safeguard memory-aligned allocation

.Rbuildignore

@@ -15,4 +15,3 @@ revdep/
 .vscode/
 new-benchmarks.R
 bench*
-revdep/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RcppThread
 Title: R-Friendly Threading in C++
-Version: 2.0.0
+Version: 2.0.1
 Authors@R: c(
     person("Thomas", "Nagler",, "mail@tnagler.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-1855-0046"))

NEWS.md

@@ -1,5 +1,14 @@
+# # RcppThread 2.0.1
+# 
+# BUG FIX
+# 
+# * safeguard construction of memory aligned objects.
+
+
 # RcppThread 2.0.0
 
+NEW FEATURES
+
 * Add R function `detectCores()` (#48).
 
 * Add classes `ProgressCounter` and `ProgressBar` for tracking progress in long-

R/inline.R

@@ -0,0 +1,10 @@
+inlineCxxPlugin <- function(...) {
+    settings <- Rcpp::Rcpp.plugin.maker(
+        include.before  = "#include <RcppThread.h>",
+        package = "RcppThread",
+        libs = if (Sys.info()["sysname"] == "Linux") "-latomic -lpthread" else ""
+    )()
+    settings$env$USE_CXX11 <- "yes"
+    settings
+}
+

cran-comments.md

@@ -1,24 +1,18 @@
-Fixed URL/DOI formatting required by Uwe Ligges via mail.
-
-The DOI in the CITATION, DESCRIPTION, and documentation is for a new JSS publication that will be registered after publication on CRAN.
-
+Fixes build warning on windows about misaligned address/allocation. Hopefully
+also the problems on Fedora, which I could not reproduce.
 
 ## Test environments
-* ubuntu 16.04 (devel, release, old-rel)
+* ubuntu 20.04 (devel, release, old-rel)
 * macOS X (release)
 * Windows Server 2019 (release)
 * CRAN win builder (devel)
+* rhub::check_for_cran()
+* rhub::check_with_sanitizers()
+* rhub::check_with_valgrind()
 
-## R CMD check results
-
-0 errors | 0 warnings | 1 note
-
-* Note caused by invalid DOI.
-
-## Reverse dependencies
-
-We checked 11 reverse dependencies (11 from CRAN), comparing R CMD check results across CRAN and dev versions of this package.
-
- * We saw 0 new problems
- * We failed to check 0 packages
+## Check status summary
+                WARN NOTE OK
+Source packages    0    0  1
+Reverse depends    1   17  1
 
+The warning in package CDSeq is known and expected.

docs/xml/classRcppThread_1_1ThreadPool.xml

@@ -4,9 +4,9 @@
     <compoundname>RcppThread::ThreadPool</compoundname>
     <includes local="no">ThreadPool.hpp</includes>
       <sectiondef kind="private-attrib">
-      <memberdef kind="variable" id="classRcppThread_1_1ThreadPool_1ae01e3405af79ea4d86d1b63b2c822311" prot="private" static="no" mutable="no">
-        <type>quickpool::ThreadPool</type>
-        <definition>quickpool::ThreadPool RcppThread::ThreadPool::pool_</definition>
+      <memberdef kind="variable" id="classRcppThread_1_1ThreadPool_1ad5e5077aa6d1b23d5344cba2fef23761" prot="private" static="no" mutable="no">
+        <type>std::unique_ptr&lt; quickpool::ThreadPool &gt;</type>
+        <definition>std::unique_ptr&lt;quickpool::ThreadPool&gt; RcppThread::ThreadPool::pool_</definition>
         <argsstring></argsstring>
         <name>pool_</name>
         <briefdescription>
@@ -15,7 +15,7 @@
         </detaileddescription>
         <inbodydescription>
         </inbodydescription>
-        <location file="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" line="65" column="27" bodyfile="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" bodystart="65" bodyend="-1"/>
+        <location file="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" line="65" column="21" bodyfile="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" bodystart="65" bodyend="-1"/>
       </memberdef>
       <memberdef kind="variable" id="classRcppThread_1_1ThreadPool_1a884ba54cc9f225392007a0736b80977d" prot="private" static="no" mutable="no">
         <type>std::thread::id</type>
@@ -393,7 +393,7 @@ Consider the following code: <programlisting><codeline><highlight class="normal"
         </detaileddescription>
         <inbodydescription>
         </inbodydescription>
-        <location file="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" line="53" column="10" bodyfile="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" bodystart="167" bodyend="197"/>
+        <location file="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" line="53" column="10" bodyfile="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" bodystart="167" bodyend="192"/>
       </memberdef>
       <memberdef kind="function" id="classRcppThread_1_1ThreadPool_1a5209d746d78202faf17524ce6bf2e94a" prot="public" static="no" const="no" explicit="no" inline="yes" virt="non-virtual">
         <templateparamlist>
@@ -463,7 +463,7 @@ Consider the following code: <programlisting><codeline><highlight class="normal"
         </detaileddescription>
         <inbodydescription>
         </inbodydescription>
-        <location file="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" line="56" column="10" bodyfile="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" bodystart="223" bodyend="226"/>
+        <location file="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" line="56" column="10" bodyfile="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" bodystart="218" bodyend="221"/>
       </memberdef>
       <memberdef kind="function" id="classRcppThread_1_1ThreadPool_1a6c93f9e84fadfdc1a3357770d47a738a" prot="public" static="no" const="no" explicit="no" inline="yes" virt="non-virtual">
         <type>void</type>
@@ -477,7 +477,7 @@ Consider the following code: <programlisting><codeline><highlight class="normal"
         </detaileddescription>
         <inbodydescription>
         </inbodydescription>
-        <location file="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" line="58" column="10" bodyfile="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" bodystart="231" bodyend="244"/>
+        <location file="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" line="58" column="10" bodyfile="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" bodystart="226" bodyend="239"/>
       </memberdef>
       <memberdef kind="function" id="classRcppThread_1_1ThreadPool_1a1ba95e4fe30c81e19c7980c865a8ce86" prot="public" static="no" const="no" explicit="no" inline="yes" virt="non-virtual">
         <type>void</type>
@@ -491,7 +491,7 @@ Consider the following code: <programlisting><codeline><highlight class="normal"
         </detaileddescription>
         <inbodydescription>
         </inbodydescription>
-        <location file="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" line="59" column="10" bodyfile="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" bodystart="248" bodyend="251"/>
+        <location file="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" line="59" column="10" bodyfile="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" bodystart="243" bodyend="246"/>
       </memberdef>
       <memberdef kind="function" id="classRcppThread_1_1ThreadPool_1a332b4f9a74d1c4e206e3957a299e0629" prot="public" static="no" const="no" explicit="no" inline="yes" virt="non-virtual">
         <type>void</type>
@@ -518,7 +518,7 @@ Consider the following code: <programlisting><codeline><highlight class="normal"
         </detaileddescription>
         <inbodydescription>
         </inbodydescription>
-        <location file="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" line="61" column="10" bodyfile="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" bodystart="256" bodyend="259"/>
+        <location file="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" line="61" column="10" bodyfile="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" bodystart="251" bodyend="254"/>
       </memberdef>
       <memberdef kind="function" id="classRcppThread_1_1ThreadPool_1aa73eb6889492403da12d60a1a92de519" prot="public" static="no" const="yes" explicit="no" inline="yes" virt="non-virtual">
         <type>size_t</type>
@@ -532,7 +532,7 @@ Consider the following code: <programlisting><codeline><highlight class="normal"
         </detaileddescription>
         <inbodydescription>
         </inbodydescription>
-        <location file="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" line="62" column="12" bodyfile="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" bodystart="263" bodyend="266"/>
+        <location file="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" line="62" column="12" bodyfile="/data/dev/r/RcppThread/inst/include/RcppThread/ThreadPool.hpp" bodystart="258" bodyend="261"/>
       </memberdef>
       </sectiondef>
       <sectiondef kind="public-static-func">
@@ -567,7 +567,7 @@ Consider the following code: <programlisting><codeline><highlight class="normal"
       <member refid="classRcppThread_1_1ThreadPool_1a884ba54cc9f225392007a0736b80977d" prot="private" virt="non-virtual"><scope>RcppThread::ThreadPool</scope><name>owner_thread_</name></member>
       <member refid="classRcppThread_1_1ThreadPool_1a86f352d702e3a8dc211838c9518a83d7" prot="public" virt="non-virtual"><scope>RcppThread::ThreadPool</scope><name>parallelFor</name></member>
       <member refid="classRcppThread_1_1ThreadPool_1a5209d746d78202faf17524ce6bf2e94a" prot="public" virt="non-virtual"><scope>RcppThread::ThreadPool</scope><name>parallelForEach</name></member>
-      <member refid="classRcppThread_1_1ThreadPool_1ae01e3405af79ea4d86d1b63b2c822311" prot="private" virt="non-virtual"><scope>RcppThread::ThreadPool</scope><name>pool_</name></member>
+      <member refid="classRcppThread_1_1ThreadPool_1ad5e5077aa6d1b23d5344cba2fef23761" prot="private" virt="non-virtual"><scope>RcppThread::ThreadPool</scope><name>pool_</name></member>
       <member refid="classRcppThread_1_1ThreadPool_1af1c8048954f42b41d19bd8fa9133490a" prot="public" virt="non-virtual"><scope>RcppThread::ThreadPool</scope><name>push</name></member>
       <member refid="classRcppThread_1_1ThreadPool_1a14e16052783d48a17791b3f29d5149f0" prot="public" virt="non-virtual"><scope>RcppThread::ThreadPool</scope><name>pushReturn</name></member>
       <member refid="classRcppThread_1_1ThreadPool_1a0967f38d786196019a06f0e65642cfb3" prot="public" virt="non-virtual"><scope>RcppThread::ThreadPool</scope><name>resize</name></member>

docs/xml/index.xml

@@ -70,7 +70,7 @@
     <member refid="classRcppThread_1_1Thread_1a1ae92afcef21111e10a96cf5f4c8c8f0" kind="function"><name>hardware_concurrency</name></member>
   </compound>
   <compound refid="classRcppThread_1_1ThreadPool" kind="class"><name>RcppThread::ThreadPool</name>
-    <member refid="classRcppThread_1_1ThreadPool_1ae01e3405af79ea4d86d1b63b2c822311" kind="variable"><name>pool_</name></member>
+    <member refid="classRcppThread_1_1ThreadPool_1ad5e5077aa6d1b23d5344cba2fef23761" kind="variable"><name>pool_</name></member>
     <member refid="classRcppThread_1_1ThreadPool_1a884ba54cc9f225392007a0736b80977d" kind="variable"><name>owner_thread_</name></member>
     <member refid="classRcppThread_1_1ThreadPool_1a83ffe33d4d776b62baf312a1c4965c08" kind="function"><name>ThreadPool</name></member>
     <member refid="classRcppThread_1_1ThreadPool_1a524ee4a9d217cba6cbdfd3405515376b" kind="function"><name>ThreadPool</name></member>

docs/xml/quickpool_8hpp.xml

@@ -8,6 +8,7 @@
     <includes local="no">exception</includes>
     <includes local="no">functional</includes>
     <includes local="no">future</includes>
+    <includes local="no">memory</includes>
     <includes local="no">mutex</includes>
     <includes local="no">numeric</includes>
     <includes local="no">thread</includes>
@@ -20,7 +21,7 @@
       <node id="6">
         <label>functional</label>
       </node>
-      <node id="9">
+      <node id="10">
         <label>numeric</label>
       </node>
       <node id="5">
@@ -52,22 +53,27 @@
         </childnode>
         <childnode refid="11" relation="include">
         </childnode>
+        <childnode refid="12" relation="include">
+        </childnode>
       </node>
       <node id="7">
         <label>future</label>
       </node>
-      <node id="11">
+      <node id="12">
         <label>vector</label>
       </node>
-      <node id="8">
+      <node id="9">
         <label>mutex</label>
       </node>
-      <node id="10">
+      <node id="11">
         <label>thread</label>
       </node>
       <node id="2">
         <label>algorithm</label>
       </node>
+      <node id="8">
+        <label>memory</label>
+      </node>
     </incdepgraph>
     <briefdescription>
     </briefdescription>

inst/include/RcppThread/ThreadPool.hpp

@@ -62,7 +62,7 @@ class ThreadPool
     size_t getNumThreads() const;
 
   private:
-    quickpool::ThreadPool pool_;
+    std::unique_ptr<quickpool::ThreadPool> pool_;
     std::thread::id owner_thread_;
 };
 
@@ -75,7 +75,7 @@ inline ThreadPool::ThreadPool()
 //! @param nWorkers number of worker threads to create; if `nWorkers = 0`, all
 //!    work pushed to the pool will be done in the main thread.
 inline ThreadPool::ThreadPool(size_t nWorkers)
-  : pool_{ nWorkers }
+  : pool_{ new quickpool::ThreadPool(nWorkers) }
   , owner_thread_{ std::this_thread::get_id() }
 {}
 
@@ -108,7 +108,7 @@ template<class F, class... Args>
 void
 ThreadPool::push(F&& f, Args&&... args)
 {
-    pool_.push(std::bind(std::forward<F>(f), std::forward<Args>(args)...));
+    pool_->push(std::bind(std::forward<F>(f), std::forward<Args>(args)...));
 }
 
 //! pushes jobs returning a value to the thread pool.
@@ -122,7 +122,7 @@ auto
 ThreadPool::pushReturn(F&& f, Args&&... args)
   -> std::future<decltype(f(args...))>
 {
-    return pool_.async(
+    return pool_->async(
       std::bind(std::forward<F>(f), std::forward<Args>(args)...));
 }
 
@@ -169,7 +169,7 @@ ThreadPool::parallelFor(int begin, int end, F f, size_t nBatches)
     if (nBatches == 0) {
         // each worker has its dedicated range, but can steal part of another
         // worker's ranges when done with own
-        auto thr = std::max(pool_.get_active_threads(), static_cast<size_t>(1));
+        auto thr = std::max(pool_->get_active_threads(), static_cast<size_t>(1));
         auto workers = quickpool::loop::create_workers<F>(f, begin, end, thr);
         for (size_t k = 0; k < thr; k++) {
             this->push([=] { workers->at(k).run(workers); });
@@ -181,17 +181,12 @@ ThreadPool::parallelFor(int begin, int end, F f, size_t nBatches)
             return;
         nBatches = std::min(nBatches, nTasks);
 
-        size_t minSize = nTasks / nBatches;
-        int remSize = nTasks % nBatches;
-
+        size_t sz = nTasks / nBatches;
+        int rem = nTasks % nBatches;
         for (size_t b = 0; b < nBatches; b++) {
-            int bSize = minSize + (remSize-- > 0);
-            this->push([=] {
-                for (int i = begin; i < begin + bSize; ++i) {
-                    f(i);
-                }
-            });
-            begin += bSize;
+            int bs = sz + (rem-- > 0);
+            this->push([=] { for (int i = begin; i < begin + bs; ++i) f(i); });
+            begin += bs;
         }
     }
 }
@@ -235,34 +230,34 @@ ThreadPool::wait()
         return;
     }
     do {
-        pool_.wait(100);
+        pool_->wait(100);
         Rcout << "";
         checkUserInterrupt();
 
-    } while (!pool_.done());
+    } while (!pool_->done());
     Rcout << "";
 }
 
 //! waits for all jobs to finish.
 inline void
 ThreadPool::join()
 {
-    pool_.wait();
+    pool_->wait();
 }
 
 //! sets the number of active threads in the pool.
 //! @param threads the desired number of threads.
 inline void
 ThreadPool::setNumThreads(size_t threads)
 {
-    pool_.set_active_threads(threads);
+    pool_->set_active_threads(threads);
 }
 
 //! gets the number of active threads in the pool.
 inline size_t
 ThreadPool::getNumThreads() const
 {
-    return pool_.get_active_threads();
+    return pool_->get_active_threads();
 }
 
 } // end namespace RcppThread