README.md

In shiauck/cummeRbund_on_RSQLite2.0: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

cummeRbund_on_RSQLite2.0

According to RSQLite 2.0, the following commands are been retired. 1. "RSQLite::make.db.names() is deprecated, please switch to DBI::dbQuoteIdentifier()." 2. "RSQLite::dbGetPreparedQuery() is deprecated, please switch to DBI::dbGetQuery(params = bind.data)."

In cummeRbund source code, the following files use "make.db.names": 1. database-setup.R 2. methods-CuffData.R

And the follwing file uses "dbGetPreparedQuery": 1. database-setup.R

In files using "make.db.names", I simply replace the command with "dbQuoteIdentifier" as RSQLite 2.0 suggested. In the file "database-setup.R", the function "bulk_insert" is been re-writed to use "dbExecute" for insertion of the given data frame.

Installation: 1. git clone https://github.com/shiauck/cummeRbund_on_RSQLite2.0.git 2. tar -czvf cummeRbund.tgz cummeRbund_on_RSQLite2.0 3. R CMD INSTALL --no-lock cummeRbund.tgz

shiauck/cummeRbund_on_RSQLite2.0 documentation built on May 5, 2019, 12:33 p.m.