[Rcppoctave-user] RcppOctave on Windows: testing needed
Dirk Eddelbuettel
edd at debian.org
Thu Oct 10 15:58:35 CEST 2013
On 10 October 2013 at 09:45, Dominick Samperi wrote:
| Your modified strtest.cpp doesn't help:
:-/
I fear Dominick is correct on the instantiation issues etc pp. Of course,
something reproducible on another OS may help.
We could at some point involve John Eaton (who I was pretty close to when
Octave was my main scripting language and kept up with for a while when I
morphed to R -- but when I stopped maintaining Octave for Debian it got
quieter). I introduced John to the R folks which made him go to one of the
earlier conference. He even hooked up an R - Octave bridge (forget though
which way it operated). Bryan Lewis is a sharp cookie who may be able to
help too, he also has a nascent R - Octave bridge (and has the best name:
Ratlab).
Dirk
|
| ** 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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--
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
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