[Bioc-devel] Attention Maintainers: still many stale S4 objects need updating

[Seth Falcon]

Hello BioC package maintainers,

Since R 2.4.0, the internal representation of S4 objects has changed.
We have detected a number of saved S4 objects hiding in rda files
inside BioC packages that were created with a pre-2.4.0 version of R
and need to be updated.

You can use updateObject in Biobase to update such objects.  The
general procedure is to update object "foo" in file "foo.rda" is:

    library(Biobase)
    load("foo.rda")
    foo = updateObject(foo)
    ## test foo looks ok
    save(foo, file="foo.rda", compress=TRUE)
    ## now quite and test the package!

Packages that have data files that need attention are:

ontoTools
    ./ontoTools/data/STMA.rda (1):
         STMA
    ./ontoTools/data/gomfAmat.rda (1):
         gomfAmat
    ./ontoTools/data/GOMF1.10.rda (1):
         GOMF1.10
    ./ontoTools/data/LL2GOMFooMap.1.10.rda (1):
         LL2GOMFooMap.1.10
    ./ontoTools/data/LL2GOMFooc1.10.rda (1):
         LL2GOMFooc1.10
    ./ontoTools/data/go1.10DAG.rda (1):
         go1.10DAG
    ./ontoTools/data/goMFamat.1.10.rda (1):
         goMFamat.1.10

pairseqsim
    [about a bazillion rda files]

stam
    ./stam/data/golubTrain.cv.rda (1):
         golubTrain.cv
    ./stam/data/golubTrain.fit.rda (1):
         golubTrain.fit

There are more details on updating on the developer wiki:

   http://wiki.fhcrc.org/bioc/HowTo/Update_ExpressionSets

I was able to automate some of the updating and have committed changes
to 14 BioC package.  If one of the packages listed below is yours,
please review my change (I ran R CMD check, but didn't look more
closely than that).

Here's my commit message:

    Update S4 objects in rda files

    I used a script to find serialized S4 instances that appeared to have
    been created with an R before the S4SXP was in place.
    
    Biobase::updateObject was then used to update the object and a new rda
    file was written.  All packages passed check after the update, but
    maintainers should review the changes.

And here is the summary of changes (note that many rda files seem to
have been created without compress=TRUE so in some cases we end up
with a nice size reduction):

 GGtools/DESCRIPTION                         |    2 +-
 GGtools/inst/fileDemos/pd.rda               |  Bin 720 -> 720 bytes
 LMGene/DESCRIPTION                          |    2 +-
 LMGene/data/sample.eS.RData                 |  Bin 39671 -> 39867 bytes
 PGSEA/DESCRIPTION                           |    2 +-
 PGSEA/data/nbEset.rda                       |  Bin 947991 -> 948196 bytes
 RBGL/DESCRIPTION                            |    2 +-
 RBGL/data/FileDep.rda                       |  Bin 392 -> 398 bytes
 ScISI/DESCRIPTION                           |    2 +-
 ScISI/data/arp23G.rda                       |  Bin 415 -> 423 bytes
 ScISI/data/arp23Y2HG.rda                    |  Bin 317 -> 320 bytes
 ScISI/data/egEBI16112.rda                   |  Bin 335 -> 339 bytes
 ScISI/data/mapping2SysG.rda                 |  Bin 315 -> 320 bytes
 ScISI/data/mappingsG.rda                    |  Bin 331 -> 336 bytes
 ScISI/inst/Scripts/C1G.rda                  |  Bin 333 -> 333 bytes
 ScISI/inst/extdata/graphs/arp23BPG.rda      |  Bin 276 -> 279 bytes
 ScISI/inst/extdata/graphs/arp23CMG.rda      |  Bin 2323 -> 399 bytes
 ScISI/inst/extdata/graphs/arp23G.rda        |  Bin 415 -> 423 bytes
 ScISI/inst/extdata/graphs/cfiaCMG.rda       |  Bin 1397 -> 361 bytes
 ScISI/inst/extdata/graphs/cfiaG.rda         |  Bin 351 -> 359 bytes
 ScISI/inst/extdata/graphs/ppi1G.rda         |  Bin 916 -> 306 bytes
 ScISI/inst/extdata/graphs/ppi2G.rda         |  Bin 916 -> 308 bytes
 affycoretools/DESCRIPTION                   |    2 +-
 affycoretools/inst/examples/exprSet2.Rdata  |  Bin 732053 -> 732264 bytes
 apComplex/DESCRIPTION                       |    2 +-
 apComplex/data/HMSPCIgraph.rda              |  Bin 37506 -> 37071 bytes
 apComplex/data/TAPgraph.rda                 |  Bin 17692 -> 17699 bytes
 apComplex/data/apEXG.rda                    |  Bin 367 -> 364 bytes
 applera/data/test.rda                       |  Bin 402075 -> 141879 bytes
 beadarraySNP/DESCRIPTION                    |    2 +-
 beadarraySNP/data/QC.260.rda                |  Bin 1285 -> 1281 bytes
 cghMCR/DESCRIPTION                          |    2 +-
 cghMCR/data/sampleData.rda                  |  Bin 1558027 -> 322315 bytes
 graph/DESCRIPTION                           |    2 +-
 graph/data/integrinMediatedCellAdhesion.rda |  Bin 2785 -> 1342 bytes
 ontoTools/DESCRIPTION                       |    4 ++--
 ontoTools/data/A.csr.rda                    |  Bin 643 -> 436 bytes
 ontoTools/data/goMFgraph.1.10.rda           |  Bin 101699 -> 103245 bytes
 ontoTools/inst/doc/sgdiOnto.pdf             |  Bin 1246523 -> 6907368 bytes
 panp/DESCRIPTION                            |    2 +-
 panp/data/gcrma.exprSet.rda                 |  Bin 1205072 -> 573504 bytes
 panp/data/test133a.rda                      |  Bin 1159421 -> 300243 bytes
 reb/DESCRIPTION                             |    2 +-
 reb/data/mcr.eset.rda                       |  Bin 480594 -> 480595 bytes
 44 files changed, 14 insertions(+), 14 deletions(-)

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org