prep for CRAN submission

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RcppHNSW
 Title: 'Rcpp' Bindings for 'hnswlib', a Library for Approximate Nearest Neighbors
-Version: 0.4.1.9000
+Version: 0.5.0
 Authors@R: c(person("James", "Melville", email = "[email protected]", 
   role = c("aut", "cre")), 
   person("Aaron", "Lun", role = "ctb"), 

NEWS.md

@@ -1,32 +1,35 @@
-# RcppHNSW 0.4.9000
+# RcppHNSW 0.5.0
 
 ## New features
 
-* For high-dimensional data, there can be a noticeable CPU overhead in copying 
-data out of the non-contiguous memory regions when row-wise data is used. If
-you wish to provide data where each *column* of the input matrix contains an
-item to be indexed/search then see the following additions to the API:
-    * For the class-based API: `addItemsCol`, `getAllNNsCol` and 
-    `getAllNNsListCol` are the column-based equivalents of `addItems`, 
-    `getAllNNs` and `getAllNNsList`, respectively. Note that the returned 
-    nearest neighbor data from `getAllNNsCol` and `getAllNNsListCol` are *also* 
-    stored by column, i.e. the matrices have dimensions `k x n` where `k` is the
-    number of neighbors, and `n` the number of items in the data being searched.
-    * For the function-based API, a new parameter `byrow` has been added to 
-    `hnsw_knn`, `hnsw_build` and `hnsw_search`. By default this is set to `TRUE`
-    and indicates that the items in the input matrix are found in each row. To 
-    pass column-stored items, set `byrow = FALSE`. Any matrices returned by 
-    `hnsw_search` and `hnsw_knn` will now follow the convention provided by the
-    value of `byrow`: i.e. if  `byrow = FALSE`, the matrices contain nearest 
-    neighbor information in each column.
-* new method: `getItems`, which returns a matrix of the data vectors in the 
-index with the specified integer identifiers. From a feature request made by
-[d4tum](https://github.com/d4tum) (<https://github.com/jlmelville/rcpphnsw/issues/18>).
+* Updated hnswlib to [version 0.7.0](https://github.com/nmslib/hnswlib/releases/tag/v0.7.0).
+Note that I made some very minor changes to the code to silence some compiler warnings. These
+changes have been submitted up-stream to the hnswlib project.
+* For high-dimensional data, there can be a noticeable CPU overhead in copying data out of the
+non-contiguous memory regions when row-wise data is used. If you wish to provide data where each
+*column* of the input matrix contains an item to be indexed/search then see the following additions
+to the API:
+  * For the class-based API: `addItemsCol`, `getAllNNsCol` and `getAllNNsListCol` are the
+  column-based equivalents of `addItems`, `getAllNNs` and `getAllNNsList`, respectively. Note that
+  the returned nearest neighbor data from `getAllNNsCol` and `getAllNNsListCol` are *also* stored
+  by column, i.e. the matrices have dimensions `k x n` where `k` is the number of neighbors, and
+  `n` the number of items in the data being searched.
+  * For the function-based API, a new parameter `byrow` has been added to `hnsw_knn`, `hnsw_build`
+  and `hnsw_search`. By default this is set to `TRUE` and indicates that the items in the input
+  matrix are found in each row. To pass column-stored items, set `byrow = FALSE`. Any matrices
+  returned by `hnsw_search` and `hnsw_knn` will now follow the convention provided by the value of
+  `byrow`: i.e. if  `byrow = FALSE`, the matrices contain nearest neighbor information in each
+  column.
+* new method: `getItems`, which returns a matrix of the data vectors in the index with the
+  specified integer identifiers. From a feature request made by [d4tum](https://github.com/d4tum)
+  (<https://github.com/jlmelville/rcpphnsw/issues/18>).
 
 ## Bug fixes and minor improvements
 
-* The `progress` parameter in the functional interface no longer does anything. When 
+* The `progress` parameter in the functional interface no longer does anything. When
 `verbose = TRUE`, a progress bar is no longer shown.
+* Due to a breaking change in roxygen2 7.0.0, there was a missing package alias in the
+documentation.
 
 # RcppHNSW 0.4.1
 

cran-comments.md

@@ -1,52 +1,65 @@
 ## Release Summary
 
-This is a patch release to fix a valgrind error that was introduced with
-the previous submission.
+This is a patch release to fix various CRAN check errors.
 
 ## Test environments
 
-* ubuntu 20.04 (on github actions), R 4.1.3, R 4.2.1, devel
-* local ubuntu 22.04 R 4.2.1
-* Windows Server 2022 (on github actions), R 4.1.3
-* local Windows 11 build, R 4.2.1
-* mac OS X Big Sur (on github actions) R 4.2.1
+* ubuntu 22.04 (on github actions), R 4.2.3, R 4.3.1, devel
+* local ubuntu 23.04 R 4.2.2
+* Debian Linux, R-devel, GCC ASAN/UBSAN (via rhub)
+* Debian Linux, R-release, GCC (via rhub)
+* Ubuntu Linux 20.04.1 LTS, R-release, GCC (via rhub)
+* Fedora Linux, R-devel, clang, gfortran (via rhub)
+* Windows Server 2022 (on github actions), R 4.2.3, R 4.3.1
+* Windows Server 2022, R-devel, 64 bit (via rhub)
+* local Windows 11 build, R 4.3.1
 * win-builder (devel)
+* mac OS X Monterey (on github actions) R 4.3.1
 
 ## R CMD check results
 
 There were no ERRORs or WARNINGs.
 
 There was one NOTE:
 
-❯ checking installed package size ... NOTE
-    installed size is  5.4Mb
-    sub-directories of 1Mb or more:
-      libs   5.1Mb
+N  checking installed package size ...
+     installed size is  6.6Mb
+     sub-directories of 1Mb or more:
+       libs   6.3Mb
 
 This is expected due to the use of C++ templates in hnswlib.
-
-There was a message about possibly mis-spelled words in DESCRIPTION:
-
-  HNSW (2:28)
 
 This is spelled correctly.
 
 ## CRAN checks
 
 There are no ERRORs or WARNINGs.
 
-There is a NOTE for all flavors about LazyData. This release fixes that NOTE.
+There is a NOTE:
+
+Check: C++ specification
+Result: NOTE
+     Specified C++11: please drop specification unless essential
+
+This submission fixes this.
+
+There is a NOTE:
+
+Check: Rd metadata
+Result: NOTE
+    Invalid package aliases in Rd file ‘RcppHnsw-package.Rd’:
+     ‘RcppHnsw-package’
 
-There are four flavors with NOTEs about installed package size 
-(r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, 
-r-oldrel-macos-x86_64). This is expected and won't be fixed.
+This submissions fixes this.
 
-There is a valgrind issue. This releases fixes that issue.
+There are four flavors with NOTEs about installed package size (r-release-macos-arm64,
+r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64). This is expected and won't be
+fixed.
 
 ## Downstream dependencies
 
-We checked 3 reverse dependencies (1 from CRAN + 2 from Bioconductor), comparing 
-R CMD check results across CRAN and dev versions of this package.
+We checked 2 reverse dependencies (0 from CRAN + 2 from Bioconductor), comparing R CMD check
+results across CRAN and dev versions of this package.
 
- * We saw 0 new problems
- * We failed to check 0 packages
+* We saw 0 new problems
+* We failed to check 0 packages