initializeScenic

[ekinsnmz]

Hello, I am trying to do initiliazing step of scenic. I tried to used fly datase. Here is my code and the error that i received. I tried to instal arrow package, but did not work. Any help to solve this problem?

code: dbFiles<- 'https://resources.aertslab.org/cistarget/databases/drosophila_melanogaster/dm6/flybase_r6.02/mc8nr/gene_based/dm6-5kb-upstream-full-tx-11species.mc8nr.genes_vs_motifs.rankings.feather'

dir.create("cisTarget_databases") setwd("cisTarget_databases")

for(featherURL in dbFiles){ download.file(featherURL, destfile=basename(featherURL)) # saved in current dir }

setwd(here::here())

Config object

dbDir="/.../cisTarget_databases" # RcisTarget databases location

org="dmel" defaultDbNames dbs <- defaultDbNames[[org]] dbs

Check if they exist:

lapply(dbs,function(x) file.exists(file.path(dbDir, x)))

for(x in dbs) { dbPath <- file.path(dbDir, x) message(paste(dbPath, " --> Exists?:", file.exists(dbPath))) }

scenicOptions <- initializeScenic(org="dmel", dbs = defaultDbNames[["dmel"]], dbDir="cisTarget_databases", nCores=4)

ERROR:

Motif databases selected: dm6-5kb-upstream-full-tx-11species.mc8nr.feather [1] "NotImplemented: Support for codec 'zstd' not built" Using the column '128up' as feature index for the ranking database. Error in (function (cond) : error in evaluating the argument 'object' in selecting a method for function 'getRanking': NotImplemented: Support for codec 'zstd' not built In order to read this file, you will need to reinstall arrow with additional features enabled. Set one of these environment variables before installing:

• LIBARROW_MINIMAL=false (for all optional features, including 'zstd')
• ARROW_WITH_ZSTD=ON (for just 'zstd')

See https://arrow.apache.org/docs/r/articles/install.html for details In addition: Warning messages: 1: In initializeScenic(org = "dmel", dbs = defaultDbNames[["dmel"]], : It was not possible to load the following databses; check whether they are downloaded correctly: dm6-5kb-upstream-full-tx-11species.mc8nr.feather 2: In RcisTarget::importRankings(dbFile, columns = rnktype) : The following columns are missing from the database: features

to load arrow: Sys.setenv("LIBARROW_BINARY" = FALSE) Sys.setenv("LIBARROW_MINIMAL" = FALSE) Sys.setenv("ARROW_R_DEV" = TRUE) install.packages("arrow") install_arrow(binary = FALSE, minimal = FALSE)

[saumyaj2001]

Has this issue been resolved? I'm having the same issue: "1: In initializeScenic(org = "dmel", dbs = defaultDbNames[["dmel"]], : It was not possible to load the following databses; check whether they are downloaded correctly: dm6-5kb-upstream-full-tx-11species.mc8nr.feather 2: In RcisTarget::importRankings(dbFile, columns = rnktype) : The following columns are missing from the database: features"

Thank you!

[abspangler13]

I'm also having this issue. Has anyone found a solution?

[xg1213]

Did you find a solution? Thanks.