I tried to first explaining the scenario.
Anyway, this seems to be the point:
Step1:
BuildGraph("POLR2A", fileSAM = "/space/datasets/ord_LiebermanAiden.sam")
no matter what body and result of this function are, the 'fileSAM'
string gets assigned to '.GlobalEnv' for subsequent reuse:
assign("file.SAM", fileSAM, envir = .GlobalEnv)
three other similar strings and the g.Edges datatable (Step2) are also
assigned to global environment.
Step2:
NormaliseEdges(edgesList=g.Edges, fileSAM = file.SAM)
the global variable 'file.SAM', that stores the string above, is used
again: THIS PRODUCES THE ERROR IN OBJECT, even though it did not give
any problem before.
Step2_BIS:
NormaliseEdges(edgesList=g.Edges, fileSAM =
"/space/datasets/ord_LiebermanAiden.sam")
pass a string instead of a global variable containing the string: THIS
DOES NOT PRODUCE ANY ERROR.
Step2_TER:
retEdges <- runNormalisation(miniEdges, file.SAM, 1, 0, 0)
manually call C++ function, using the global variable 'file.SAM'
(miniEdges is a data.frame): THIS DOES NOT PRODUCE ANY ERROR.
The 'runNormalisation' function's signature:
SEXP runNormalisation(Rcpp::DataFrame mEd, std::string samfile, int
nwrks, float e_lm, int chunk)
The code executed within these functions does not seem to play a part in
the error. to me it looks like it has to do with 'file.SAM' scope, or
with variables declared in GlobalEnv in general, but I might be wrong.
Also, it wasn't a problem until early this morning!
Regards,
Fabio
On 08/07/2015 02:19 PM, Dirk Eddelbuettel wrote:
On 7 August 2015 at 13:40, Fabio Tordini wrote:
| Hello,
| I already read the discussion about the issue in object, but I can't
| find a way out!
We can't either.
You supplied a screenful of email but __no reproducible code__ exhibiting an
error we can reproduce. Nobody can help you based on what you wrote here.
Dirk
| That problem came out all of a sudden, in a function that has always
| worked and has not been modified so far.
|
| I describe the problem here. if more code might help, I'll provide it.
|
|
| I have an R function named 'NormaliseEdges', where I set up variables
| and objects and then call:
| retEdges <- runNormalisation(miniEdges, fileSAM, numWrks, edgesProb, grain)
|
| the function called is a c++ function defined as:
| // [[Rcpp::export]]
| SEXP runNormalisation(DataFrame mEd, std::string samfile, int nwrks,
| float e_lm, int chunk)
|
| never had any problems with that.
|
| today it started to crash with the above error.
| Weirdly, this happens only when I call the R function, like:
| NormaliseEdges(g.Edges, file.SAM)
| Error: not compatible with requested type
| Called from: runNormalisation(miniEdges, fileSAM, numWrks, edgesProb, grain)
|
| if I simply call the c++ function it works fine
| retEdges <- runNormalisation(miniEdges, file.SAM, 1, 0, 0)
|
| I double-checked that 'miniEdges' is a data.frame (and it is); also, it
| has always been.
|
|
| I fear this might have something to do with other modifications in other
| files, that somehow affected the whole? is it possible?
| I don't see any other error!
|
|
| Regards,
| Fabio
|
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