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Error in doc_parse_raw #164

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chreman opened this issue May 16, 2018 · 3 comments
Closed

Error in doc_parse_raw #164

chreman opened this issue May 16, 2018 · 3 comments
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bug
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v0.9

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@chreman
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chreman commented May 16, 2018 •
edited by sckott
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Session Info 
> devtools::session_info()
Session info -------------------------------------------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.4.4 (2018-03-15)
 system   x86_64, linux-gnu           
 ui       RStudio (1.1.447)           
 language de_AT:de                    
 collate  de_AT.UTF-8                 
 tz       Europe/Vienna               
 date     2018-05-16                  

Packages -----------------------------------------------------------------------------------------------------------------------------------------------
 package     * version    date       source                              
 assertthat    0.2.0      2017-04-11 CRAN (R 3.4.4)                      
 base        * 3.4.4      2018-03-16 local                               
 bibtex        0.4.2      2017-06-30 CRAN (R 3.4.4)                      
 bindr         0.1.1      2018-03-13 CRAN (R 3.4.4)                      
 bindrcpp      0.2.2      2018-03-29 CRAN (R 3.4.4)                      
 bitops        1.0-6      2013-08-17 CRAN (R 3.4.4)                      
 caTools       1.17.1     2014-09-10 CRAN (R 3.4.4)                      
 codetools     0.2-15     2016-10-05 CRAN (R 3.3.1)                      
 compiler      3.4.4      2018-03-16 local                               
 crul          0.5.2      2018-02-24 CRAN (R 3.4.4)                      
 curl          3.2        2018-03-28 CRAN (R 3.4.4)                      
 data.table    1.10.4-3   2017-10-27 CRAN (R 3.4.4)                      
 datasets    * 3.4.4      2018-03-16 local                               
 devtools      1.13.5     2018-02-18 CRAN (R 3.4.4)                      
 digest        0.6.15     2018-01-28 CRAN (R 3.4.4)                      
 doParallel  * 1.0.11     2017-09-28 CRAN (R 3.4.4)                      
 dplyr         0.7.4      2017-09-28 CRAN (R 3.4.4)                      
 DT            0.4        2018-01-30 CRAN (R 3.4.4)                      
 ecodist     * 2.0.1      2017-07-13 CRAN (R 3.4.4)                      
 foreach     * 1.4.4      2017-12-12 CRAN (R 3.4.4)                      
 foreign     * 0.8-70     2018-04-23 CRAN (R 3.4.4)                      
 fossil      * 0.3.7      2012-03-30 CRAN (R 3.4.4)                      
 gdata         2.18.0     2017-06-06 CRAN (R 3.4.4)                      
 glue          1.2.0      2017-10-29 CRAN (R 3.4.4)                      
 GMD         * 0.3.3      2016-12-27 CRAN (R 3.4.4)                      
 gplots        3.0.1      2016-03-30 CRAN (R 3.4.4)                      
 graphics    * 3.4.4      2018-03-16 local                               
 grDevices   * 3.4.4      2018-03-16 local                               
 grid          3.4.4      2018-03-16 local                               
 gtools        3.5.0      2015-05-29 CRAN (R 3.4.4)                      
 hms           0.4.2      2018-03-10 CRAN (R 3.4.4)                      
 htmltools     0.3.6      2017-04-28 CRAN (R 3.4.4)                      
 htmlwidgets   1.2        2018-04-19 CRAN (R 3.4.4)                      
 httpcode      0.2.0      2016-11-14 CRAN (R 3.4.4)                      
 httpuv        1.4.1      2018-04-21 CRAN (R 3.4.4)                      
 httr          1.3.1      2017-08-20 CRAN (R 3.4.4)                      
 iterators   * 1.0.9      2017-12-12 CRAN (R 3.4.4)                      
 jsonlite    * 1.5        2017-06-01 CRAN (R 3.4.4)                      
 KernSmooth    2.23-15    2015-06-29 CRAN (R 3.4.0)                      
 later         0.7.1      2018-03-07 CRAN (R 3.4.4)                      
 lattice       0.20-35    2017-03-25 CRAN (R 3.3.3)                      
 magrittr      1.5        2014-11-22 CRAN (R 3.4.4)                      
 maps        * 3.3.0      2018-04-03 CRAN (R 3.4.4)                      
 MASS        * 7.3-50     2018-04-30 CRAN (R 3.4.4)                      
 memoise       1.1.0      2017-04-21 CRAN (R 3.4.4)                      
 methods     * 3.4.4      2018-03-16 local                               
 mime          0.5        2016-07-07 CRAN (R 3.4.4)                      
 miniUI        0.1.1      2016-01-15 CRAN (R 3.4.4)                      
 NLP         * 0.1-11     2017-08-15 CRAN (R 3.4.4)                      
 parallel    * 3.4.4      2018-03-16 local                               
 parfossil   * 0.2.0      2012-10-29 CRAN (R 3.4.4)                      
 pillar        1.2.2      2018-04-26 CRAN (R 3.4.4)                      
 pkgconfig     2.0.1      2017-03-21 CRAN (R 3.4.4)                      
 plyr        * 1.8.4      2016-06-08 CRAN (R 3.4.4)                      
 promises      1.0.1      2018-04-13 CRAN (R 3.4.4)                      
 proxy       * 0.4-20     2017-12-12 url                                 
 R6            2.2.2      2017-06-17 CRAN (R 3.4.4)                      
 rAltmetric  * 0.7.9000   2018-04-30 Github (ropensci/rAltmetric@fff961e)
 Rcpp          0.12.16    2018-03-13 CRAN (R 3.4.4)                      
 rcrossref   * 0.8.1.9511 2018-04-30 Github (ropensci/rcrossref@c80444e) 
 readr         1.1.1      2017-05-16 CRAN (R 3.4.4)                      
 rlang         0.2.0      2018-02-20 CRAN (R 3.4.4)                      
 rlist         0.4.6.1    2016-04-04 CRAN (R 3.4.4)                      
 ropenaire   * 0.1.6.9433 2018-04-30 Github (sckott/ropenaire@26f564a)   
 rstudioapi  * 0.7        2017-09-07 CRAN (R 3.4.4)                      
 shapefiles  * 0.7        2013-01-26 CRAN (R 3.4.4)                      
 shiny         1.0.5      2017-08-23 CRAN (R 3.4.4)                      
 slam          0.1-43     2018-04-23 CRAN (R 3.4.4)                      
 SnowballC   * 0.5.1      2014-08-09 CRAN (R 3.4.4)                      
 sp          * 1.2-7      2018-01-19 CRAN (R 3.4.4)                      
 stats       * 3.4.4      2018-03-16 local                               
 stringdist  * 0.9.4.7    2018-03-13 CRAN (R 3.4.4)                      
 stringi     * 1.1.7      2018-03-12 CRAN (R 3.4.4)                      
 stringr     * 1.3.0      2018-02-19 CRAN (R 3.4.4)                      
 tibble        1.4.2      2018-01-22 CRAN (R 3.4.4)                      
 tm          * 0.6        2014-06-11 url                                 
 tools         3.4.4      2018-03-16 local                               
 triebeard     0.3.0      2016-08-04 CRAN (R 3.4.4)                      
 urltools      1.7.0      2018-01-20 CRAN (R 3.4.4)                      
 utils       * 3.4.4      2018-03-16 local                               
 withr         2.1.2      2018-03-15 CRAN (R 3.4.4)                      
 xml2        * 1.2.0      2018-01-24 CRAN (R 3.4.4)                      
 xtable        1.8-2      2016-02-05 CRAN (R 3.4.4)

In some cases, there appears to be an unexpected response from crossref - manual check looks like either a bad DOI or bad response.

[1] "Error in doc_parse_raw(x, encoding = encoding, base_url = base_url, as_html = as_html, : Opening and ending tag mismatch: link line 5 and head [76]\n 10.1155_2014/154376.full.pdf"
@sckott
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sckott commented May 16, 2018

Thanks, but can you show the code that created that error?

@chreman
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chreman commented May 16, 2018

ah yes sorry, example:

library('rcrossref')
doi <- "10.1155_2014/154376.full.pdf"
cr_citation_count(doi=doi)
cr_citation_count(doi=doi, async=TRUE)

@sckott sckott added this to the v0.8.4 milestone May 18, 2018
@sckott sckott added the bug label May 18, 2018
@sckott sckott modified the milestones: v0.8.4, v0.9 May 18, 2018
sckott added a commit that referenced this issue May 18, 2018
@sckott
fix #164 throw warning on bad DOI, and hard return NA
5344fb7
@sckott
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sckott commented May 18, 2018

hmm, not a valid DOI https://doi.org/10.1155_2014/154376.full.pdf

reinstall from async branch and try again now - throwing warning and NA on invalid DOIs so that it doesn't interrupt

@sckott sckott closed this as completed May 18, 2018
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