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lgatto / synapter

Label-free data analysis pipeline for optimal identification and quantitation
https://lgatto.github.io/synapter/
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synapter 1.99 fails to build on bioc #136

Closed sgibb closed 6 years ago

sgibb commented 7 years ago

Dear @lgatto, it seems that some files for the vignette are missing. Could you please have a look: https://bioconductor.org/checkResults/devel/bioc-LATEST/synapter/

   ‘fragmentmatching.Rmd’ using ‘UTF-8’ 
Warning in readLines(if (is.character(input2)) { :
  cannot open file './Foreword.md': No such file or directory
Quitting from lines 37-37 (./Foreword.md) 
Error in readLines(if (is.character(input2)) { : 
  cannot open the connection
lgatto commented 7 years ago

Strange??? 2017-04-07-074600_771x322_scrot

lgatto commented 7 years ago

These files are not copied into inst/docs, hence the error.

lgatto commented 7 years ago

The files are currently duplicated, which is not nice. But I would prefer to have them in the vignettes directory, rather than (only) in inst/doc, but not sure how and why at the moment. Maybe renaming them Rmd, which will get them copied over?

sgibb commented 7 years ago

I am not convinced that copying the to inst/doc or renaming them into Rmd will solve the problem. I am not sure why it fails on bioc because locally and on travis it builds without copying/renaming.

sgibb commented 7 years ago

BTW it should be the same vignette setup as used in MSnbase.

lgatto commented 7 years ago

I tested the above locally, which is why I ended up committing to Bioc. Trying again.

lgatto commented 7 years ago

I confirm that things check fine locally - no idea why/what on Bioc. I hope it will fix itself!

lgatto commented 7 years ago

1.99.0 now builds - probably something on their side. I won't do any change now, but we should remove the files in inst/doc in the new release (unless things break before). Let's close this issue after the release.