Closed gbss2 closed 9 months ago
Hi!
Hmm, the data(entrez2symbol_hs)
call that throws the error in 1.5.0 is calling a built in data set belonging to superFreq. I honestly don't know how the back end of data()
works, but I'd guess that it has to be either an issue with the superFreq installation that didn't install that data set, or that there is an issue with finding the data set... You can try just
library(superFreq)
data(entrez2symbol_hs)
in a fresh R session, and see if that works. You can also try
data(package='superFreq')
which returns
Data sets in package ‘superFreq’:
entrez2symbol_hs
entrez2symbol_mm
for me. Might be clues to the cause of the error in there.
If you can't solve it, then you should be able to install older version of superFreq. Use the ref setting in install_github
, and point to the 1.4.5 commit, i believe this one: https://github.com/ChristofferFlensburg/superFreq/commit/99584742099b33310f96a4bfb3a9fd179274d5cb
In general I'll be less keen to support older versions, but we all do whatever makes things work, so no judgement if that turns out to be the easiest way to get your data analysed.
Good luck, let me know if you need more help.
Just an update, I had a local user report the same problem with the missing data set, so I'll be able to look into that closer. Good chance I'll push a fix for that out this week, but no promises ofc.
Ok, seems I just forgot to git add the data directory to my local repo, so the data didn't get pushed to github. Oopsie. 😬
But it explains why it passed my (local) tests but didn't work for you, or others, and why you didn't get any hits on a search... I pushed the data to live in version 1.5.1, and it worked for at least one other user, so re-install and rerun, and it should work. 🤞
Let me know if it doesn't.
Hi @ChristofferFlensburg,
We are facing some errors in SuperFreq trying to infer CNAs on RNA data.
The first error was related to the issue #100 (R 4.3.1 and SuperFreq 1.4.4):
To solve this issue, we updated to the latest version on Github (SuperFreq 1.5.0). However, another error, now related to the annotation popped up:
I looked up the code and found out that there is no previous reference to the object entrez2symbol_hs, and this may be generating the error. Is there a way to install version 1.4.5, cited on #100, or a workaround to this new error?
The run log from the last attempt is posted below:
Many thanks for your work; I appreciate it. Let me know if you need any more information or if I can assist in any way. Thank you!
Regards,