[Rcppoctave-user] RcppOctave on Windows: testing needed

[Dominick Samperi]

Your modified strtest.cpp doesn't help:

** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
sh: line 1: 28714 Abort trap: 6
'/Library/Frameworks/R.framework/Resources/bin/R' --no-save --slave 2>&1 <
'/var/folders/fq/2th4vc9n1mq9cxv5nl9bmzkc0000gn/T//RtmpSQ4FV7/file6fc0345d6d7c'
R(28714) malloc: *** error for object 0x7fff7a01b570: pointer being freed
was not allocated
*** set a breakpoint in malloc_error_break to debug
ERROR: loading failed
* removing ‘/Users/dsamperi/Library/R/3.0/library/Rcpp’
* restoring previous ‘/Users/dsamperi/Library/R/3.0/library/Rcpp’


On Thu, Oct 10, 2013 at 4:18 AM, Renaud Gaujoux <
renaud at mancala.cbio.uct.ac.za> wrote:

> Can you try with this modified version of the file?
> I wrapped the const char* strings into std::string, maybe this will make
> Mac happier.
>
> Let's communicate on this Mac issue off Rcpp-devel list for now on, since
> it is not directly related to Rcpp, but keep rcppoctave-user (where we are
> currently alone with Dirk :)). I will send a summary of the findings at the
> end. People that are keen to participate can subscribe to the
> rcppoctave-user list:
>
> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>
>
>
>
> On 10 October 2013 07:01, Dominick Samperi <djsamperi at gmail.com> wrote:
>
>> It appears that there is some conflict between Rcpp and Octave under
>> Mac OS X that doesn't depend on the design of RcppOctave. Just
>> drop the files strtest.cpp and Makevars (attached) into Rcpp/src and
>> run R CMD INSTALL Rcpp. This leads to a memory error. The file
>> strtest.cpp was stripped out of rcpp_octave.cpp, but it does not
>> use RcppOctave or Rcpp (it is just a trivial Octave client).
>>
>> Since the problem is OS-dependent, it might have something do to
>> with static initializers in the Octave string_vector class, or perhaps
>> there
>> is a MacOS-specific conflict with std::string.
>>
>>
>>
>> On Wed, Oct 9, 2013 at 4:21 AM, Renaud Gaujoux <
>> renaud at mancala.cbio.uct.ac.za> wrote:
>>
>>> You are a resourceful person Dominick! :D
>>> I was not thinking in going Mac for now, because I can't test anything,
>>> but it will be great if we manage our way through it as well.
>>>
>>> 1. In src/modules/Makefile.in, the '-F' flag (for framework) is not
>>>>      recognized by mkoctfile, so I added this temporary work-around:
>>>>
>>>> #R_LDFLAGS = @R_LDFLAGS@
>>>> R_LDFLAGS = -L/Library/Frameworks/R.framework/Libraries -lR
>>>>
>>>
>>> One can probably test for Mac in configure.in and tweak the R_LDFLAGS
>>> for this platform only.
>>>
>>>>
>>>> 2. Parsing the man files o_whatever.Rd fails (attempt to
>>>>     free an unallocated pointer), so I removed all of these
>>>>     man pages for now (the failure occurs in
>>>>    <R>/src/library/tools/R/Rd.R, function .build_Rd_db(),
>>>>    where .fetch_Rd_object is applied to each Rd file).
>>>>
>>>
>>> The o_*.Rd files document more R-friendly wrappers to octave functions.
>>> They contain \Sexp statements that retrieve Octave help files of the
>>> associated function via RcppOctave o_help function:
>>>
>>> \Sexpr[results=rd,stage=render]{RcppOctave::o_help(<octave_function_name>,
>>> format='rd')}
>>>
>>> For packages that contain such expressions in man pages, R CMD build
>>> also generate the manual pdf, by installing the package in a temp directory
>>> and evaluating the code in all \Sexpr statements. On Windows, R CMD INSTALL
>>> --build also renders the man pages.
>>> So the issue will probably solves away when the package loads properly.
>>>
>>> For quick testing compilation and load on Windows, I run R CMD INSTALL
>>> directly on the package source directory with flag --no-help. To ensure a
>>> fresh compilation at each run I use --preclean which runs the cleanup
>>> script, and removes everything, including the .o, .so, .dll, .oct files:
>>>
>>> # mkdir libtest
>>> R --vanilla CMD INSTALL -l libtest --no-help --preclean pkg_src_directory
>>>
>>>
>>>> 3. With these changes the build gets to the point where
>>>>     the install process checks if the package can be
>>>>     loaded, and fails with:
>>>>
>>>> ** testing if installed package can be loaded
>>>> sh: line 1: 55395 Abort trap: 6
>>>> '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --slave 2>&1 <
>>>> '/var/folders/fq/2th4vc9n1mq9cxv5nl9bmzkc0000gn/T//RtmpbjkEA7/filed5d471d0dd21'
>>>> R(55395) malloc: *** error for object 0x7fff7684d570: pointer being
>>>> freed was not allocated
>>>> *** set a breakpoint in malloc_error_break to debug
>>>> ERROR: loading failed
>>>> * removing ‘/Users/dsamperi/Library/R/3.0/library/RcppOctave’
>>>> * restoring previous ‘/Users/dsamperi/Library/R/3.0/library/RcppOctave’
>>>>
>>>> 4. If I ignore this and try to run library(RcppOctave) in R I get:
>>>>
>>>> > library(RcppOctave)
>>>> Loading required package: Rcpp
>>>> Loading required package: pkgmaker
>>>> Loading required package: registry
>>>> R(55403) malloc: *** error for object 0x7fff7684d570: pointer being
>>>> freed was not allocated
>>>> *** set a breakpoint in malloc_error_break to debug
>>>> Abort trap: 6
>>>>
>>>> 5. Setting the breakpoint as instructed was not very helpful
>>>> as the malloc code does not have symbols and cannot be
>>>> traced.
>>>>
>>>>
>>> I will double check for bad allocations in the code, but will
>>> unfortunately be limited in my ability to debug this.
>>>
>>> Renaud
>>>
>>>
>>
>>
>
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