getLindelScores Error

[ericmalekos]

Hi, I'm running into the following error when I try to run getLindelScores as described in the documentation/

> flank5 <- "ACCTTTTAATCGA" #13bp
> spacer <- "TGCTGATGCTAGATATTAAG" #20bp
> pam    <- "TGG" #3bp
> flank3 <- "CTTTTAATCGATGCTGATGCTAGATATTA" #29bp
> input <- paste0(flank5, spacer, pam, flank3)
> results <- getLindelScores(input)
Error in checkForRemoteErrors(lapply(cl, recvResult)) : 
  one node produced an error: error in evaluating the argument 'x' in selecting a method for function 'query': Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
✖ Problematic argument:
• ..1 = Inf
ℹ Did you misspell an argument name?

I have run many of the other methods without issue - the exception being getDeepHFScores, which I have opened a separate issue for.

Session info:
> sessionInfo(package = NULL)
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Pop!_OS 22.04 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/Los_Angeles
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] crisprScore_1.4.0     crisprScoreData_1.4.0 ExperimentHub_2.8.1   AnnotationHub_3.8.0   BiocFileCache_2.8.0   dbplyr_2.4.0         
[7] BiocGenerics_0.46.0  

[Jfortin1]

Hi @ericmalekos, we fixed a few bugs today; could you try 1.7.2 of the devel branch to see if you have the same problems?

[ericmalekos]

Hi @Jfortin1 I'm having an odd error with Bioconductor requiring R 4.4 which is not released yet.

> BiocManager::install(version="devel")
Error: Bioconductor version '3.19' requires R version '4.4'; use `version = '3.18'`
  with R version 4.3; see https://bioconductor.org/install

When I instead try the devtools install option I only see up to version 1.6.0 available for install.

> install_github("crisprVerse/crisprScore")
Downloading GitHub repo crisprVerse/crisprScore@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
...
34: crisprSco... (1.4.0     -> 1.6.0    ) [CRAN]

So you have suggestions for downloading 1.7.2?

[ericmalekos]

Doh! I should've had the sense to try BiocManager::install(version="3.18"). The install works as expected now. It might be good to update the README so to reduce confusion.

It is working now!