Comments (4)
Thanks - ctrdata
runs on some servers on the internet where dependencies can be installed. Perhaps shinyapps.io
lacks external depencies needed for certain registers (CTGOV
, EUCTR
, ISRCTN
; see https://github.com/rfhb/ctrdata#2-command-line-tools-perl-sed-and-php-52-or-higher). Try using CTGOV2
or CTIS
, which have no depencies besides R packages that should be provisioned when deploying to shinyapps.io
.
from ctrdata.
Indeed using CTGOV2 instead of CTGOV solved the issue.
Thank you very much for your quick help!
see https://github.com/rfhb/ctrdata#2-command-line-tools-perl-sed-and-php-52-or-higher).
(...) These are required for ctrLoadQueryIntoDb(), the main function of package ctrdata (see Example workflow), to work with the registers EUCTR, CTGOV, ISRCTN (but are not required to work with CTIS); (...)
By the way, you may want to consider mentioning that CTGOV2 also have no dependencies on that section of the readme
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@machado-t Today's development version ca7f243 should work with all registers in the hosted environment because all dependencies on command line tools were removed, see https://rfhb.github.io/ctrdata/news/index.html#improvements-1-15-2-9002. Install and use with remotes::install_github("rfhb/ctrdata", dependencies = TRUE)
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That's great news! Thank you so much! I will test this soon.
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Related Issues (20)
- dbGetFieldsIntoDf() not working for fields with mixed array and other types HOT 1
- failing if path to package contains space HOT 1
- trial ids are incompletely deduplicated with preferregister="EUCTR" HOT 1
- Example code doesn't work HOT 2
- ctrLoadQueryIntoDb works on windows but not ubuntu HOT 7
- Erroneous entries in register fields (e.g. date) not flagged with dbGetFieldsIntoDf() HOT 1
- Error message printed with ctrLoadQueryIntoDb() HOT 1
- Trial records not imported into database - stack error
- CTGOV changed website layout HOT 9
- Manual input of trial IDs instead of search functions HOT 5
- Feature request: extract EUCTR results data HOT 1
- Variable fields in EUCTR are not always retrieved HOT 14
- When downloading results from EUCTR, sometimes fails due to error with invalid argument HOT 2
- When downloading result PDFs from EUCTR, sometimes get error of file not found HOT 1
- Certain result documents are causing an error: "No such file or directory" HOT 3
- invalid numeric literal when accumulating information in database HOT 1
- CTGOV2 API call does not filter by study sponsor HOT 7
- Invalid numeric literal HOT 6
- How to cite this package? HOT 3
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