Here's an updated version of the patch that fixes a stack imbalance bug.
N.B: the patch seems to work fine with R-3.0.2 too.
On Wed, Mar 5, 2014 at 5:16 PM, Karl Forner <karl.for...@gmail.com> wrote:
> Hello,
>
> I submit a patch for review that implements code coverage tracing in
> the R interpreter.
> It records the lines that are actually executed and their associated
> frequency for which srcref information is available.
>
> I perfectly understands that this patch will not make its way inside R
> as it is, that they are many concerns of stability, compatibility,
> maintenance and so on.
> I would like to have the code reviewed, and proper guidance on how to
> get this feature available at one point in R, in base R or as a
> package or patch if other people are interested.
>
> Usage
> --------
> Rcov_start()
> # your code to trace here
> res <- Rcov_stop()
>
> res is currently a hashed env, with traced source filenames associated
> with 2-columns matrices holding the line numbers and their
> frequencies.
>
>
> How it works
> -----------------
> I added a test in getSrcref(), that records the line numbers if code
> coverage is started.
> The overhead should be minimal since for a given file, subsequent
> covered lines will be stored
> in constant time. I use a hased env to store the occurrences by file.
>
> I added two entry points in the utils package (Rcov_start() and Rcov_stop())
>
>
> Example
> -------------
> * untar the latest R-devel and cd into it
> * patch -p1 < rdev-cov-patch.txt
> * ./configure [... ] && make && [sudo] make install
> * install the devtools package
> * run the following script using Rscript
>
> library(methods)
> library(devtools)
> pkg <- download.packages('testthat', '.', repos = "http://stat.ethz.ch/CRAN";)
> untar(pkg[1, 2])
>
> Rcov_start()
> test('testthat')
> env <- Rcov_stop()
>
> res <- lapply(ls(env), get, envir = env)
> names(res) <- ls(env)
> print(res)
>
>
> This will hopefully output something like:
> $`.../testthat/R/auto-test.r`
> [,1] [,2]
> [1,] 33 1
> [2,] 80 1
>
> $`.../testthat/R/colour-text.r`
> [,1] [,2]
> [1,] 18 1
> [2,] 19 106
> [3,] 20 106
> [4,] 22 106
> [5,] 23 106
> [6,] 40 1
> [7,] 59 1
> [8,] 70 1
> [9,] 71 106
> ...
>
>
> Karl Forner
>
>
> Disclaimer
> -------------
> There are probably bugs and ugly statements, but this is just a proof
> of concept. This is untested and only run on a linux x86_64
diff -urN -x '.*' R-devel/src/library/utils/man/Rcov_start.Rd
R-develcov/src/library/utils/man/Rcov_start.Rd
--- R-devel/src/library/utils/man/Rcov_start.Rd 1970-01-01 01:00:00.000000000
+0100
+++ R-develcov/src/library/utils/man/Rcov_start.Rd 2014-03-07
18:41:33.117646470 +0100
@@ -0,0 +1,26 @@
+% File src/library/utils/man/Rcov_start.Rd
+% Part of the R package, http://www.R-project.org
+% Copyright 1995-2010 R Core Team
+% Distributed under GPL 2 or later
+
+\name{Rcov_start}
+\alias{Rcov_start}
+\title{Start Code Coverage analysis of R's Execution}
+\description{
+ Start Code Coverage analysis of the execution of \R expressions.
+}
+\usage{
+Rcov_start(nb_lines = 10000L, growth_rate = 2)
+}
+\arguments{
+ \item{nb_lines}{
+ Initial max number of lines per source file.
+ }
+ \item{growth_rate}{
+ growth factor of the line numbers vectors per filename.
+ If a reached line number L is greater than nb_lines, the vector will
+ be reallocated with provisional size of growth_rate * L.
+ }
+}
+
+\keyword{utilities}
diff -urN -x '.*' R-devel/src/library/utils/man/Rcov_stop.Rd
R-develcov/src/library/utils/man/Rcov_stop.Rd
--- R-devel/src/library/utils/man/Rcov_stop.Rd 1970-01-01 01:00:00.000000000
+0100
+++ R-develcov/src/library/utils/man/Rcov_stop.Rd 2014-03-07
18:41:33.117646470 +0100
@@ -0,0 +1,20 @@
+% File src/library/utils/man/Rcov_stop.Rd
+% Part of the R package, http://www.R-project.org
+% Copyright 1995-2010 R Core Team
+% Distributed under GPL 2 or later
+
+\name{Rcov_stop}
+\alias{Rcov_stop}
+\title{Start Code Coverage analysis of R's Execution}
+\description{
+ Start Code Coverage analysis of the execution of \R expressions.
+}
+\usage{
+Rcov_stop()
+}
+
+\value{
+ a named list of integer vectors holding occurrences counts (line number,
frequency)
+ , named after the covered source file names.
+}
+\keyword{utilities}
diff -urN -x '.*' R-devel/src/library/utils/NAMESPACE
R-develcov/src/library/utils/NAMESPACE
--- R-devel/src/library/utils/NAMESPACE 2013-09-10 03:04:59.000000000 +0200
+++ R-develcov/src/library/utils/NAMESPACE 2014-03-07 18:41:33.121646470
+0100
@@ -1,7 +1,7 @@
# Refer to all C routines by their name prefixed by C_
useDynLib(utils, .registration = TRUE, .fixes = "C_")
-export("?", .DollarNames, CRAN.packages, Rprof, Rprofmem, RShowDoc,
+export("?", .DollarNames, CRAN.packages, Rcov_start, Rcov_stop, Rprof,
Rprofmem, RShowDoc,
RSiteSearch, URLdecode, URLencode, View, adist, alarm, apropos,
aregexec, argsAnywhere, assignInMyNamespace, assignInNamespace,
as.roman, as.person, as.personList, as.relistable, aspell,
diff -urN -x '.*' R-devel/src/library/utils/R/Rcov.R
R-develcov/src/library/utils/R/Rcov.R
--- R-devel/src/library/utils/R/Rcov.R 1970-01-01 01:00:00.000000000 +0100
+++ R-develcov/src/library/utils/R/Rcov.R 2014-03-07 18:41:33.121646470
+0100
@@ -0,0 +1,27 @@
+# File src/library/utils/R/Rcov.R
+# Part of the R package, http://www.R-project.org
+#
+# Copyright (C) 1995-2013 The R Core Team
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# A copy of the GNU General Public License is available at
+# http://www.r-project.org/Licenses/
+
+Rcov_start <- function(nb_lines = 10000L, growth_rate = 2)
+{
+ invisible(.External(C_Rcov_start, nb_lines, growth_rate))
+}
+
+
+Rcov_stop <- function() {
+ invisible(.External(C_Rcov_stop))
+}
diff -urN -x '.*' R-devel/src/library/utils/src/init.c
R-develcov/src/library/utils/src/init.c
--- R-devel/src/library/utils/src/init.c 2014-01-08 18:06:33.000000000
+0100
+++ R-develcov/src/library/utils/src/init.c 2014-03-07 18:41:33.129646469
+0100
@@ -74,6 +74,8 @@
static const R_ExternalMethodDef ExtEntries[] = {
EXTDEF(download, 5),
EXTDEF(unzip, 7),
+ EXTDEF(Rcov_start, 2),
+ EXTDEF(Rcov_stop, 0),
EXTDEF(Rprof, 8),
EXTDEF(Rprofmem, 3),
diff -urN -x '.*' R-devel/src/library/utils/src/utils.c
R-develcov/src/library/utils/src/utils.c
--- R-devel/src/library/utils/src/utils.c 2012-10-01 17:52:17.000000000
+0200
+++ R-develcov/src/library/utils/src/utils.c 2014-03-07 18:41:33.129646469
+0100
@@ -27,6 +27,22 @@
#include "utils.h"
/* from src/main/eval.c */
+void do_Rcov_start(int nb_lines, double growth_rate);
+SEXP do_Rcov_stop(void);
+
+SEXP Rcov_start(SEXP args)
+{
+ do_Rcov_start(asInteger(CADR(args)), asReal(CADDR(args)));
+ return R_NilValue; /* -Wall */
+}
+
+
+SEXP Rcov_stop(void)
+{
+ return do_Rcov_stop();
+}
+
+/* from src/main/eval.c */
SEXP do_Rprof(SEXP args);
SEXP Rprof(SEXP args)
diff -urN -x '.*' R-devel/src/library/utils/src/utils.h
R-develcov/src/library/utils/src/utils.h
--- R-devel/src/library/utils/src/utils.h 2014-01-06 03:04:59.000000000
+0100
+++ R-develcov/src/library/utils/src/utils.h 2014-03-07 18:41:33.129646469
+0100
@@ -26,6 +26,8 @@
SEXP objectSize(SEXP s);
SEXP unzip(SEXP args);
+SEXP Rcov_start(SEXP args);
+SEXP Rcov_stop(void);
SEXP Rprof(SEXP args);
SEXP Rprofmem(SEXP args);
diff -urN -x '.*' R-devel/src/main/eval.c R-develcov/src/main/eval.c
--- R-devel/src/main/eval.c 2014-02-21 03:03:36.000000000 +0100
+++ R-develcov/src/main/eval.c 2014-03-07 18:41:33.133646469 +0100
@@ -37,6 +37,202 @@
static SEXP bcEval(SEXP, SEXP, Rboolean);
+
+static int R_Code_Coverage = 0;
+#define R_CODE_COVERAGE
+#ifdef R_CODE_COVERAGE
+
+/* A Simple mechanism for implementing code coverage.
+ When code coverage is enables (via the R_Code_Coverage global var),
+ each call to the getSrcref() function will record the current srcref
filename and line
+ number.
+ The code coverage support is controlled by the R_CODE_COVERAGE preprocessor
define.
+
+ The actual implementation consists for the moment in intercepting
getSrcref() calls,
+ then calling the record_code_coverage() function.
+ The code coverage tracing is activating by calling the do_Rcov() (Rcov from
R) function.
+
+ Karl Forner
+ */
+
+/* global variable: hit lines freqs: a HashedEnv by filename */
+static SEXP R_Cov_freqs_hash = NULL;
+
+/* create a new non-sparsed vector of line frequencies at least of length size.
+ * Depending on the do_Rcov_start params nb_lines and growth_rate,
+ * it will allocate an actual size of either nb_lines or size * growth_rate
+ */
+static SEXP cov_new_lines_vector(int size) {
+ SEXP sexp, lines;
+ int nb_lines, i;
+ int *tab;
+ double growth_rate;
+
+ sexp = findVarInFrame(R_Cov_freqs_hash, install(".nb_lines"));
+ nb_lines = INTEGER(sexp)[0];
+ if (size > nb_lines) {
+ sexp = findVarInFrame(R_Cov_freqs_hash,
install(".growth_rate"));
+ growth_rate = REAL(sexp)[0];
+ size = (int)(size * growth_rate);
+ } else {
+ size = nb_lines;
+ }
+
+ PROTECT(lines = allocVector(INTSXP, size));
+ tab = INTEGER(lines);
+ for (i = 0; i < size; ++i)
+ tab[i] = 0;
+ UNPROTECT(1);
+ return lines;
+}
+
+/* store a new line occurrence in R_Cov_freqs_hash for filename */
+static void cov_store_new_line(const char* filename, int line) {
+ SEXP lines, lines2;
+ int len, i, *t1, *t2;
+
+ lines = findVarInFrame(R_Cov_freqs_hash, install(filename));
+ if (lines == R_UnboundValue) { /* new file */
+ lines = cov_new_lines_vector(line + 1);
+ defineVar(install(filename), lines, R_Cov_freqs_hash);
+ }
+ if (length(lines) <= line) {
+ /* lines vector too short */
+ PROTECT(lines2 = cov_new_lines_vector(line + 1)); /* should
allocate (line+1)*growth_rate */
+ len = length(lines);
+ i = 0;
+ t1 = INTEGER(lines);
+ t2 = INTEGER(lines2);
+ for (i = 0; i < len; ++i)
+ lines2[i] = lines[i];
+ defineVar(install(filename), lines2, R_Cov_freqs_hash);
+ lines = lines2;
+ UNPROTECT(1);
+ }
+
+ INTEGER(lines)[line]++;
+}
+
+/* maybe store a new srcref in R_Cov_freqs_hash */
+static void record_code_coverage(SEXP srcref)
+{
+ if (srcref && !isNull(srcref)) {
+ int fnum, line = asInteger(srcref);
+
+ SEXP srcfile = getAttrib(srcref, R_SrcfileSymbol);
+ const char *filename;
+
+ if (!srcfile || TYPEOF(srcfile) != ENVSXP) return;
+ srcfile = findVar(install("filename"), srcfile);
+ if (TYPEOF(srcfile) != STRSXP || !length(srcfile)) return;
+
+ filename = CHAR(STRING_ELT(srcfile, 0));
+ cov_store_new_line(filename, line);
+ }
+}
+
+
+/* This initiates the code coverage tracing.
+ * nb_lines is the initial size of frequencies vectors per file.
+ * If a line number L is encountered s.t L >=nb_lines, the vector will be
extended
+ * to L * growth_rate
+ */
+void do_Rcov_start(int nb_lines, double growth_rate)
+{
+ SEXP sexp;
+
+ if (growth_rate < 1.1)
+ growth_rate = 1.1;
+
+ if (R_Code_Coverage) return;
+ R_Code_Coverage = 1;
+ if (R_Cov_freqs_hash != NULL)
+ R_ReleaseObject(R_Cov_freqs_hash);
+
+ /* put the params nb_lines and growth_rate as hidden vars of the hashed
env */
+ R_Cov_freqs_hash = R_NewHashedEnv(R_NilValue, ScalarInteger(0));
+ R_PreserveObject(R_Cov_freqs_hash);
+ PROTECT(sexp = ScalarInteger(nb_lines));
+ defineVar(install(".nb_lines"), sexp, R_Cov_freqs_hash);
+
+ PROTECT(sexp = ScalarReal(growth_rate));
+ defineVar(install(".growth_rate"), sexp, R_Cov_freqs_hash);
+
+ UNPROTECT(2);
+}
+
+/* Ends the code coverage tracing.
+ * and returns an environment with symbols named after the covered source
files and values
+ * matrices of dim n*2, which first column is the line number and the second
the nb of occurrences
+ */
+SEXP do_Rcov_stop(void)
+{
+ SEXP names, lines, mat, key, res;
+ int n, i, j, k, nb_lines, non_empty_lines, *tab, *m;
+
+ /* stop the code covered tracing */
+ R_Code_Coverage = 0;
+
+ /* convert frequencies by line to matrix N*2 of lines, freq */
+ PROTECT(names = R_lsInternal(R_Cov_freqs_hash, FALSE));
+ n = length(names);
+
+ for (i = 0; i < n; ++i) {
+ key = install(CHAR(STRING_ELT(names, i)));
+ lines = findVarInFrame(R_Cov_freqs_hash, key);
+
+ tab = INTEGER(lines);
+ nb_lines = length(lines);
+ non_empty_lines = 0;
+ for (j = 0; j < nb_lines; ++j)
+ if (tab[j])
+ ++non_empty_lines;
+
+ PROTECT(mat = allocMatrix(INTSXP, non_empty_lines, 2));
+ m = INTEGER(mat);
+ k = 0;
+ for (j = 0; j < nb_lines; ++j) {
+ if (tab[j]) {
+ m[k] = j;
+ m[k + non_empty_lines] = tab[j];
+ ++k;
+ }
+ }
+
+ defineVar(key, mat, R_Cov_freqs_hash);
+ UNPROTECT(1); /* mat */
+ }
+ UNPROTECT(1); /* names */
+
+ res = R_Cov_freqs_hash;
+ R_ReleaseObject(R_Cov_freqs_hash);
+ R_Cov_freqs_hash = NULL;
+
+ return res;
+}
+
+
+#else /* not R_CODE_COVERAGE */
+
+void do_Rcov_start(int nb_lines, int growth_rate)
+{
+ error(_("do_Rcov_start: R code coverage is not available on this system"));
+ return R_NilValue; /* -Wall */
+}
+
+SEXP do_Rcov_stop()
+{
+ error(_("do_Rcov_stop: R code coverage is not available on this system"));
+ R_Code_Coverage = 0;
+}
+
+
+#endif
+
+
+
+
+
/* BC_PROILFING needs to be defined here and in registration.c */
/*#define BC_PROFILING*/
#ifdef BC_PROFILING
@@ -851,10 +1047,17 @@
&& length(srcrefs) > ind
&& !isNull(result = VECTOR_ELT(srcrefs, ind))
&& TYPEOF(result) == INTSXP
- && length(result) >= 6)
- return result;
- else
- return R_NilValue;
+ && length(result) >= 6) {
+
+#ifdef R_CODE_COVERAGE
+ if (R_Code_Coverage) record_code_coverage(result);
+#endif
+
+ } else {
+ result = R_NilValue;
+ }
+
+ return result;
}
SEXP applyClosure(SEXP call, SEXP op, SEXP arglist, SEXP rho, SEXP suppliedenv)
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