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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
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
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
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
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
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
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
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
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
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:
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
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
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