I confirm you have a solution with GitHub Rcpp.
Thanks very much for your effort.
pj
On Mon, Feb 1, 2016 at 12:06 PM, Qiang Kou wrote:
> Hi, Paul,
>
> I am sorry I deleted the branch after merging.
>
> You can just do as Jonathan said.
>
> Best wishes,
>
> KK
>
> On Mon, Feb 1, 2016 at 11:16 A
Hi, Paul,
I am sorry I deleted the branch after merging.
You can just do as Jonathan said.
Best wishes,
KK
On Mon, Feb 1, 2016 at 11:16 AM, Paul Johnson wrote:
> Thanks, KK for studying this one.
>
> Am I doing this wrong?
>
> > devtools::install_github("thirdwing/Rcpp", ref = "subsetter")
>
Any reason not to get it from RcppCore/Rcpp? History shows the fix was
pulled in: https://github.com/RcppCore/Rcpp/commits/master
On my end, I just installed Rcpp via
> install_github("RcppCore/Rcpp")
and then re-installed openxlsx from CRAN via
> install.packages("openxlsx")
The script I ha
Thanks, KK for studying this one.
Am I doing this wrong?
> devtools::install_github("thirdwing/Rcpp", ref = "subsetter")
Downloading GitHub repo thirdwing/Rcpp@subsetter
from URL https://api.github.com/repos/thirdwing/Rcpp/zipball/subsetter
Error in download(dest, src, auth) : Not Found (HTTP 404
On 30 January 2016 at 13:58, Kevin Ushey wrote:
| And I now have a MRE:
|
| #include
| using namespace Rcpp;
|
| // [[Rcpp::export]]
| IntegerVector ouch(IntegerVector x, IntegerVector y) {
| IntegerVector result;
| result = x[y - 1];
| return result;
| }
|
| /*** R
| x <- 1:1E6
| y <- 1
And I now have a MRE:
#include
using namespace Rcpp;
// [[Rcpp::export]]
IntegerVector ouch(IntegerVector x, IntegerVector y) {
IntegerVector result;
result = x[y - 1];
return result;
}
/*** R
x <- 1:1E6
y <- 1:1E6
gctorture(TRUE)
x <- ouch(x, y)
gctorture(FALSE)
*/
This fails pretty rel
I think I know what's going on now. Effectively, we're 'evaluating'
the sugar proxy vector, getting a pointer to a (temporary,
unprotected) R data structure, and then storing that pointer. Later,
when we attempt to allocate the output vector (with `no_init`) the GC
runs and cleans up our pointer.
Another thing confused me is the segfault only happens when the
IntegerVector is significantly long.
Best,
KK
On Sat, Jan 30, 2016 at 2:57 AM, Kevin Ushey wrote:
> Hmm, I have one thought: we try to re-use the indices from an
> IntegerVector, but the type here is actually a sugar type:
>
>
Hmm, I have one thought: we try to re-use the indices from an
IntegerVector, but the type here is actually a sugar type:
Rcpp::SubsetProxy<13, Rcpp::PreserveStorage, 13, true,
Rcpp::sugar::Minus_Vector_Primitive<13, true, Rcpp::Vector<13,
Rcpp::PreserveStorage> > >::get_vec (this=)
Ie
On 29 January 2016 at 17:55, Qiang Kou wrote:
| Hi, Paul, can you try my fork of Rcpp? You can install it by the line below:
|
| devtools::install_github("thirdwing/Rcpp", ref = "subsetter")
|
| This fixed the segfault on my Ubuntu machine.
Yay. Nice work!
| The difference can be found from [
Hi, Paul, can you try my fork of Rcpp? You can install it by the line below:
devtools::install_github("thirdwing/Rcpp", ref = "subsetter")
This fixed the segfault on my Ubuntu machine.
The difference can be found from [1].
In *subsetter*, if an IntegerVector passed in, we will try to reuse it.
Hi, Kevin, I was also trying to track this down yesterday.
>From the debugging info below, *indices_n* is not equal to length of
*indices*, which I don't quite understand.
Program received signal SIGSEGV, Segmentation fault.
0x72ed5c4e in Rcpp::SubsetProxy<13, Rcpp::PreserveStorage, 13,
On 29 January 2016 at 11:27, Kevin Ushey wrote:
| When I add some debug printing to the associated subscripting line
|
(https://github.com/awalker89/openxlsx/blob/b92bb3acdd6ea759be928c298c6faeef2f26fa3e/src/cppFunctions.cpp#L2608),
| I see:
|
|colNumbers.size(): 98,03,150
|charCols.size
When I add some debug printing to the associated subscripting line
(https://github.com/awalker89/openxlsx/blob/b92bb3acdd6ea759be928c298c6faeef2f26fa3e/src/cppFunctions.cpp#L2608),
I see:
colNumbers.size(): 98,03,150
charCols.size(): 95,94,546
It looks to me like the package is erroneously
On 28 January 2016 at 21:47, Paul Johnson wrote:
| Thanks.
|
| On Thu, Jan 28, 2016 at 2:42 PM, Dirk Eddelbuettel wrote:
| >
| > Paul,
| >
| > I can reproduce the segfault on Ubuntu 15.10, "everything current".
| > Definitely a valid bug report, though a 30mb xlsx may not qualify as
| > minimal.
Thanks.
On Thu, Jan 28, 2016 at 2:42 PM, Dirk Eddelbuettel wrote:
>
> Paul,
>
> I can reproduce the segfault on Ubuntu 15.10, "everything current".
> Definitely a valid bug report, though a 30mb xlsx may not qualify as
> minimal.
>
I'm glad I did not attach it to an email, then :)
The data xlsx
On 28 January 2016 at 17:42, Qiang Kou wrote:
| No errors on OSX with R 3.2.2.
|
| Rcpp and openxlsx are installed from CRAN with type = "source".
Very helpful -- thank you!
Dirk
--
http://dirk.eddelbuettel.com | @eddelbuettel | [email protected]
___
No errors on OSX with R 3.2.2.
Rcpp and openxlsx are installed from CRAN with type = "source".
KK
On Thu, Jan 28, 2016 at 4:59 PM, Dirk Eddelbuettel wrote:
>
> Paul,
>
> It does not appear to be a new bug. As this was easily scriptable, I tested
> Rcpp 0.12.3, 0.12.2, 0.12.1, 0.12.0, 0.11.6, 0
Paul,
It does not appear to be a new bug. As this was easily scriptable, I tested
Rcpp 0.12.3, 0.12.2, 0.12.1, 0.12.0, 0.11.6, 0.11.5 and 0.11.4 -- all by
getting the tarball off CRAN, installing, re-installing openxlsx and then
running your script. They all died by segfault.
It may be an old bu
Paul,
I can reproduce the segfault on Ubuntu 15.10, "everything current".
Definitely a valid bug report, though a 30mb xlsx may not qualify as
minimal.
I won't have time to look at this for a while though so if you find that
downgrading helps that may be your best bet.
Thanks for the report. I
Thanks -- this is helpful. Based on the stack trace, it looks like the
error is coming out of here:
https://github.com/awalker89/openxlsx/blob/b92bb3acdd6ea759be928c298c6faeef2f26fa3e/src/cppFunctions.cpp#L2608
Whether this is an error in the Rcpp SubsetProxy class, or the vectors
the package aut
Thanks. It has been a while since I used gdb, and I can't recall doing
it with R.
It looks discouraging to me because I see "" in the
symbols. I have to re-learn what symbols are and where to get them.
I deleted openxlsx and got clean re-install before trying this.
What's this one mean?
warnin
A C++ stack trace would be very helpful. Can you try running R with gdb, e.g.
R -d gdb -f example.R
where 'example.R' is the path to your script that reproduces the
segfault? Hopefully, 'gdb' can provide more context on where the error
is occurring.
For what it's worth, the file did open suc
Paul,
Advice is always the same: fresh compilation of all dependent packages.
Dirk
--
http://dirk.eddelbuettel.com | @eddelbuettel | [email protected]
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