curl config bug?
maelle opened this issue · 10 comments
maelle commented
library("fulltext")
res1 <- ft_search(query = 'biology', from = 'entrez', limit = 5)
ft_links(res1)
#> Only 5 found for Entrez, proceeding...
#> Error in curl::curl_fetch_memory(url, handle = handle): Error in the HTTP2 framing layer
Created on 2019-03-18 by the reprex package (v0.2.1)
Session info
devtools::session_info()
#> ─ Session info ──────────────────────────────────────────────────────────
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#>
#> [1] /home/maelle/R/x86_64-pc-linux-gnu-library/3.4
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library
Looks like jeroen/curl#156
sckott commented
thanks @maelle !
does this suggestion help? jeroen/curl#156 (comment)
maelle commented
Where would I write it? I am trying to knit the README
sckott commented
okay, reinstall from master - then try
ft_links(res1, config=httr::verbose())
and report back the verbose http outout
maelle commented
library("fulltext")
res1 <- ft_search(query = 'biology', from = 'entrez', limit = 5)
ft_links(res1, config = httr::verbose())
#> Error in curl::curl_fetch_memory(url, handle = handle): Error in the HTTP2 framing layer
Created on 2019-03-21 by the reprex package (v0.2.1)
Session info
devtools::session_info()
#> ─ Session info ──────────────────────────────────────────────────────────
#> setting value
#> version R version 3.4.4 (2018-03-15)
#> os Ubuntu 18.04.2 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language en_US
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz Europe/Paris
#> date 2019-03-21
#>
#> ─ Packages ──────────────────────────────────────────────────────────────
#> package * version date lib
#> aRxiv 0.5.16 2017-04-28 [1]
#> assertthat 0.2.0 2017-04-11 [1]
#> backports 1.1.3 2018-12-14 [1]
#> bibtex 0.4.2 2017-06-30 [1]
#> callr 3.2.0 2019-03-15 [1]
#> cli 1.1.0 2019-03-19 [1]
#> colorspace 1.4-1 2019-03-18 [1]
#> crayon 1.3.4 2017-09-16 [1]
#> crul 0.7.0 2019-01-04 [1]
#> curl 3.3 2019-01-10 [1]
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#> DT 0.5 2018-11-05 [1]
#> evaluate 0.13 2019-02-12 [1]
#> fs 1.2.6 2018-08-23 [1]
#> fulltext * 1.2.0.9310 2019-03-21 [1]
#> ggplot2 3.1.0 2018-10-25 [1]
#> glue 1.3.1 2019-03-19 [1]
#> gtable 0.2.0 2016-02-26 [1]
#> highr 0.7 2018-06-09 [1]
#> hoardr 0.5.2 2018-12-02 [1]
#> htmltools 0.3.6 2017-04-28 [1]
#> htmlwidgets 1.3 2018-09-30 [1]
#> httpcode 0.2.0 2016-11-14 [1]
#> httpuv 1.5.0 2019-03-15 [1]
#> httr 1.4.0 2018-12-11 [1]
#> jsonlite 1.6 2018-12-07 [1]
#> knitr 1.22 2019-03-08 [1]
#> later 0.8.0 2019-02-11 [1]
#> lazyeval 0.2.2 2019-03-15 [1]
#> lubridate 1.7.4 2018-04-11 [1]
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#> whisker 0.3-2 2013-04-28 [1]
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#> source
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#> local
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#>
#> [1] /home/maelle/R/x86_64-pc-linux-gnu-library/3.4
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library
sckott commented
hmm, I found a little bug, just fixed #203 , so install again - Also, reprex doens't show the curl vebose output - can you paste in that output manually or maybe ther'es a reprex setting to show the curl outupt
maelle commented
Here's what I get
-> GET /entrez/eutils/esearch.fcgi?db=pubmed&term=10.1016%2Fj.celrep.2017.05.019%5Bdoi%5D%20OR%2010.3791%2F58664%5Bdoi%5D%20OR%2010.1038%2Fs41380-018-0231-1%5Bdoi%5D%20OR%2010.1038%2Fs41380-018-0247-6%5Bdoi%5D%20OR%20NA%5Bdoi%5D&retmode=xml&usehistory=n&email=david.winter%40gmail.com&tool=rentrez HTTP/2
-> Host: eutils.ncbi.nlm.nih.gov
-> User-Agent: libcurl/7.58.0 r-curl/3.3 httr/1.4.0
-> Accept-Encoding: gzip, deflate
-> Cookie: ncbi_sid=3A71884A51D5C153_D4D9SID
-> Accept: application/json, text/xml, application/xml, */*
->
Error in curl::curl_fetch_memory(url, handle = handle) :
Error in the HTTP2 framing layer
sckott commented
can you try ft_links(res1, config = c(httr::verbose(), httr::config(http_version=0L)))
maelle commented
-> GET /entrez/eutils/esearch.fcgi?db=pubmed&term=10.1016%2Fj.celrep.2017.05.019%5Bdoi%5D%20OR%2010.3791%2F58664%5Bdoi%5D%20OR%2010.1038%2Fs41380-018-0231-1%5Bdoi%5D%20OR%2010.1038%2Fs41380-018-0247-6%5Bdoi%5D%20OR%20NA%5Bdoi%5D&retmode=xml&usehistory=n&email=david.winter%40gmail.com&tool=rentrez HTTP/2
-> Host: eutils.ncbi.nlm.nih.gov
-> User-Agent: libcurl/7.58.0 r-curl/3.3 httr/1.4.0
-> Accept-Encoding: gzip, deflate
-> Cookie: ncbi_sid=51453EFDBC3A648D_4EB6SID
-> Accept: application/json, text/xml, application/xml, */*
->
<- HTTP/2 200
<- date: Fri, 22 Mar 2019 17:52:46 GMT
<- server: Finatra
<- strict-transport-security: max-age=31536000; includeSubDomains; preload
<- content-security-policy: upgrade-insecure-requests
<- x-ratelimit-remaining: 1
<- ncbi-phid: 322C1335D2DEB7E5000021FA4DBA6593.1.1.m_2
<- cache-control: private
<- l5d-success-class: 1.0
<- ncbi-sid: 51453EFDBC3A648D_4EB6SID
<- content-encoding: gzip
<- x-ratelimit-limit: 3
<- access-control-allow-origin: *
<- content-type: text/xml; charset=UTF-8
<- set-cookie: ncbi_sid=51453EFDBC3A648D_4EB6SID; domain=.nih.gov; path=/; expires=Sun, 22 Mar 2020 17:52:46 GMT
<- x-ua-compatible: IE=Edge
<- x-xss-protection: 1; mode=block
<-
-> GET /entrez/eutils/elink.fcgi?db=&dbfrom=pubmed&cmd=llinks&id=30663642%2C30242229%2C30242228%2C28564607&email=david.winter%40gmail.com&tool=rentrez HTTP/2
-> Host: eutils.ncbi.nlm.nih.gov
-> User-Agent: libcurl/7.58.0 r-curl/3.3 httr/1.4.0
-> Accept-Encoding: gzip, deflate
-> Cookie: ncbi_sid=51453EFDBC3A648D_4EB6SID
-> Accept: application/json, text/xml, application/xml, */*
->
Error in curl::curl_fetch_memory(url, handle = handle) :
Error in the HTTP2 framing layer
sckott commented
still can't replicate this, closing for now