.
I updated all the packages
Tried this: install.packages(c("Rcpp", "httpuv", "shiny"))
Loaded Rcpp and httpuv separately
tried to run like this runApp('app1',host="127.0.0.1",port = 3894)
// tried other ports as well.
But nothing works.
(Please note that, I don't know whether it's relevant but GoogleVis Demo worked on my RStudio.)
#roboticman
My recommendation is first to test and confirm R is correctly setup on your machine. We can then move to harness a Shiny demonstration application and confirm if that works.
https://technophobe01.shinyapps.io/WorldBank/
First step:
Can you please run the following command via R, this should download and install shiny and its dependencies...
> install.packages("shiny", dependencies = TRUE)
If things work after this, great. If not, well, then let's check your R configuration:
Validate R Install
To check your configuration, my recommendation is you launch R on your machine and run the following tests and post back the output.
> R
> sessionInfo()
Sys.setenv(LC_COLLATE = "C", LC_TIME = "C", LANGUAGE = "en")
library("tools")
testInstalledBasic("both")
testInstalledPackages(scope = "base")
testInstalledPackages(scope = "recommended")
testInstalledBasic("internet")
Once you post the output of the above command set, we can move to work through the example 'World Bank', and see if we can determine the problem.
Take care
Try this:
library(shiny)
runExample("01_hello", host = "0.0.0.0", port = 9999).
runApp will also work:
shiny::runApp(host = "127.0.0.1", port = 9999)
I am trying to fetch tweets using searchTwitter() and/or userTimeline()
I want to fetch maximum number tweets allowed to fetch by twitterR API (I believe that limit is around 3000.)
But in result I'm only getting very few posts (like 83 or 146). I'm sure there are more number of posts, when I check the Timeline of that user (via browser or app) I see there are more than 3000 posts.
Below is the message I get.
r_stats <- searchTwitter("#ChangeToMeIs", n=2000)
Warning message:
In doRppAPICall("search/tweets", n, params = params, retryOnRateLimit = retryOnRateLimit, :
2000 tweets were requested but the API can only return 83
Is there anything I am missing on?
PS: I've checked all related question before posting. Before marking duplicate, please help me with the solution.
Actually, you are using is the Twitter Search API and it only returns a sample of results, not the comprehensive search.
What you need is Twitter Streaming API.
Please note that the Twitter search API does not return an exhaustive
list of tweets that match your search criteria, as Twitter only makes
available a sample of recent tweets. For a more comprehensive search,
you will need to use the Twitter streaming API, creating a database of
results and regularly updating them, or use an online service that can
do this for you.
Source: https://colinpriest.com/2015/07/04/tutorial-using-r-and-twitter-to-analyse-consumer-sentiment/
I install the library twitteR from git hub and this is quite important that the version is from git not CRAN
Than set up
setup_twitter_oauth("xxxxxxx", "xxxxx")
and than you can use the commends as
To get twitts from users timeline
ut <- userTimeline('xxxx', n=2000)
ut <- twListToDF(ut)
or to search for specific hastags
tweets<-twListToDF(searchTwitter("#f1", n=5000))
It works perfect for me
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=Swedish_Sweden.1252 LC_CTYPE=Swedish_Sweden.1252 LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C LC_TIME=Swedish_Sweden.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] twitteR_1.1.9
loaded via a namespace (and not attached):
[1] bit_1.1-12 httr_1.1.0 rjson_0.2.15 plyr_1.8.3 R6_2.1.2 rsconnect_0.4.1.11 DBI_0.3.1 tools_3.2.2
[9] whisker_0.3-2 yaml_2.1.13 Rcpp_0.12.4 bit64_0.9-5 rCharts_0.4.5 RJSONIO_1.3-0 grid_3.2.2 lattice_0.20-33
Since twitteR is going to be deprecated, what you need to do is install rtweet.
Here is the code:
# Install and load the 'rtweet' package
install.packages("rtweet")
library(rtweet)
# whatever name you assigned to your created app
appname <- "tweet-search-app"
# api key (example below is not a real key)
key <- "9GmBeouvgfdljlBLryeIeqCHEt"
# api secret (example below is not a real key)
secret <- "ugdfdgdgrxOzjhlkhlxgdxllhoiofdtrrdytszghcv"
# create token named "twitter_token"
twitter_token <- create_token(
app = appname,
consumer_key = key,
consumer_secret = secret)
# Retrieve tweets for a particular hashtag
r_stats <- search_tweets("#ChangeToMeIs", n = 2000, token = twitter_token)
I am retrieving online XML data using the XML R packages. My issue is that the UTF-8 encoding is lost during the call to xmlToList : for instance, 'é' are replaced by 'é'. This happens during the XML parsing.
Here is a code snippet, with an example of encoding lost and another where encoding is kept (depending of the data source) :
library(XML)
library(RCurl)
url = "http://www.bdm.insee.fr/series/sdmx/data/DEFAILLANCES-ENT-FR-ACT/M.AZ+BE.BRUT+CVS-CJO?lastNObservations=2"
res <- getURL(url)
xmlToList(res)
# encoding lost
url2 = "http://www.bdm.insee.fr/series/sdmx/conceptscheme/"
res2 <- getURL(url2)
xmlToList(res2)
# encoding kept
Why the behaviour about encoding is different ? I tried to set .encoding = "UTF-8" in getURL, and to enc2utf8(res) but that makes no change.
Any help is welcome !
Thanks,
Jérémy
R version 3.2.1 (2015-06-18)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RCurl_1.95-4.7 bitops_1.0-6 XML_3.98-1.3
loaded via a namespace (and not attached):
[1] tools_3.2.1
You are trying to read SDMX documents in R. I would suggest to use the rsdmx package that makes easier the reading of SDMX documents. The package is available on CRAN, you can also access the latest version on Github.
rsdmx allows you to read SDMX documents by file or url, e.g.
require(rsdmx)
sdmx = readSDMX("http://www.bdm.insee.fr/series/sdmx/data/DEFAILLANCES-ENT-FR-ACT/M.AZ+BE.BRUT+CVS-CJO?lastNObservations=2")
as.data.frame(sdmx)
Another approach is to use the web-service interface to embedded data providers, and INSEE is one of them. Try:
sdmx <- readSDMX(providerId = "INSEE", resource = "data",
flowRef = "DEFAILLANCES-ENT-FR-ACT",
key = "M.AZ+BE.BRUT+CVS-CJO", key.mode = "SDMX",
start = 2010, end = 2015)
as.data.frame(sdmx)
AFAIK the package also contains issues to the character encoding, but i'm currently investigating a solution to make available soon in the package. Calling getURL(file, .encoding="UTF-8") properly retrieves data, but encoding is lost calling xml functions.
Note: I also see you use a parameter lastNObservations. For the moment the web-service interface does not support extra parameters, but it may be made available quite easily if you need it.
I solved the problem by moving R installation directory out of disk C. Thanks Joris for the great suggestions! I think the R core team should also take this as a bug and do something against the protecting mechanism of windows xp.
Dear Community:
While using the BIOMOD packages in R, I always get the following problem:
Error in xzfile(file, "wb", compression = 9) : cannot open the connection
In addition: Warning message:
In xzfile(file, "wb", compression = 9) :
cannot initialize lzma encoder, error 5
It was said by the author of the package and also in the help file of "save" that the problem should be caused by lack of permission to write. However, as I am logging in as administative account and have assess to all operations, I have no idea what the problem is. Can anybody help me out? I really need to run the package now. Thanks in advance~
Sincerely,
Marco
Below is the illustration in the help file of "save":
The most common reason for failure is lack of write permission in
the current directory. For 'save.image' and for saving at the end
of a session this will shown by messages like
Error in gzfile(file, "wb") : unable to open connection
In addition: Warning message:
In gzfile(file, "wb") :
cannot open compressed file '.RDataTmp',
probable reason 'Permission denied'
The defaults were changed to use compressed saves for 'save' in
2.3.0 and for 'save.image' in 2.4.0. Any recent version of R can
read compressed save files, and a compressed file can be
uncompressed (by 'gzip -d') for use with very old versions of R.*
Sorry for the ommision of the information:
Here is the sessionInfo():
> sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=Chinese_People's Republic of China.936
[2] LC_CTYPE=Chinese_People's Republic of China.936
[3] LC_MONETARY=Chinese_People's Republic of China.936
[4] LC_NUMERIC=C
[5] LC_TIME=Chinese_People's Republic of China.936
attached base packages:
[1] splines stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] BIOMOD_1.1-6.8 foreign_0.8-42 gam_1.04
[4] randomForest_4.6-2 mda_0.4-1 class_7.3-3
[7] gbm_1.6-3.1 lattice_0.19-17 MASS_7.3-11
[10] Design_2.3-0 Hmisc_3.8-3 survival_2.36-5
[13] rpart_3.1-48 nnet_7.3-1 ade4_1.4-16
[16] rgdal_0.6-33 dismo_0.5-19 rJava_0.9-0
[19] raster_1.7-47 sp_0.9-78
loaded via a namespace (and not attached):
[1] cluster_1.13.3 grid_2.12.2 tools_2.12.2
Now I found that the problem come form the lzma encoder in doing "save":
> x<-runif(100)
> save(x, file = "F:/test.gzip", compress='gzip')
> save(x, file = "F:/test.xz", compress='xz')
Error in xzfile(file, "wb", compression = 9) : cannot open the connection
>
I had a similar issue when trying to project to a new scenario (a tables containing columns corresponding to the predictor variables) after having run the modeling procedure using 8 models.
The first table (approx 250,000 rows) ran fine, and I was able to save the results as a .csv file. However the second one (approx 380,000 rows) resulted in the above error message, and some of the files were not written to the project folder.
I have since cut all the tables down to a maximum of 260,000 rows and I no longer recieve the error message. It was a bit of a pain doing it in multiple runs, but once I had written the script once, I just used find and replace in MS Word to change it for each run.