<div dir="ltr">Hi, Paul,<div><br></div><div>I am sorry I deleted the branch after merging.</div><div><br></div><div>You can just do as Jonathan said.</div><div><br></div><div>Best wishes,</div><div><br></div><div>KK</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Feb 1, 2016 at 11:16 AM, Paul Johnson <span dir="ltr"><<a href="mailto:pauljohn32@gmail.com" target="_blank">pauljohn32@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Thanks, KK for studying this one.<br>
<br>
Am I doing this wrong?<br>
<span class=""><br>
> devtools::install_github("thirdwing/Rcpp", ref = "subsetter")<br>
</span>Downloading GitHub repo thirdwing/Rcpp@subsetter<br>
from URL <a href="https://api.github.com/repos/thirdwing/Rcpp/zipball/subsetter" rel="noreferrer" target="_blank">https://api.github.com/repos/thirdwing/Rcpp/zipball/subsetter</a><br>
Error in download(dest, src, auth) : Not Found (HTTP 404).<br>
> sessionInfo()<br>
<span class="">R version 3.2.3 (2015-12-10)<br>
Platform: x86_64-pc-linux-gnu (64-bit)<br>
Running under: Ubuntu 15.10<br>
<br>
locale:<br>
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C<br>
</span><span class=""> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8<br>
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8<br>
</span> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C<br>
 [9] LC_ADDRESS=C               LC_TELEPHONE=C<br>
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C<br>
<br>
attached base packages:<br>
[1] stats     graphics  grDevices utils     datasets  methods   base<br>
<span class=""><br>
loaded via a namespace (and not attached):<br>
</span>[1] httr_1.1.0      R6_2.1.1        tools_3.2.3     curl_0.9.5<br>
[5] memoise_0.2.1   git2r_0.13.1    digest_0.6.8    devtools_1.10.0<br>
<br>
<br>
I'm glad I found MLPACK while looking at your GitHub. That has neat<br>
features, which I'll try out. We have a big data workgroup here and<br>
I'll look smart.<br>
<div class="HOEnZb"><div class="h5"><br>
<br>
On Fri, Jan 29, 2016 at 4:55 PM, Qiang Kou <<a href="mailto:qkou@umail.iu.edu">qkou@umail.iu.edu</a>> wrote:<br>
> Hi, Paul, can you try my fork of Rcpp? You can install it by the line below:<br>
><br>
> devtools::install_github("thirdwing/Rcpp", ref = "subsetter")<br>
><br>
> This fixed the segfault on my Ubuntu machine.<br>
><br>
> The difference can be found from [1].<br>
><br>
> In subsetter, if an IntegerVector passed in, we will try to reuse it. This<br>
> led to a segfault in this case, which I don't know why.<br>
><br>
> Dirk and Kevin, do you have any thoughts on it?<br>
><br>
> Best wishes,<br>
><br>
> KK<br>
><br>
> [1]<br>
> <a href="https://github.com/thirdwing/Rcpp/commit/216c5220bcb84778a656b3496d0f1803b973ef61" rel="noreferrer" target="_blank">https://github.com/thirdwing/Rcpp/commit/216c5220bcb84778a656b3496d0f1803b973ef61</a><br>
><br>
><br>
> On Fri, Jan 29, 2016 at 3:00 PM, Qiang Kou <<a href="mailto:qkou@umail.iu.edu">qkou@umail.iu.edu</a>> wrote:<br>
>><br>
>> Hi, Kevin, I was also trying to track this down yesterday.<br>
>><br>
>> From the debugging info below, indices_n is not equal to length of<br>
>> indices, which I don't quite understand.<br>
>><br>
>> Program received signal SIGSEGV, Segmentation fault.<br>
>><br>
>> 0x00007ffff2ed5c4e in Rcpp::SubsetProxy<13, Rcpp::PreserveStorage, 13,<br>
>> true, Rcpp::sugar::Minus_Vector_Primitive<13, true, Rcpp::Vector<13,<br>
>> Rcpp::PreserveStorage> > >::get_vec (this=this@entry=0x7fffffff79a0)<br>
>><br>
>>     at<br>
>> /usr/local/lib/R/site-library/Rcpp/include/Rcpp/vector/Subsetter.h:200<br>
>><br>
>> 199             output[i] = lhs[ indices[i] ];<br>
>><br>
>> (gdb) p i<br>
>><br>
>> $1 = 33622<br>
>><br>
>> (gdb) p indices[i]<br>
>><br>
>> Cannot access memory at address 0x34c6e000<br>
>><br>
>> (gdb) p indices_n<br>
>><br>
>> $2 = 9594546<br>
>><br>
>><br>
>> On Fri, Jan 29, 2016 at 2:29 PM, Dirk Eddelbuettel <<a href="mailto:edd@debian.org">edd@debian.org</a>> wrote:<br>
>>><br>
>>><br>
>>> On 29 January 2016 at 11:27, Kevin Ushey wrote:<br>
>>> | When I add some debug printing to the associated subscripting line<br>
>>> |<br>
>>> (<a href="https://github.com/awalker89/openxlsx/blob/b92bb3acdd6ea759be928c298c6faeef2f26fa3e/src/cppFunctions.cpp#L2608" rel="noreferrer" target="_blank">https://github.com/awalker89/openxlsx/blob/b92bb3acdd6ea759be928c298c6faeef2f26fa3e/src/cppFunctions.cpp#L2608</a>),<br>
>>> | I see:<br>
>>> |<br>
>>> |    colNumbers.size(): 98,03,150<br>
>>> |    charCols.size(): 95,94,546<br>
>>> |<br>
>>> | It looks to me like the package is erroneously attempting to subset<br>
>>> | vectors of different sizes, causing out-of-bounds reads.<br>
>>><br>
>>> Nice work.<br>
>>><br>
>>> | Unfortunately, Rcpp is not detecting or warning about this...<br>
>>> |<br>
>>> | Either way, I believe this is a bug in the openxlsx package, but Rcpp<br>
>>> | should be checking / reporting this.<br>
>>><br>
>>> With (Rcpp)Armadillo you do have an option of turning this on/off. With<br>
>>> Rcpp<br>
>>> alone not quite.<br>
>>><br>
>>> Dirk<br>
>>><br>
>>> --<br>
>>> <a href="http://dirk.eddelbuettel.com" rel="noreferrer" target="_blank">http://dirk.eddelbuettel.com</a> | @eddelbuettel | <a href="mailto:edd@debian.org">edd@debian.org</a><br>
>>> _______________________________________________<br>
>>> Rcpp-devel mailing list<br>
>>> <a href="mailto:Rcpp-devel@lists.r-forge.r-project.org">Rcpp-devel@lists.r-forge.r-project.org</a><br>
>>> <a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel" rel="noreferrer" target="_blank">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel</a><br>
>><br>
>><br>
>><br>
>><br>
>> --<br>
>> Qiang Kou<br>
>> <a href="mailto:qkou@umail.iu.edu">qkou@umail.iu.edu</a><br>
>> School of Informatics and Computing, Indiana University<br>
>><br>
><br>
><br>
><br>
> --<br>
> Qiang Kou<br>
> <a href="mailto:qkou@umail.iu.edu">qkou@umail.iu.edu</a><br>
> School of Informatics and Computing, Indiana University<br>
><br>
><br>
> _______________________________________________<br>
> Rcpp-devel mailing list<br>
> <a href="mailto:Rcpp-devel@lists.r-forge.r-project.org">Rcpp-devel@lists.r-forge.r-project.org</a><br>
> <a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel" rel="noreferrer" target="_blank">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel</a><br>
<br>
<br>
<br>
--<br>
</div></div><div class="HOEnZb"><div class="h5">Paul E. Johnson<br>
Professor, Political Science        Director<br>
1541 Lilac Lane, Room 504      Center for Research Methods<br>
University of Kansas                 University of Kansas<br>
<a href="http://pj.freefaculty.org" rel="noreferrer" target="_blank">http://pj.freefaculty.org</a>              <a href="http://crmda.ku.edu" rel="noreferrer" target="_blank">http://crmda.ku.edu</a><br>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr">Qiang Kou<div><a href="mailto:qkou@umail.iu.edu" target="_blank">qkou@umail.iu.edu</a><br><div>School of Informatics and Computing, Indiana University</div><div><br></div></div></div></div>
</div>