stefanedwards/r-string

Automatically exported from code.google.com/p/r-string

r-string's Issues

Add data cache building.

We need to add (and test) the building of a data-object.

Original issue reported on code.google.com by stefan.mckinnon.edwards on 9 Oct 2012 at 7:45

Make test routine for mapped data.

Up to now we only test the hardcoded ensembl* data; but we also need to make a 
routine that makes fictional mappings to an integer based identifier.

Original issue reported on code.google.com by stefan.mckinnon.edwards on 9 Oct 2012 at 8:35

• Blocking: #4

Add support for STITCH

Add support for STITCH, http://stitch.embl.de/.

Downloads and format seem similar 
(http://stitch.embl.de/cgi/show_download_page.pl?UserId=8lY1X1dK7HHW&sessionId=c
UISm2e96R8k).

Original issue reported on code.google.com by stefan.mckinnon.edwards on 2 Apr 2013 at 8:11

Improve documentation on STRING.db!

Generally, documentation on STRING.db needs heavily improvement.

Original issue reported on code.google.com by stefan.mckinnon.edwards on 8 Oct 2012 at 7:33

dbconn() and dbfile() are not exported!

What steps will reproduce the problem?
1. Install a spin-off library, e.g. STRING.Hs.db.
2. Load the library in R.
3. Try to access STRING.Hs_dbconn().


I believe they simply need to be stated in NAMESPACE.

Original issue reported on code.google.com by stefan.mckinnon.edwards on 29 Jan 2013 at 6:42

Create data-package based on test-data.

We need one of the STRING.T1.db, STRING.T2.db and STRING.T2.db packages for 
testing full functionality and setup of packages.

Original issue reported on code.google.com by stefan.mckinnon.edwards on 9 Oct 2012 at 8:22

• Blocked on: #5

Remove support for DB Schema 0.1

The presence of DB Schema 0.1 is a nuisance for development. Remove them, but 
keep function name structures (e.g. getPPI.0.2).

Original issue reported on code.google.com by stefan.mckinnon.edwards on 9 Oct 2012 at 7:48

Add method to get all protein-links

Lina wanted to retrieve all protein-linkts. Let's add this functionality.


This was the conclusion of how it should be done, circa:

sql <- "SELECT g1.gene as id1, g2.gene as id2, score FROM ensembl 
        INNER JOIN ensembl_ids AS g1 ON g1.id=id1 
        INNER JOIN ensembl_ids AS g2 ON g2.id=id2 
        WHERE score >= @score ORDER BY id1 LIMIT 10;"
threshold <- 800
dbGetQuery(STRING.Hs.db:::STRING.Hs_dbconn(), sql, data.frame(score=threshold))
#               id1             id2 score
#1  ENSP00000000233 ENSP00000234313   904
#2  ENSP00000000233 ENSP00000254584   982
#3  ENSP00000000233 ENSP00000262305   921
#4  ENSP00000000233 ENSP00000281419   891
#5  ENSP00000000233 ENSP00000296557   967
#6  ENSP00000000233 ENSP00000350199   958
#7  ENSP00000000233 ENSP00000350297   939
#8  ENSP00000000233 ENSP00000354398   818
#9  ENSP00000000233 ENSP00000355153   949
#10 ENSP00000000233 ENSP00000355759   865




* Lina from ki.se wrote personally to me around 28. jan 2013.

Original issue reported on code.google.com by stefan.mckinnon.edwards on 2 Apr 2013 at 7:41

Add function for retrieving all protein-links above a threshold.

This function was in the initial developing phase. How come it disappeared? 

Anyhow, we want to add a function:
getAllPPI in STRING.db/R/generics.R
which returns a data-frame.
And similar:
STRING.{organism-shortname}.AllPPI in STRING.db/inst/extdata/all.funcs.R

Original issue reported on code.google.com by stefan.mckinnon.edwards on 29 Jan 2013 at 6:49

• Merged into: #10

R CMD check is not successful on an organism package.

What steps will reproduce the problem?
1. Run build.packages.R
2. Run `R CMD check STRING.Bt.db`

What is the expected output? What do you see instead?
Notable errors:
* checking whether the namespace can be loaded with stated dependencies ... 
WARNING
Error: .onLoad failed in loadNamespace() for 'STRING.Bt.db', details:
  call: is(object, Cl)
  error: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': Error in do.call(as.character(drvName), list(...)) : 
  could not find function "SQLite"
Calls: <Anonymous> -> .valueClassTest -> is -> is -> do.call
Execution halted

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.



* checking whether the namespace can be unloaded cleanly ... WARNING
Error: .onLoad failed in loadNamespace() for 'STRING.Bt.db', details:
  call: is(object, Cl)
  error: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': Error in do.call(as.character(drvName), list(...)) : 
  could not find function "SQLite"
Calls: <Anonymous> -> .valueClassTest -> is -> is -> do.call
Execution halted


* checking Rd cross-references ... WARNING
Unknown package(s) 'STRING.Bt_dbconn' in Rd xrefs



Additional errors in log for pdf and data compression optimisation. 

Original issue reported on code.google.com by stefan.mckinnon.edwards on 2 Apr 2013 at 8:57

Attachments:

• 00check.log

R CMD Check does not like require(RSQLite) in .onLoad

In all.funcs.R, usage of dbConnect and RSQLite gives errors:

  * checking R code for possible problems ... NOTE
  File ‘STRING.T1.db/R/all.funcs.R’:
    .onLoad calls:
      require(RSQLite)

  Package startup functions should not change the search path.
  See section ‘Good practice’ in ?.onAttach.

Original issue reported on code.google.com by stefan.mckinnon.edwards on 23 Oct 2012 at 10:17

makePackage needs argument build

An extra argument is needed for makePackage-function, to indicate whether the 
package should be built to a zipped file.

Original issue reported on code.google.com by stefan.mckinnon.edwards on 23 Oct 2012 at 6:00