Error in dbFileConnect(file)

[sunliang3361]

Hi, When I try to run your sample code and data, I found the following error messages, do you know what my problem is? I can successfully load all required R packages. Thank you

-------error message below_---------

suppressPackageStartupMessages(library(SummarizedExperiment)) se <- tximeta(coldata) importing quantifications reading in files with read_tsv 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 found matching transcriptome: [ Gencode - Homo sapiens - release 29 ] loading existing TxDb created: 2020-06-05 21:23:05 Error in dbFileConnect(file) : DB file '/Users/xxx/Library/Caches/BiocFileCache/13d2eae3fb0a_13d2eae3fb0a.sqlite' not found

[sunliang3361]

These are all codes: library(tximeta) library(fishpond) library(macrophage)

library(swish)

dir <- system.file("extdata", package="macrophage") coldata <- read.csv(file.path(dir, "coldata.csv")) coldata <- coldata[,c(1,2,3,5)] names(coldata) <- c("names","id","line","condition") coldata$files <- file.path(dir, "quants", coldata$names, "quant.sf.gz") all(file.exists(coldata$files))

suppressPackageStartupMessages(library(SummarizedExperiment))

se <- tximeta(coldata)

[mikelove]

This is actually a tximeta issue, so maybe you can post either on that GitHub or on https://support.bioconductor.org if the following link doesn't help:

https://bioconductor.org/packages/release/bioc/vignettes/tximeta/inst/doc/tximeta.html#errors_connecting_to_a_database

What happened is that the files in the cache were removed but not by BiocFileCache which manages the cache directory. So BiocFileCache throws an error when the file it expects to be present is not.