Add support for dtCMatrix&dsCMatrix #135

binxiangni · 2017-06-14T21:34:17Z

Now I just add codes for the conversion of dtCMatrix and dsCMatrix here in order to partially solve the issue#17 and issue#114. More conversion of sparse matrix would be added soon. Please do me a favor to check the code style or anything else important.

coatless · 2017-06-14T21:44:34Z

inst/include/RcppArmadilloAs.h


            // Setting the sentinel
-            arma::access::rw(res.col_ptrs[(unsigned) dims[1] + 1]) =
+            arma::access::rw(res.col_ptrs[static_cast<unsigned>(ncol + 1)]) =


+1 for the static_cast usage.

coatless · 2017-06-14T21:51:54Z

inst/include/RcppArmadilloAs.h

-            std::copy(x.begin(), x.end(), arma::access::rwp(res.values));
+            // Get the type of sparse matrix
+            std::string type = Rcpp::as<std::string>(mat.slot("class"));
+            if (type == "dgCMatrix"){


Stylistically... @eddelbuettel will complain that you did not put a space between ) and {.

coatless · 2017-06-14T21:53:35Z

Could you add unit tests that verify your assertion?

https://github.com/RcppCore/RcppArmadillo/blob/master/inst/unitTests/runit.sparse.R
https://github.com/RcppCore/RcppArmadillo/blob/master/inst/unitTests/cpp/sparse.cpp

eddelbuettel · 2017-06-14T21:59:16Z

Nice! And don't worry too about indentation -- following what is in the other files in the repo is a good plan.

binxiangni · 2017-06-15T03:17:36Z

I am curious about the meaning of the first dot and triple colons in the following codes:

    .setUp <- RcppArmadillo:::unit_test_setup("sparse.cpp")

coatless · 2017-06-15T04:50:14Z

Generally, the . preceding a function or variable name is meant to hide it from users in a way that is similar to how dotfiles are hidden on most file systems. Basically, these functions and variables are to be considered internal components of the package that shouldn't be modified.

Regarding the :::, this relates to package namespaces. When you call library(pkgname), you are loading all of the packages exported functions and variables into the search path. If you do not, one way to access a package's function is to prefix it with the package name and two colons, e.g. pkgname::function(). Now, you might have components that are not exported because they are internal components as mentioned above. To access these internal values, you can add one additional colon after the package name but before a function or variable, e.g. RcppArmadillo:::unit_test_setup, and viola you have access to it outside the package.

You might want to glance at Double Colon and Triple Colon Operators help doc article for more.

thirdwing · 2017-06-15T17:24:35Z

inst/include/RcppArmadilloAs.h

@@ -77,7 +77,9 @@ namespace traits {
    private:
        MATRIX mat ;
    };
-
+
+    // 14 June 2017


I think we don't have time in other place, right?

I just followed the style of the source code. There are also dates there

It doesn't matter. Let's focus on the unit test.

thirdwing · 2017-06-15T17:27:48Z

inst/include/RcppArmadilloAs.h

-            std::copy(p.begin(), p.end(), arma::access::rwp(res.col_ptrs));
-            std::copy(x.begin(), x.end(), arma::access::rwp(res.values));
+            // Get the type of sparse matrix
+            std::string type = Rcpp::as<std::string>(mat.slot("class"));


Maybe we can print some message when converting the matrix type?

Like "Converting dgCMatrix into Armadillo type".

What is your opinion? @coatless

eddelbuettel · 2017-06-15T17:51:34Z

IIRC the sample() code by Christian has dates in it. I am with you that it is somewhat redundant given the commit logs. But hey, documentation is good.

As for printing message: Hm. Maybe if and only if a verbose flag or option is set?

coatless · 2017-06-15T18:42:27Z

Perhaps a set of debug macros similar to what Rcpp does for some of the String and general conversions?

c.f.

https://github.com/RcppCore/Rcpp/blob/8f2a101789b29e572bf3abe5115d9ddb48c1b0c7/inst/include/Rcpp/String.h#L30-L41

https://github.com/RcppCore/Rcpp/blob/6f81b4684481dbd9bb554dd95e66725fc3b63a8c/inst/include/Rcpp/vector/converter.h#L50

So, we would have

#define DEBUG_RCPPARMADILLO_SPARSE

Then something print status of conversion to console with Rprintf() instead of Rcpp::Rcout?

eddelbuettel · 2017-06-15T19:03:34Z

Let's not get distracted. This is Binxiang's issue ticket on something different.

We can always print some debug text during development and clean up before releases. No biggie either way.

eddelbuettel · 2017-06-16T11:07:46Z

@binxiangni The pull request looks really good. Two more suggestions / requests

Tests would be excellent, and if you look at the existing directory it should become clear how to add them. If it is not, well then we can merge this as is and open a new branch just for tests. They are important and a key part of how we do things.
ChangeLog entries would be nice. That gets autoformatted if you use Emacs, it is pretty easy to do by hand as well. Date, name and email with two spaces, then a bullet point for each changed file with a summary.

Can we add that?

binxiangni · 2017-06-16T12:58:58Z

@eddelbuettel Sorry for delay. I'll do that ASAP. Please do not merge for now. I understand the importance of test.

As I mentioned before, my broken laptop quite let me down. Yesterday I tried to use Ubuntu Server in the digitalocean as KK suggests and set up a GUI for further working environment, but GUI didn't work. I'll go to a local dealer to get a new laptop today. After that, I can go back to the right track. Apologize again!

eddelbuettel · 2017-06-16T14:38:50Z

No worry, you are doing great. We could do it as two PRs as well but may as well have you expand this one.

eddelbuettel · 2017-06-16T14:39:30Z

Oh, and sorry about the hardware troubles.

@coatless Any way a student can access a proper and current dev env on campus? Isn't that what the VM pool is for? But not outside of classes?

binxiangni · 2017-06-16T15:56:46Z

The local dealer also tells me that I can get the laptop after 10 days. 😭
Now I try to install Rstudio in the ubuntu server in the digitalocean. There is a step not making sense to me

RStudio can be access through port 8787.

Do you have any idea?

eddelbuettel · 2017-06-16T16:22:11Z

Sure. Standard RStudio Server use via a webbrowser. See eg https://support.rstudio.com/hc/en-us/articles/200552306-Accessing-RStudio-Server-Open-Source

Really no resources on campus?

binxiangni · 2017-06-16T20:03:38Z

I can access the computer in the computer lab, but have no admin right to install package like Armadillo. But for now, I have an old laptop from my friend and at least it can run the build check in the RStudio. Previously, I think I have to install C++ Armadillo library. Maybe I am wrong. Only if the build check runs and no error occurs, that means it passes the test, right?

eddelbuettel · 2017-06-16T20:12:30Z

Also, you could just use GitHub and Travis CI. If you clone RcppArmadillo you have a working .travis.yml. So you just need to turn on Travis CI for your account as everything else is already there. (For what it is worth, the first Google hit was this tutorial.)

coatless · 2017-06-16T21:05:33Z

Just to give a heads up, I've put in a request to get @binxiangni access to a linux machine on campus. I'll let you know what happens. (It likely won't be until Monday since it's almost 5 o'clock.)

eddelbuettel · 2017-06-16T23:17:06Z

Thanks for adding tests. Looks like one failed ... but I am about to cook dinner so can't check now.

I am sure we'll get it sorted out.

binxiangni · 2017-06-17T00:24:31Z

I find where the bug is:
'S4' was not declared in this scope
I just fixed apparent bugs but don't know how to include S4 in the scope.

thirdwing · 2017-06-17T05:03:05Z

inst/unitTests/cpp/sparse.cpp

+    int nrow = dims[0];
+    int ncol = dims[1];
+
+    // Creating an empty SpMat


I think what we want to test is arma::sp_mat res = Rcpp::as<arma::sp_mat>(S);

The converting code has been added into the as implementation and we want to test.

binxiangni · 2017-06-17T14:45:06Z

I did unit test locally and it shows R CMD check succeeded, which I guess means that the unit tests pass. But there is a warning: Problems with news in 'inst/NEWS.Rd':. Anyone can give me a hint?

eddelbuettel · 2017-06-17T15:21:54Z

Problems with news in 'inst/NEWS.Rd'

That usually means a closing } is missing or in the wrong. And as you didn't touch the file, not your problem :)

I can take a look in a bit. Just in a from a long run...

eddelbuettel · 2017-06-17T17:10:43Z

Passes with flying colors for me too!

Add support for dtCMatrix&dsCMatrix

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coatless reviewed Jun 14, 2017

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thirdwing reviewed Jun 15, 2017

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thirdwing approved these changes Jun 15, 2017

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thirdwing reviewed Jun 15, 2017

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Indentation

409c2f0

Add unit test for dtc2dgc

c74a0b8

Fix bug

04faf58

thirdwing reviewed Jun 17, 2017

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Add unit tests for dtCMatrix & dsCMatrix

ba58bd2

binxiangni added 3 commits June 17, 2017 11:19

Add conversion and unit tests for dtCMatrix & dsCMatrix

ecbb0d0

Update ChangeLog

f5d2f74

Add unit test for low triangle dsCMatrix

457c6c2

thirdwing approved these changes Jun 17, 2017

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eddelbuettel merged commit ab72955 into RcppCore:master Jun 18, 2017

eddelbuettel mentioned this pull request Jun 18, 2017

Add conversion & unit tests for dgT, dtT & dsTMatrix #136

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Add support for dtCMatrix&dsCMatrix #135

Add support for dtCMatrix&dsCMatrix #135

binxiangni commented Jun 14, 2017

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Add support for dtCMatrix&dsCMatrix #135

Add support for dtCMatrix&dsCMatrix #135

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