Error importing DwC file from URL

[Daphnisd]

> devtools::session_info() Session info ------------------------------------------------------------------------------------------------------------  setting  value                         version  R version 3.4.1 (2017-06-30)  system   x86_64, mingw32               ui       RStudio (1.0.143)             language (EN)                          collate  English_United States.1252    tz       Europe/Paris                  date     2017-07-18                    Packages ----------------------------------------------------------------------------------------------------------------  package    * version date       source          base       * 3.4.1   2017-06-30 local           compiler     3.4.1   2017-06-30 local           data.table   1.10.4  2017-02-01 CRAN (R 3.4.0)  datasets   * 3.4.1   2017-06-30 local           devtools   * 1.13.2  2017-06-02 CRAN (R 3.4.1)  digest       0.6.12  2017-01-27 CRAN (R 3.4.1)  EML          1.0.3   2017-05-01 CRAN (R 3.4.1)  finch      * 0.1.0   2016-12-23 CRAN (R 3.4.1)  graphics   * 3.4.1   2017-06-30 local           grDevices  * 3.4.1   2017-06-30 local           memoise      1.1.0   2017-04-21 CRAN (R 3.4.1)  methods    * 3.4.1   2017-06-30 local           plyr         1.8.4   2016-06-08 CRAN (R 3.4.1)  rappdirs     0.3.1   2016-03-28 CRAN (R 3.4.1)  Rcpp         0.12.12 2017-07-15 CRAN (R 3.4.1)  stats      * 3.4.1   2017-06-30 local           tools        3.4.1   2017-06-30 local           utils      * 3.4.1   2017-06-30 local           uuid         0.1-2   2015-07-28 CRAN (R 3.4.0)  withr        1.0.2   2016-06-20 CRAN (R 3.4.1)  xml2         1.1.1   2017-01-24 CRAN (R 3.4.1)
--

I get the following error:

file <- "http://ipt.vliz.be/eurobis/archive.do?r=nbn_ga000467&v=1.1"
out <- dwca_read(file, read = TRUE)
File in cache
Error in if (grepl("<|>", x)) { : argument is of length zero

but the following works fine:

file <- "dwca-nbn_ga000467-v1.1.zip"
out <- dwca_read(file, read = TRUE)

[sckott]

Thanks for the report @Daphnisd - I'll have a look

[sckott]

I think its an issue that was fixed in #17 - try reinstall from github devtools::install_github("ropensci/finch") , restart R session, then try again

[Daphnisd]

installing from devtools and restarting R did not resolve the issue.
I still have:

file <- "http://ipt.vliz.be/eurobis/archive.do?r=nbn_ga000467&v=1.1" >
out <- dwca_read(file, read = TRUE)
File in cache Error in if (grepl("<|>", x)) { : argument is of length zero

> devtools::session_info() Session info ------------------------------------------------------------------------------------------------------------  setting  value                         version  R version 3.4.1 (2017-06-30)  system   x86_64, mingw32               ui       RStudio (1.0.143)             language (EN)                          collate  English_United States.1252    tz       Europe/Paris                  date     2017-07-19                    Packages ----------------------------------------------------------------------------------------------------------------  package    * version    date       source                           base       * 3.4.1      2017-06-30 local                            compiler     3.4.1      2017-06-30 local                            data.table   1.10.4     2017-02-01 CRAN (R 3.4.0)                   datasets   * 3.4.1      2017-06-30 local                            devtools     1.13.2     2017-06-02 CRAN (R 3.4.1)                   digest       0.6.12     2017-01-27 CRAN (R 3.4.1)                   EML          1.0.3      2017-05-01 CRAN (R 3.4.1)                   finch      * 0.1.0.9000 2017-07-19 Github (ropensci/finch@d7db645)  graphics   * 3.4.1      2017-06-30 local                            grDevices  * 3.4.1      2017-06-30 local                            memoise      1.1.0      2017-04-21 CRAN (R 3.4.1)                   methods    * 3.4.1      2017-06-30 local                            plyr         1.8.4      2016-06-08 CRAN (R 3.4.1)                   rappdirs     0.3.1      2016-03-28 CRAN (R 3.4.1)                   Rcpp         0.12.12    2017-07-15 CRAN (R 3.4.1)                   stats      * 3.4.1      2017-06-30 local                            tools        3.4.1      2017-06-30 local                            utils      * 3.4.1      2017-06-30 local                            uuid         0.1-2      2015-07-28 CRAN (R 3.4.0)                   withr        1.0.2      2016-06-20 CRAN (R 3.4.1)                   xml2         1.1.1      2017-01-24 CRAN (R 3.4.1)
--

[sckott]

@Daphnisd okay, will have another look at it

[sckott]

@Daphnisd can you run that again and then run traceback() after that error happens and paste in those error messages

[Daphnisd]

file <- "http://ipt.vliz.be/eurobis/archive.do?r=nbn_ga000467&v=1.1"
out <- dwca_read(file, read = TRUE)
File in cache
Error in if (grepl("<|>", x)) { : argument is of length zero
traceback()
5: read_xml.character(grep("meta.xml", x, value = TRUE))
4: read_xml(grep("meta.xml", x, value = TRUE))
3: data_paths(ff)
2: parse_dwca(x)
1: dwca_read(file, read = TRUE)
--

[sckott]

thx. interesting, it's an error in xml2. will look into that

[sckott]

@Daphnisd Just ran this on a windows VM with same R version and I think same Windows OS version and I can't replicate your error.

I don't think it's an xml2 problem since we have the same version.

Can you start with a fresh R session, make sure you have finch v0.1.0.9000 installed by doing packgeVersion("finch") then try your eg again - do you get the same error and if so, do traceback again

[Daphnisd]

My colleague who has the same system just installed R and does not encounter an issue running the code. However, reinstalling R, and R studio (while deleting all directories) does not solve it on my system (I tried 3 times,...) . You know how I can do a clean reinstall?

[sckott]

@Daphnisd since it may be an xml2 package problem can you install that package, though it may already be installed, load it, and try to run examples from xml2::read_xml

[Daphnisd]

I have no issue running any of the examples.

[sckott]

@Daphnisd okay, thanks

[albenson-usgs]

@Daphnisd Were you able to get this error resolved? I'm running into it myself.

[Daphnisd]

No, I still have the error, as does a colleague of mine. But another colleague who has the same system which installed R for the first time and did not encounter any issues. I should check on a clean computer which additional R package or other software makes it break.

[pieterprovoost]

I have this issue intermittently on mac, and am able to solve it by clearing the file cache:

dwca_cache_delete_all(force = TRUE)

[albenson-usgs]

Yep, that fixed it. Thanks @pieterprovoost

[sckott]

thanks @pieterprovoost for the help here - will look into cache interference here

[Daphnisd]

Indeed that fixed it here too. Thnx!

[sckott]

if okay with you i want to keep this open to look if there's anything I can fix in the pkg so this problem can be avoided in the future

[sckott]

closing for now, if it comes up again i can can re-open