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akoyabio / phenoptrReports

Create analysis reports from inForm data.
https://akoyabio.github.io/phenoptrReports
zlib License
15 stars 7 forks source link

File Akoya.png not found in resource path #28

Closed drstitch closed 4 years ago

drstitch commented 5 years ago

Hi,

I'm trying to test my data set. But, some error occurs when "consolidate and summarize" in R addin.

Reading "1_BR 1801Scan3[14061,47724]_cell_seg_data". Data is already in microns, no conversion performed Writing report for "1_BR 1801Scan3[14061,47724]_cell_seg_data". File Akoya.png not found in resource path Unable to write summary report pandoc document conversion failed with error 99 Writing consolidated data. Writing report for consolidated data. File Akoya.png not found in resource path Unable to write summary report pandoc document conversion failed with error 99 Done!

Could you tell me how to fix it? thanks!

AB-Kent commented 4 years ago

The recent update of the rmarkdown package to version 1.16 introduced a bug which impacts phenoptrReports. The symptom is that report generation fails with the error File Akoya.png not found in resource path If you get this error, the simplest fix is to update to the development version of rmarkdown, which has been fixed. Update with the R command remotes::install_github("rstudio/rmarkdown")

If you have not updated rmarkdown, I recommend waiting for version 1.17.

The rmarkdown issue is here: https://github.com/rstudio/rmarkdown/issues/1667

drstitch commented 4 years ago

fantastic. Thanks!

AB-Kent commented 4 years ago

Note: the rmarkdown package is now at version 2.0. This bug has been fixed and there is no longer any need to install from github.