From peter.ruckdeschel at web.de  Tue May 10 20:25:44 2016
From: peter.ruckdeschel at web.de (Peter Ruckdeschel)
Date: Tue, 10 May 2016 20:25:44 +0200
Subject: [Rd] Storage of byte code-compiled functions in sysdata.rda
In-Reply-To: <alpine.DEB.2.10.1605051445500.12737@luke-Latitude>
References: <5725ED5B.20208@web.de>
	<704D9B27-D7A7-4B46-A2F4-82E0582AC6B5@uiowa.edu>
	<5725F98E.5040609@web.de>
	<alpine.DEB.2.10.1605051445500.12737@luke-Latitude>
Message-ID: <b7aa89a1-9c7a-6bc8-c7e8-c0e7d933bd29@web.de>

Dear Luke,

thanks for taking a look at our problem and for checking it out, in particular for
sending us the tool function getbc.

This really sounds like we have somehow messed up our chain with different versions
of the byte-code compiler. We will try and fix this and will let you know if we succeed.

Thanks again, Peter


Am 05.05.2016 um 22:07 schrieb luke-tierney at uiowa.edu:
> I can't reproduce the more complex version. But the package on CRAN
> fails in the same way on 3.2.3 and 3.3.0.
>
> The problem is that your sysdata.rda includes a function that is
> generating this error. If you do
>
> f <- getFromNamespace(".RMXE", ns ="RobAStRDA")[["GEVFamily"]][["fun.N"]][[1]]
> g <- get("fct", environment(f))
>
> and look at the byte code for g with compiler::disassemble or the
> utility I'll paste in below you get
>
>> getbc(g)
> list(8L, BCMISMATCH.OP)
>
> The only way you can get a file like this is to byte compile and save
> in a version of R with a newer byte code version (the 8L) and then
> load and resave in an older version of R. If you load and run this
> code in an older (or newer) version of R it will revert to the
> standard interpeter using eval but will issue a warning once per
> session. If you try to run it in an R with byte code version 8L you
> get this error.
>
> I can make a small change to that this becomes a once-per-session
> warning, but even then you won't actually be running compiled code.
>
> So I think your task is to figure out how you are ended up with a
> sysdata.rda file created in this incompatible way. Something to look
> for might be whether a call from within your R-devel somehow manages
> to run an R process with an older R version.
>
> Let me know what you find out.
>
> luke
>
> Here is the little utility, adapted from compiler::disassemble:
>
> getbc <- function (code) 
> {
>      .CodeSym <- as.name(".Code")
>      disasm.const <- function(x) if (typeof(x) == "list" && length(x) >
>          0 && identical(x[[1]], .CodeSym))
>          disasm(x)
>      else x
>      disasm <- function(code) {
>          code[[2]] <- compiler:::bcDecode(code[[2]])
>          code[[3]] <- lapply(code[[3]], disasm.const)
>          code
>      }
>      if (typeof(code) == "closure") {
>          code <- .Internal(bodyCode(code))
>          if (typeof(code) != "bytecode")
>              stop("function is not compiled")
>      }
>      invisible(dput(disasm(.Internal(disassemble(code)))[[2]]))
> }
>
> On Sun, 1 May 2016, Peter Ruckdeschel wrote:
>
>> Thanks, Luke, for having a look to it.
>>
>> Sure, I can give you some reproducible example -- even in two degrees of
>> completeness ;-): see below.
>>
>> Thanks again, Peter
>>
>> %-----------------------------------
>> (I) first example
>> %-----------------------------------
>> Just to reproduce the error, on r-devel, try:
>>
>> install.packages("RobAStRDA")
>> require(RobAStRDA)
>> getFromNamespace(".RMXE", ns = "RobAStRDA")[["GEVFamily"]][["fun.N"]][[1]](1.3)
>>
>> %-----------------------------------
>> (II) an example also giving the context
>> %-----------------------------------
>> For the "complete" story, not only the R-code needs to be given, but also the
>> preparation steps to produce the packages on the right R version;
>>
>> so please follow steps (1)--(6) below; I am not 100% sure whether this already gives
>> you all information needed for this, but if not so please let me know.
>>
>> (1) create a minimal R-package "InterpolTry"
>>      with byte-compilation on in the DESCRIPTION file
>>      and with stats::approxfun imported in the NAMESPACE file
>>
>> (2) in an R session on R-devel do
>>
>> require(InterpolTry)
>> x <- 1:100
>> y <- 1:100
>> fun <- approxfun(x,y)
>> ## revise the next line accordingly to your local settings
>> SrcRPathInterpolTry <- <path_to_(source-)R-folder_of_InterpolTry>
>> RdaFile <- file.path(SrcRPathInterpolTry, "sysdata.rda")
>> save(fun, file = RdaFile)
>> tools::resaveRdaFiles(RdaFile)
>>
>> (3) re-build package InterpolTry and re-install it
>>
>> (4) create a minimal R package "UseInterpolTry", again
>>      with byte-compilation on in the DESCRIPTION file
>>      and with stats::approxfun and package "InterpolTry"
>>      imported in the NAMESPACE file
>>
>> (5) in the R folder of R package "UseInterpolTry" write a function
>>      useInterpolFct()  which goes like this
>>
>>      useInterpolFct <- function(x){
>>               fun <- getFromNamespace("fun", ns = "InterpolTry")
>>               fun(x)
>>      }
>>
>>     export this function in the namespace and create an .Rd file to it
>>
>> (6) (re-)build package "UseInterpolTry" and (re-)install it and try
>>
>> require(UseInterpolTry)
>> useInterpolFct(5)
>>
>> Steps (1)--(6) work with R-3.1.3, but no longer with R-devel.
>>
>>
>>
>> Am 01.05.2016 um 14:12 schrieb Tierney, Luke:
>>> Can you provide a complete reproducible example?
>>>
>>> Sent from my iPhone
>>>
>>>> On May 1, 2016, at 6:51 AM, Peter Ruckdeschel <peter.ruckdeschel at web.de> wrote:
>>>>
>>>> Hi r-devels,
>>>>
>>>> we are seeing a new problem with our packages RobAStRDA (just new on CRAN, thanks
>>>> to Uwe and Kurt!) and RobExtremes (to be submitted).
>>>>
>>>> It must be something recent with the way you internally treat/store byte-code compiled
>>>> functions, as we have no problems with R-3.1.3, but do see an "Error in fct(x) : byte code
>>>> version mismatch" with R-devel SVNrev r70532.
>>>>
>>>> Background:
>>>> Starting from several x-y grids, in the sysdata.rda file of RobAStRDA, we store the results
>>>> of calls to approxfun/splinefun to these grids from within a session with pkg RobAStRDA
>>>> require()d.  From pkg RobExtremes we then call these interpolating functions by means of
>>>> a call (essentially) as:
>>>>
>>>> getFromNamespace(".RMXE", ns = "RobAStRDA")[["GEVFamily"]][["fun.N"]][[1]](1.3)
>>>>
>>>> upon which we get the announced "Error in fct(x) : byte code version mismatch" while the same
>>>> code does work for R-3.1.3.
>>>>
>>>> The list element "fun.N" in the above call already accounts for a different behaviour for
>>>> pre R-3.0.0 (would have given "fun.O") and post R-3.0.0 ("fun.N") results of approxfun/
>>>> splinefun, but the interpolating functions in branch "fun.N" have been produced in
>>>> R-devel SVNrev r70532, so we would have expected our code getFromNamespace(.....) above to
>>>> work in R-devel as well.
>>>>
>>>> Could you give us any hints how to
>>>>
>>>> (a) store the interpolating functions resulting from approxfun/splinefun in pkg RobAStRDA
>>>>    correctly in recent R-versions and
>>>> (b) call these functions in pkg RobExtremes ?
>>>>
>>>> We already did import stats::approxfun and stats::splinefun into the NAMESPACEs of pkgs
>>>> RobAStRDA and RobExtremes.
>>>>
>>>> Thanks for your help already,
>>>> Peter
>>>>
>>>>
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[Rd] Storage of byte code-compiled functions in sysdata.rda
Peter Ruckdeschel