version 1.0-4

DESCRIPTION

@@ -1,7 +1,7 @@
 Encoding: UTF-8
 Package: RPostgres
-Version: 1.0-3
-Date: 2017-12-06
+Version: 1.0-4
+Date: 2017-12-20
 Title: 'Rcpp' Interface to 'PostgreSQL'
 Authors@R: c(
     person("Hadley", "Wickham", role = "aut"),
@@ -16,6 +16,10 @@ Authors@R: c(
 Description: 
     Fully 'DBI'-compliant 'Rcpp'-backed interface to 'PostgreSQL' <https://www.postgresql.org/>,
     an open-source relational database.
+URL: https://github.com/r-dbi/RPostgres
+BugReports: https://github.com/r-dbi/RPostgres/issues
+SystemRequirements: libpq >= 9.0: libpq-dev (deb) or postgresql-devel
+        (rpm)
 License: GPL-2
 LazyLoad: true
 Depends: R (>= 3.1.0)
@@ -28,7 +32,7 @@ Collate: 'PqDriver.R' 'PqConnection.R' 'PqResult.R' 'RPostgres-pkg.R'
         'transactions.R' 'utils.R'
 RoxygenNote: 6.0.1
 NeedsCompilation: yes
-Packaged: 2017-12-06 00:17:52 UTC; muelleki
+Packaged: 2017-12-20 13:58:34 UTC; muelleki
 Author: Hadley Wickham [aut],
   Jeroen Ooms [aut],
   Kirill Müller [cre],
@@ -39,4 +43,4 @@ Author: Hadley Wickham [aut],
   Kungliga Tekniska Högskolan [ctb] (Source code for timegm)
 Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
 Repository: CRAN
-Date/Publication: 2017-12-06 10:21:43 UTC
+Date/Publication: 2017-12-20 15:50:56 UTC

MD5

@@ -1,6 +1,6 @@
-488ff95ba8e2d7e9719b961276dff586 *DESCRIPTION
+4832eb107246f1c494d8b0a0a12e0426 *DESCRIPTION
 feec1bfbc596fa53152300f94a3a7ab7 *NAMESPACE
-466d97216e230f9984d18d9eba02221e *NEWS.md
+4f803550504bcf1c80e414b6d4dab64b *NEWS.md
 d3949d39c6e0d3ebb30f5f47e69ed7d2 *R/PqConnection.R
 03a867755b841450b855879abbf62b30 *R/PqDriver.R
 b91897c5beee9b99af6fd55051171a80 *R/PqResult.R
@@ -11,36 +11,36 @@ ff99d2cac7decf472cd0bc8291a78e49 *R/default.R
 178feaef07207f895f30fd44b038ace6 *R/tables.R
 bbad0daadf44d8a9a43a0a720bef3803 *R/transactions.R
 c3efac6c8ef323cae26e037cce6c0d16 *R/utils.R
-f3da0de24104764362936f522e26ec6f *README.md
-8131313a7c1ae9b3ca097dc23a33918d *configure
+f68cbc04ffaf966382f11d77aff0ada5 *README.md
+593b73f88532bd8bca65acc012047767 *configure
 d41d8cd98f00b204e9800998ecf8427e *configure.win
 254056c489b1f3e7cc8cdc9fe4a14255 *man/Postgres.Rd
 fcfcf00fa9190113b6ee073f9fd11e2c *man/PqConnection-class.Rd
 26ccd704aecacc6484f3ea5b2e3eaa5f *man/PqDriver-class.Rd
 6ebae0927715384b8e90764e3ad2ba87 *man/PqResult-class.Rd
-16132b2b8d5c154d5ad5f9f4bf63cc81 *man/RPostgres-package.Rd
+fb4dbf64f44d7e1bdbb2c89f242429e4 *man/RPostgres-package.Rd
 3968c41c099acd7c228e85cc99655961 *man/dbConnect-PqDriver-method.Rd
 dda833f4b2c036ce15b0555c49add570 *man/dbDataType.Rd
 549393f4e48dad8a411932f23b543930 *man/postgres-query.Rd
 8e99dd84756b338faa2981ff82a8bfc0 *man/postgres-tables.Rd
 068c48521487f453e0c5b15bc6605cfe *man/postgres-transactions.Rd
 0f380511ba5e72720224904f24e3a42b *man/postgresHasDefault.Rd
 c4a8dbefb34cf9b1b599d26fc3ab3612 *man/quote.Rd
-fac812734f22d35b7a19561ea33d2a7c *src/DbColumn.cpp
+a567f5b302cec3ac90c52fd40be56c7d *src/DbColumn.cpp
 0d0f6283e1aee5ba374ac6c30ce35a57 *src/DbColumn.h
 1bead3e4afde4eb4237507be9fd81801 *src/DbColumnDataSource.cpp
 c1bd654b0f1d00b85c0213fb15266100 *src/DbColumnDataSource.h
 b54f1bed5e031730d84ea6ac5678d57c *src/DbColumnDataSourceFactory.cpp
 bdb2b7ed1a0c451b46b90f5ba0cae405 *src/DbColumnDataSourceFactory.h
 1ba5afa61895d800dbe19155f7d2c492 *src/DbColumnDataType.h
-4d4e148248bbebe297320f33a3244def *src/DbColumnStorage.cpp
+42a9a49f416883265bc88ef5d9b35b9a *src/DbColumnStorage.cpp
 00308bd348a82fa234bc3faf490c3bb5 *src/DbColumnStorage.h
-e6793b8d19bb3599363801a69f689fb7 *src/DbConnection.cpp
+b568eeeb2a620abb473f6e96e925dc9e *src/DbConnection.cpp
 91fd7039d2c543d73abf05c10937928a *src/DbConnection.h
 52f74e46125617344b9ef6c064922057 *src/DbDataFrame.cpp
 ce8cede04ec884229dfec09a95128ad9 *src/DbDataFrame.h
-add0543c36d85ecd4d07d3aec205a3d1 *src/DbResult.cpp
-a924adc6fcb47073a85a603d579bb3fc *src/DbResult.h
+548a2a51f2beb996158270d790cfb7d2 *src/DbResult.cpp
+8fcd22187e896f842ec2a034eeca9844 *src/DbResult.h
 111e1efb50ff675feb507ea42a24b300 *src/Makevars.in
 c5a5d51517569b4577b384cbbc412ad5 *src/Makevars.win
 16024658adfb1ccb34b929298ac0396e *src/PqColumnDataSource.cpp
@@ -49,8 +49,8 @@ d94f34a4e740f7d2f7b1f46c5bbc9411 *src/PqColumnDataSourceFactory.cpp
 5932e6e86bc3c43a31954bfd1dac8117 *src/PqColumnDataSourceFactory.h
 8dd8d1fe7af6e996859ef849d6b72993 *src/PqDataFrame.cpp
 3fb6f7104460055e29d87402ef538b55 *src/PqDataFrame.h
-f0cc2e38a2445b24a32298045d42396b *src/PqResultImpl.cpp
-68d9a7002c6ded7a86df79e6281b367c *src/PqResultImpl.h
+d73945444948561434167824978e0d2e *src/PqResultImpl.cpp
+53c364304523ba77289d3c77c6ff9b33 *src/PqResultImpl.h
 4601b2b6e925fa6761186d25fa93f9f5 *src/PqResultSource.cpp
 e2d8563ac79450e3f2347ebc5259ba0e *src/PqResultSource.h
 74630eb1d3dd72f0e20c90f0deac0ba6 *src/RPostgres-init.c
@@ -74,7 +74,7 @@ f251e8d8c1249e774674be514615eeec *tests/testthat/helper-with_table.R
 000f052dbee7a744d411e507f6efbb9e *tests/testthat/test-DBItest.R
 29890f7f72946cbf870c714ebeaee604 *tests/testthat/test-bigint.R
 d0d355c427d7373ab8e6a85d655a381b *tests/testthat/test-data-type.R
-3fb2c6809894d3fc84a1832ca0509707 *tests/testthat/test-dbConnect.R
+1eb01045fcf55d6094c6d528af1df1af *tests/testthat/test-dbConnect.R
 9939d01b8b9c8b6c138e1466a1a74c09 *tests/testthat/test-dbGetQuery.R
 dfc643c4d14d440fb7b02648551dca58 *tests/testthat/test-dbWriteTable.R
 07ec38d74f52ade1ddc67997730ad1ca *tests/testthat/test-encoding.R

NEWS.md

@@ -1,3 +1,12 @@
+# RPostgres 1.0-4 (2017-12-20)
+
+- Only call `PQcancel()` if the query hasn't completed, fixes transactions on Amazon RedShift (#159, @mmuurr).
+- Fix installation on MacOS.
+- Check libpq version in configure script (need at least 9.0).
+- Fix UBSAN warning: reference binding to null pointer (#156).
+- Fix rchk warning: PROTECT internal temporary SEXP objects (#157).
+- Fix severe memory leak when fetching results (#154).
+
 # RPostgres 1.0-3 (2017-12-01)
 
 Initial release, compliant to the DBI specification.

README.md

@@ -9,17 +9,18 @@ RPostgres is an DBI-compliant interface to the postgres database. It's a ground-
 * Automatically cleans up open connections and result sets, ensuring that you
   don't need to worry about leaking connections or memory.
 
-* Is a little faster, saving ~5 ms per query. (For refernce, it takes around 5ms
+* Is a little faster, saving ~5 ms per query. (For reference, it takes around 5ms
   to retrive a 1000 x 25 result set from a local database, so this is 
   decent speed up for smaller queries.)
 
 * A simplified build process that relies on system libpq.
 
 ## Installation
-
-RPostgres isn't available from CRAN yet, but you can get it from github with:
-
 ```R
+# Install the latest RPostgres release from CRAN:
+install.packages("RPostgres")
+
+# Or the the development version from GitHub:
 # install.packages("remotes")
 remotes::install_github("r-dbi/RPostgres")
 ```

configure

@@ -22,18 +22,22 @@ PKG_LIBS_STATIC="-lpq -lssl -lcrypto -lldap"
 if [ $(command -v pkg-config) ]; then
   PKGCONFIG_CFLAGS=$(pkg-config --cflags --silence-errors ${PKG_CONFIG_NAME})
   PKGCONFIG_LIBS=$(pkg-config --libs --silence-errors ${PKG_CONFIG_NAME})
+  PKGCONFIG_MODVERSION=$(pkg-config --modversion --silence-errors ${PKG_CONFIG_NAME})
 
   # MacOS seems to ship a broken libpq.pc file
-  if [[ "$PKGCONFIG_CFLAGS" == *"Internal.sdk"* ]]; then
-    unset PKGCONFIG_CFLAGS
-    unset PKGCONFIG_LIBS
+  if [[ "$OSTYPE" == "darwin"* ]]; then
+    if [[ "$PKGCONFIG_CFLAGS" == *"Internal.sdk"* ]] || [[ -z "$PKGCONFIG_CFLAGS" ]]; then
+      unset PKGCONFIG_CFLAGS
+      unset PKGCONFIG_LIBS
+    fi
   fi
 fi
 
 # pg_config values (if available)
 if [ $(command -v pg_config) ]; then
   PG_INC_DIR=$(pg_config --includedir)
   PG_LIB_DIR=$(pg_config --libdir)
+  PG_VERSION=$(pg_config --version)
 fi
 
 # Note that cflags may be empty in case of success
@@ -42,11 +46,15 @@ if [ "$INCLUDE_DIR" ] || [ "$LIB_DIR" ]; then
   PKG_CFLAGS="-I$INCLUDE_DIR $PKG_CFLAGS"
   PKG_LIBS="-L$LIB_DIR $PKG_LIBS"
 elif [ "$PKGCONFIG_CFLAGS" ] || [ "$PKGCONFIG_LIBS" ]; then
-  echo "Using pkg-config cflags and libs!"
+  echo "Found pkg-config cflags and libs ($PKG_CONFIG_NAME $PKGCONFIG_MODVERSION)!"
   PKG_CFLAGS=${PKGCONFIG_CFLAGS}
   PKG_LIBS=${PKGCONFIG_LIBS}
 elif [ "$PG_INC_DIR" ] || [ "$PG_LIB_DIR" ]; then
-  echo "Using pg_config includedir and libdir!"
+  echo "Found pg_config includedir and libdir ($PG_VERSION)!"
+  if [[ "$PG_VERSION" == "PostgreSQL 8"* ]]; then
+    echo "This version of libpq is too old! We need at least 9.0!"
+    exit 1
+  fi
   PKG_CFLAGS="-I${PG_INC_DIR}"
   PKG_LIBS="-L${PG_LIB_DIR} ${PKG_LIBS}"
 elif [[ "$OSTYPE" == "darwin"* ]]; then
@@ -94,11 +102,10 @@ fi
 
 # Write to Makevars
 sed -e "s|@cflags@|$PKG_CFLAGS|" -e "s|@libs@|$PKG_LIBS|" src/Makevars.in > src/Makevars.new
-if [ ! -f src/Makevars.new ] || (which diff > /dev/null && ! diff -q src/Makevars src/Makevars.new); then
-  mv src/Makevars.new src/Makevars
-else
-  rm src/Makevars.new
+if [ ! -f src/Makevars ] || (which diff > /dev/null && ! diff -q src/Makevars src/Makevars.new); then
+  cp -f src/Makevars.new src/Makevars
 fi
+rm -f src/Makevars.new
 
 # Success
 exit 0

src/DbColumn.cpp

@@ -72,12 +72,13 @@ void DbColumn::warn_type_conflicts(const String& name) const {
 
 DbColumn::operator SEXP() const {
   DATA_TYPE dt = get_last_storage()->get_data_type();
-  SEXP ret = DbColumnStorage::allocate(n, dt);
+  SEXP ret = PROTECT(DbColumnStorage::allocate(n, dt));
   int pos = 0;
   for (size_t k = 0; k < storage.size(); ++k) {
     const DbColumnStorage& current = storage[k];
     pos += current.copy_to(ret, dt, pos);
   }
+  UNPROTECT(1);
   return ret;
 }
 

src/DbColumnStorage.cpp

@@ -38,9 +38,10 @@ SEXP DbColumnStorage::allocate(const R_xlen_t length, DATA_TYPE dt) {
   SEXPTYPE type = sexptype_from_datatype(dt);
   RObject class_ = class_from_datatype(dt);
 
-  SEXP ret = Rf_allocVector(type, length);
+  SEXP ret = PROTECT(Rf_allocVector(type, length));
   if (!Rf_isNull(class_)) Rf_setAttrib(ret, R_ClassSymbol, class_);
   set_attribs_from_datatype(ret, dt);
+  UNPROTECT(1);
   return ret;
 }
 
@@ -209,7 +210,8 @@ Rcpp::RObject DbColumnStorage::class_from_datatype(DATA_TYPE dt) {
 void DbColumnStorage::set_attribs_from_datatype(SEXP x, DATA_TYPE dt) {
   switch (dt) {
   case DT_TIME:
-    Rf_setAttrib(x, CharacterVector::create("units"), CharacterVector::create("secs"));
+    Rf_setAttrib(x, PROTECT(CharacterVector::create("units")), PROTECT(CharacterVector::create("secs")));
+    UNPROTECT(2);
     break;
 
   default:

src/DbConnection.cpp

@@ -1,6 +1,7 @@
 #include "pch.h"
 #include "DbConnection.h"
 #include "encode.h"
+#include "DbResult.h"
 
 
 DbConnection::DbConnection(std::vector<std::string> keys, std::vector<std::string> values) :
@@ -44,34 +45,45 @@ PGconn* DbConnection::conn() {
 }
 
 void DbConnection::set_current_result(const DbResult* pResult) {
-  // Cancels previous query, if needed.
+  // same result pointer, nothing to do.
   if (pResult == pCurrentResult_)
     return;
 
+  // try to clean up remnants of any previous queries.
+  // (even if (the new) pResult is NULL, we should try to reset the back-end.)
   if (pCurrentResult_ != NULL) {
-    if (pResult != NULL)
-      warning("Cancelling previous query");
+    if (pResult != NULL) {
+      warning("Closing open result set, cancelling previous query");
+    }
 
     cleanup_query();
   }
+
   pCurrentResult_ = pResult;
 }
 
+
+/**
+ * Documentation for canceling queries:
+ * https://www.postgresql.org/docs/9.6/static/libpq-cancel.html
+ **/
 void DbConnection::cancel_query() {
   check_connection();
 
-  // Cancel running query
+  // first allocate a 'cancel command' data structure.
+  // should only return NULL if either:
+  //  * the connection is NULL or
+  //  * the connection is invalid.
   PGcancel* cancel = PQgetCancel(pConn_);
-  if (cancel == NULL) {
-    warning("Failed to cancel running query");
-    return;
-  }
+  if (cancel == NULL) stop("Connection error detected via PQgetCancel()");
 
+  // PQcancel() actually issues the cancel command to the backend.
   char errbuf[256];
   if (!PQcancel(cancel, errbuf, sizeof(errbuf))) {
     warning(errbuf);
   }
 
+  // free up the data structure allocated by PQgetCancel().
   PQfreeCancel(cancel);
 }
 
@@ -217,6 +229,8 @@ void DbConnection::conn_stop(PGconn* conn, const char* msg) {
 }
 
 void DbConnection::cleanup_query() {
-  cancel_query();
+  if(pCurrentResult_ != NULL && !(pCurrentResult_->complete())) {
+    cancel_query();
+  }
   finish_query();
 }

src/DbResult.cpp

@@ -50,8 +50,8 @@ int DbResult::n_rows_fetched() {
   return impl->n_rows_fetched();
 }
 
-bool DbResult::complete() {
-  return impl->complete();
+bool DbResult::complete() const {
+  return (impl == NULL) || impl->complete();
 }
 
 List DbResult::get_column_info() {

src/DbResult.h

@@ -25,7 +25,7 @@ class DbResult : boost::noncopyable {
   ~DbResult();
 
 public:
-  bool complete();
+  bool complete() const;
   bool active() const;
   int n_rows_fetched();
   int n_rows_affected();