I recently started working with RNA-Seq and I reached the step where I analyze my data using cummeRbund. I thought of doing some tutorials first to get to know the package, but I'm having problems with that.

I followed the instructions in the sample workflow:

source("https://bioconductor.org/biocLite.R")
biocLite("cummeRbund")
library(cummeRbund)

cuff <- readCufflinks(dir=system.file("extdata", package="cummeRbund"))

But when I run the readCufflinks command, the following errors appear:

Creating database /Library/Frameworks/R.framework/Versions/3.4/Resources/library/cummeRbund/extdata/cuffData.db
Reading Run Info File /Library/Frameworks/R.framework/Versions/3.4/Resources/library/cummeRbund/extdata/run.info
Writing runInfo Table
Reading Read Group Info  /Library/Frameworks/R.framework/Versions/3.4/Resources/library/cummeRbund/extdata/read_groups.info
Writing replicates Table
Reading /Library/Frameworks/R.framework/Versions/3.4/Resources/library/cummeRbund/extdata/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Error: Column name mismatch.
In addition: There were 50 or more warnings (use warnings() to see the first 50)

I thought it was weird.  Would this be an issue of installation? Any help is welcomed!

Some guys suggested that I should install RSQLite1.1-2, not 2.0​. But when I installed 2.0 vesion, "Error: package or namespace load failed for ‘Gviz’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])", there are RSQLite need >= 2.0 to load Gviz​.

Hello,

I am facing the exact issue. Were you able to get through this error? 
Please let me know

Thanks,