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Error while using occ_download() #333

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damianooldoni opened this issue Dec 3, 2018 · 7 comments
Closed

Error while using occ_download() #333

damianooldoni opened this issue Dec 3, 2018 · 7 comments
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Bug
Milestone
v1.2

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@damianooldoni
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While attempting to download occurrence data, I get today this error message Error in x$http_status() : attempt to apply non-function. Below all message:

* Connection 1 seems to be dead!
* Closing connection 1
* schannel: shutting down SSL/TLS connection with api.gbif.org port 443
* schannel: clear security context handle
*   Trying 130.225.43.2...
* TCP_NODELAY set
* Connected to api.gbif.org (130.225.43.2) port 443 (#2)
* schannel: SSL/TLS connection with api.gbif.org port 443 (step 1/3)
* schannel: disabled server certificate revocation checks
* schannel: sending initial handshake data: sending 176 bytes...
* schannel: sent initial handshake data: sent 176 bytes
* schannel: SSL/TLS connection with api.gbif.org port 443 (step 2/3)
* schannel: failed to receive handshake, need more data
* schannel: SSL/TLS connection with api.gbif.org port 443 (step 2/3)
* schannel: encrypted data got 4096
* schannel: encrypted data buffer: offset 4096 length 4096
* schannel: encrypted data length: 3998
* schannel: encrypted data buffer: offset 3998 length 4096
* schannel: received incomplete message, need more data
* schannel: SSL/TLS connection with api.gbif.org port 443 (step 2/3)
* schannel: encrypted data got 1024
* schannel: encrypted data buffer: offset 5022 length 5022
* schannel: encrypted data length: 313
* schannel: encrypted data buffer: offset 313 length 5022
* schannel: received incomplete message, need more data
* schannel: SSL/TLS connection with api.gbif.org port 443 (step 2/3)
* schannel: encrypted data got 34
* schannel: encrypted data buffer: offset 347 length 5022
* schannel: sending next handshake data: sending 166 bytes...
* schannel: SSL/TLS connection with api.gbif.org port 443 (step 2/3)
* schannel: encrypted data got 91
* schannel: encrypted data buffer: offset 91 length 5022
* schannel: SSL/TLS handshake complete
* schannel: SSL/TLS connection with api.gbif.org port 443 (step 3/3)
* schannel: stored credential handle in session cache
* Server auth using Basic with user 'damiano.oldoni'
> POST /v1/occurrence/download/request HTTP/1.1
Host: api.gbif.org
Authorization: Basic ZGFtaWFuby5vbGRvbmk6dmViZWxvdHRv
Accept-Encoding: gzip, deflate
User-Agent: r-curl/3.2 crul/0.6.0 rOpenSci(rgbif/1.1.0)
X-USER-AGENT: r-curl/3.2 crul/0.6.0 rOpenSci(rgbif/1.1.0)
Content-Type: application/json
Accept: application/json
Content-Length: 1124

* upload completely sent off: 1124 out of 1124 bytes
* schannel: client wants to read 16384 bytes
* schannel: encdata_buffer resized 17408
* schannel: encrypted data buffer: offset 0 length 17408
* schannel: encrypted data got 469
* schannel: encrypted data buffer: offset 469 length 17408
* schannel: decrypted data length: 400
* schannel: decrypted data added: 400
* schannel: decrypted data cached: offset 400 length 16384
* schannel: encrypted data buffer: offset 0 length 17408
* schannel: decrypted data buffer: offset 400 length 16384
* schannel: schannel_recv cleanup
* schannel: decrypted data returned 400
* schannel: decrypted data buffer: offset 0 length 16384
< HTTP/1.1 406 Not Acceptable
< Date: Mon, 03 Dec 2018 14:27:12 GMT
< Access-Control-Allow-Origin: *
< Access-Control-Allow-Methods: HEAD, GET, POST, DELETE, PUT, OPTIONS
< Content-Length: 0
< Server: Jetty(9.3.z-SNAPSHOT)
< X-API-URL: /v1/occurrence/download/request
< Cache-Control: no-cache, no-store, must-revalidate
< X-Varnish: 44696595
< Age: 0
< Via: 1.1 varnish (VError in x$http_status() : attempt to apply non-function
arnish/5.2)
< Connection: keep-alive
< 
* Connection #2 to host api.gbif.org left intact

I asked to a colleague to install (for the first time ever) and load rgbif package on his Windows laptop. I used my credentials on his laptop for triggering the download. He gets the same error message. Does somebody have an idea about the reason of this problem?
Thanks!

Session Info 
> devtools::session_info()
Session info -----------------------------------------------------------------
 setting  value                       
 version  R version 3.5.1 (2018-07-02)
 system   x86_64, mingw32             
 ui       RStudio (1.1.453)           
 language (EN)                        
 collate  English_United States.1252  
 tz       Europe/Paris                
 date     2018-12-03                  

Packages ---------------------------------------------------------------------
 package    * version     date       source                          
 assertthat   0.2.0       2017-04-11 CRAN (R 3.5.1)                  
 backports    1.1.2       2017-12-13 CRAN (R 3.5.0)                  
 base       * 3.5.1       2018-07-02 local                           
 colorspace   1.3-2       2016-12-14 CRAN (R 3.5.1)                  
 compiler     3.5.1       2018-07-02 local                           
 crayon       1.3.4       2017-09-16 CRAN (R 3.5.1)                  
 crul         0.6.0       2018-07-10 CRAN (R 3.5.1)                  
 curl         3.2         2018-03-28 CRAN (R 3.5.1)                  
 data.table   1.11.8      2018-09-30 CRAN (R 3.5.1)                  
 datasets   * 3.5.1       2018-07-02 local                           
 devtools     1.13.6      2018-06-27 CRAN (R 3.5.1)                  
 digest       0.6.16      2018-08-22 CRAN (R 3.5.1)                  
 dplyr        0.7.99.9000 2018-11-26 Github (tidyverse/dplyr@22d6a33)
 evaluate     0.11        2018-07-17 CRAN (R 3.5.1)                  
 geoaxe       0.1.0       2016-02-19 CRAN (R 3.5.1)                  
 ggplot2      3.1.0       2018-10-25 CRAN (R 3.5.1)                  
 glue         1.3.0       2018-07-17 CRAN (R 3.5.1)                  
 graphics   * 3.5.1       2018-07-02 local                           
 grDevices  * 3.5.1       2018-07-02 local                           
 grid         3.5.1       2018-07-02 local                           
 gtable       0.2.0       2016-02-26 CRAN (R 3.5.1)                  
 htmltools    0.3.6       2017-04-28 CRAN (R 3.5.1)                  
 httpcode     0.2.0       2016-11-14 CRAN (R 3.5.0)                  
 httr         1.3.1       2017-08-20 CRAN (R 3.5.1)                  
 jsonlite     1.5         2017-06-01 CRAN (R 3.5.1)                  
 knitr        1.20        2018-02-20 CRAN (R 3.5.1)                  
 lattice      0.20-35     2017-03-25 CRAN (R 3.5.1)                  
 lazyeval     0.2.1       2017-10-29 CRAN (R 3.5.1)                  
 magrittr     1.5         2014-11-22 CRAN (R 3.5.1)                  
 memoise      1.1.0       2017-04-21 CRAN (R 3.5.1)                  
 methods    * 3.5.1       2018-07-02 local                           
 munsell      0.5.0       2018-06-12 CRAN (R 3.5.1)                  
 oai          0.2.2       2016-11-24 CRAN (R 3.5.1)                  
 pillar       1.3.0.9001  2018-11-06 Github (r-lib/pillar@c5bf622)   
 pkgconfig    2.0.2       2018-08-16 CRAN (R 3.5.1)                  
 plyr         1.8.4       2016-06-08 CRAN (R 3.5.1)                  
 purrr        0.2.5       2018-05-29 CRAN (R 3.5.1)                  
 R6           2.3.0       2018-10-04 CRAN (R 3.5.1)                  
 Rcpp         1.0.0.1     2018-12-03 Github (RcppCore/Rcpp@0664c1a)  
 rgbif      * 1.1.0       2018-10-19 CRAN (R 3.5.1)                  
 rgeos        0.3-28      2018-06-08 CRAN (R 3.5.1)                  
 rlang        0.3.0.9000  2018-12-03 Github (r-lib/rlang@035d279)    
 rmarkdown    1.10        2018-06-11 CRAN (R 3.5.1)                  
 rprojroot    1.3-2       2018-01-03 CRAN (R 3.5.1)                  
 rstudioapi   0.7         2017-09-07 CRAN (R 3.5.1)                  
 scales       1.0.0       2018-08-09 CRAN (R 3.5.1)                  
 sp           1.3-1       2018-06-05 CRAN (R 3.5.1)                  
 stats      * 3.5.1       2018-07-02 local                           
 stringi      1.1.7       2018-03-12 CRAN (R 3.5.0)                  
 stringr      1.3.1       2018-05-10 CRAN (R 3.5.1)                  
 tibble       1.4.2       2018-01-22 CRAN (R 3.5.1)                  
 tidyselect   0.2.5       2018-10-11 CRAN (R 3.5.1)                  
 tools        3.5.1       2018-07-02 local                           
 triebeard    0.3.0       2016-08-04 CRAN (R 3.5.1)                  
 urltools     1.7.0       2018-01-20 CRAN (R 3.5.1)                  
 utils      * 3.5.1       2018-07-02 local                           
 whisker      0.3-2       2013-04-28 CRAN (R 3.5.1)                  
 withr        2.1.2       2018-03-15 CRAN (R 3.5.1)                  
 xml2         1.2.0       2018-01-24 CRAN (R 3.5.1)                  
 yaml         2.2.0       2018-07-25 CRAN (R 3.5.1)
@sckott sckott added the Bug label Dec 3, 2018
@sckott
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sckott commented Dec 3, 2018

thanks for the report @damianooldoni will have a look

sckott added a commit that referenced this issue Dec 3, 2018
@sckott
#333 fix to catch_err() internal fxn for occ_download
9325a21 
was accidentally using httr function, swapped to use crul equivalent R6 method
bump dev version
@sckott
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sckott commented Dec 3, 2018

@damianooldoni reinstall from here and try again. However, you should still get an HTTP request error from GBIF - not sure why we're suddenly getting 406 HTTP errors.

@sckott
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sckott commented Dec 3, 2018

emailed the GBIF mailing list, hopefully will get this sorted soon

@damianooldoni
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Yes, I hope so. Many thanks!

@sckott
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sckott commented Dec 4, 2018

It seems to be working again now - they must have fixed something. Can you test again?

@damianooldoni
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Thanks Scott. Yes, it works fine now. Issue can be closed for what I can see.

@sckott
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sckott commented Dec 5, 2018

great, glad it works now

@sckott sckott closed this as completed Dec 5, 2018
@sckott sckott added this to the v1.2 milestone Feb 26, 2019
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