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 <[email protected]> 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 <[email protected]> | 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 <[email protected]> | 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 | [email protected] | > | > | > | > | > -- | > Thank you, Terrance Savitsky | > | > _______________________________________________ | > Rcpp-devel mailing list | > [email protected] | > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel | | | | | -- | Thank you, Terrance Savitsky -- http://dirk.eddelbuettel.com | @eddelbuettel | [email protected] _______________________________________________ Rcpp-devel mailing list [email protected] https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
