[Rcpp-devel] Fwd: CRAN submission growfunctions 0.1

[Dirk Eddelbuettel]

Hi Terrance,

On 9 August 2014 at 16:58, terrance savitsky wrote:
| Hi Guys, 
|  
| I embed a data list object of dgCMatrix elements (produced in the same manner
| as used in package, growfunctions) in an .RData file located in the sparseList
| \data folder. I'm not sure what script and data ASAN uses to conduct the memory
| check.  I'm guessing the package examples are run.  So I added an example that
| loads the .RData object embedded with this toy package, sparseList.  Please
| pardon me if my understanding is off.   I also embedd an R script in the single

It's not complicated. 

'R CMD check' needs a code path that does this, which can be as simple as an
example section in the manual page (mayne you meant this by 'added an
example').  Or something tickled via a test script in tests/.

You submitted a CRAN package. It has testable code. It failed. We now need a
_minimal reproducible example_, ideally without a long tail of dependencies,
to examine it.

| toy package .cpp file that generates the same data (list object of dgCMatrix
| objects created using R::Matrix) and runs an example.
|  
| Terrance
| ​
| 
| [icon_10_ge] sparseList_1.1.tar.gz

Can you update to a version which loads data and passes down to the code
which was seen to tickle this?

And then place it somewhere where we can get it with a simple wget or curl call.

Thanks, Dirk
 ​
 
| 
| On Sat, Aug 9, 2014 at 3:02 PM, Kevin Ushey <kevinushey at gmail.com> wrote:
| 
|     Hi Terrance,
| 
|     Can you please try to construct a reproducible example based on the
|     (tagged, potentially offending) line of code -- that is,
| 
|         #4 0x7f79b6541df0 in IGMRFDPMIX
|     /data/gannet/ripley/R/packages/tests-49x/growfunctions/src/dpmix.cpp:63
| 
|     which has the line:
| 
|         C(k,0)          = as<sp_mat>(Cr[k]);
| 
|     Can you construct a small, reproducible example using objects 'C',
|     'Cr' as you construct in the package, and then see if that gives a
|     similar error?
| 
|     Preferably you can construct this using Rcpp Attributes, so an example
|     of the form
| 
|         // [[Rcpp::depends(RcppArmadillo)]]
| 
|         #include <RcppArmadillo.h>
|         using namespace Rcpp;
| 
|         // [[Rcpp::export]]
|         SEXP test(SEXP C, SEXP Cr) {
|           ... use C, Cr as above...
|         }
| 
|         /*** R
|         ... construct C, Cr on the R side as necessary ...
|         */
| 
|     That way, we can 'sourceCpp' it and immediately investigate.
| 
|     Thanks,
|     Kevin
| 
|     On Sat, Aug 9, 2014 at 11:31 AM, terrance savitsky <tds151 at gmail.com>
|     wrote:
|     > Dirk,  Thanks much for taking the time to investigate this issue.  I've
|     > created a package (sparseList_1.0.tar.gz) with a minimal example of what
|     > writing from a list of dgCMatrix matrices at the R layer to a field
|     <sp_mat>.
|     > I had intended to install boot2docker and use load your R-devel set-up to
|     a
|     > container so that I could replicate the ASAN-generated error.  Its taking
|     me
|     > longer than I'd hoped, however, so - for now - I include the package
|     tarball
|     > with the minimal example and also an R script (sparse_list_to_field.R) so
|     > that you may see what the function does.
|     > Terrance
|     >  sparse_list_to_field.R
|     >
|     >  sparseList_1.0.tar.gz
|     >
|     >
|     >
|     > On Sat, Aug 9, 2014 at 11:50 AM, Dirk Eddelbuettel <edd at debian.org>
|     wrote:
|     >>
|     >>
|     >> Terrance,
|     >>
|     >> So I took a look with one of the prebuilt versions of R using the Docker
|     >> container I prepare (see the blog / sanitizers write-up I linked to) as
|     I
|     >> realized that we had a Rcpp Gallery post similar to what that as<>
|     >> conversion
|     >> does.
|     >>
|     >> And no issue with that code.
|     >>
|     >> From a brief look at your package it seems like you are pushing the
|     >> envelope
|     >> a lot harder with fields and list of sparse matrices ( in dpmix.cpp,
|     where
|     >> another ASAN log pointed to ) so you may have to debug around there.
|     >>
|     >> A small reproducible example would surely help us. So far I don't have
|     one
|     >> for as<sp_mat>.
|     >>
|     >> Dirk
|     >>
|     >> --
|     >> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
|     >
|     >
|     >
|     >
|     > --
|     > Thank you, Terrance Savitsky
|     >
|     > _______________________________________________
|     > Rcpp-devel mailing list
|     > Rcpp-devel at lists.r-forge.r-project.org
|     > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
| 
| 
| 
| 
| --
| Thank you, Terrance Savitsky

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org