Back to Multiple platform build/check report for BioC 3.20:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 182/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocNeighbors 1.23.0  (landing page)
Aaron Lun
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/BiocNeighbors
git_branch: devel
git_last_commit: e0cd963
git_last_commit_date: 2024-04-30 11:07:34 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  

CHECK results for BiocNeighbors on palomino6

To the developers/maintainers of the BiocNeighbors package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocNeighbors.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BiocNeighbors
Version: 1.23.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocNeighbors.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BiocNeighbors_1.23.0.tar.gz
StartedAt: 2024-07-15 22:06:08 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 22:11:45 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 337.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BiocNeighbors.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocNeighbors.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BiocNeighbors_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/BiocNeighbors.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BiocNeighbors/DESCRIPTION' ... OK
* this is package 'BiocNeighbors' version '1.23.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BiocNeighbors' can be installed ... WARNING
Found the following significant warnings:
  annoy/annoylib.h:1115:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
  annoy/annoylib.h:1305:20: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
  annoy/annoylib.h:1305:20: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/BiocNeighbors.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... WARNING
checkRd: (5) BiocNeighborIndex.Rd:24: \item in \describe must have non-empty label
checkRd: (5) BiocNeighborIndex.Rd:25: \item in \describe must have non-empty label
checkRd: (5) BiocNeighborIndex.Rd:26: \item in \describe must have non-empty label
checkRd: (5) BiocNeighborIndex.Rd:27: \item in \describe must have non-empty label
checkRd: (5) BiocNeighborParam.Rd:18: \item in \describe must have non-empty label
checkRd: (5) BiocNeighborParam.Rd:19: \item in \describe must have non-empty label
checkRd: (5) BiocNeighborParam.Rd:20: \item in \describe must have non-empty label
checkRd: (5) BiocNeighborParam.Rd:21: \item in \describe must have non-empty label
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/BiocNeighbors/libs/x64/BiocNeighbors.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
findNeighbors-functions 5.57   0.45    6.01
findKNN-functions       5.81   0.02    4.54
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/BiocNeighbors.Rcheck/00check.log'
for details.

Installation output

BiocNeighbors.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BiocNeighbors
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'BiocNeighbors' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
using C++11
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c annoy.cpp -o annoy.o
In file included from annoy/RcppAnnoy.h:24,
                 from annoy.h:8,
                 from annoy.cpp:1:
annoy/annoylib.h: In instantiation of 'bool AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::load(const char*, bool, char**) [with S = int; T = float; Distance = Manhattan; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]':
annoy.cpp:7:13:   required from 'Annoy<Distance>::Annoy(int, const std::string&, double) [with Distance = Manhattan; std::string = std::__cxx11::basic_string<char>]'
annoy.cpp:93:16:   required from here
annoy/annoylib.h:1115:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1115 |     if (_verbose) showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ~~~~~~~~~~~~~
      |                                                                             |
      |                                                                             std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1115:39: note: format string is defined here
 1115 |     if (_verbose) showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                                     ~~^
      |                                       |
      |                                       long unsigned int
      |                                     %llu
annoy/annoylib.h: In instantiation of 'bool AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::load(const char*, bool, char**) [with S = int; T = float; Distance = Euclidean; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]':
annoy.cpp:7:13:   required from 'Annoy<Distance>::Annoy(int, const std::string&, double) [with Distance = Euclidean; std::string = std::__cxx11::basic_string<char>]'
annoy.cpp:94:16:   required from here
annoy/annoylib.h:1115:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1115 |     if (_verbose) showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ~~~~~~~~~~~~~
      |                                                                             |
      |                                                                             std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1115:39: note: format string is defined here
 1115 |     if (_verbose) showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                                     ~~^
      |                                       |
      |                                       long unsigned int
      |                                     %llu
annoy/annoylib.h: In instantiation of 'S AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::_make_tree(const std::vector<T>&, bool, Random&, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Euclidean; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]':
annoy/annoylib.h:1185:30:   required from 'void AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::thread_build(int, int, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Euclidean; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]'
annoy/annoylib.h:1407:24:   required from 'static void AnnoyIndexSingleThreadedBuildPolicy::build(AnnoyIndex<S, T, D, Random, AnnoyIndexSingleThreadedBuildPolicy>*, int, int) [with S = int; T = float; D = Euclidean; Random = Kiss64Random]'
annoy/annoylib.h:966:46:   required from 'bool AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::build(int, int, char**) [with S = int; T = float; Distance = Euclidean; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]'
annoy/annoylib.h:951:8:   required from here
annoy/annoylib.h:1305:20: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1306 |           children_indices[0].size(), children_indices[1].size());
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                   |
      |                                   std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1305:55: note: format string is defined here
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                     ~~^
      |                                                       |
      |                                                       long int
      |                                                     %lld
annoy/annoylib.h:1305:20: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1306 |           children_indices[0].size(), children_indices[1].size());
      |                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                               |
      |                                                               std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1305:79: note: format string is defined here
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                                             ~~^
      |                                                                               |
      |                                                                               long int
      |                                                                             %lld
annoy/annoylib.h: In instantiation of 'S AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::_make_tree(const std::vector<T>&, bool, Random&, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Manhattan; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]':
annoy/annoylib.h:1185:30:   required from 'void AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::thread_build(int, int, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Manhattan; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]'
annoy/annoylib.h:1407:24:   required from 'static void AnnoyIndexSingleThreadedBuildPolicy::build(AnnoyIndex<S, T, D, Random, AnnoyIndexSingleThreadedBuildPolicy>*, int, int) [with S = int; T = float; D = Manhattan; Random = Kiss64Random]'
annoy/annoylib.h:966:46:   required from 'bool AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::build(int, int, char**) [with S = int; T = float; Distance = Manhattan; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]'
annoy/annoylib.h:951:8:   required from here
annoy/annoylib.h:1305:20: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1306 |           children_indices[0].size(), children_indices[1].size());
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                   |
      |                                   std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1305:55: note: format string is defined here
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                     ~~^
      |                                                       |
      |                                                       long int
      |                                                     %lld
annoy/annoylib.h:1305:20: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1306 |           children_indices[0].size(), children_indices[1].size());
      |                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                               |
      |                                                               std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1305:79: note: format string is defined here
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                                             ~~^
      |                                                                               |
      |                                                                               long int
      |                                                                             %lld
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c build_annoy.cpp -o build_annoy.o
In file included from annoy/RcppAnnoy.h:24,
                 from annoy.h:8,
                 from build_annoy.cpp:1:
annoy/annoylib.h: In instantiation of 'bool AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::load(const char*, bool, char**) [with S = int; T = float; Distance = Manhattan; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]':
annoy/annoylib.h:1032:14:   required from 'bool AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::save(const char*, bool, char**) [with S = int; T = float; Distance = Manhattan; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]'
build_annoy.cpp:17:13:   required from 'Rcpp::RObject build_annoy_internal(Rcpp::NumericMatrix, int, const std::string&) [with Distance = Manhattan; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericMatrix = Rcpp::Matrix<14>; std::string = std::__cxx11::basic_string<char>]'
build_annoy.cpp:25:47:   required from here
annoy/annoylib.h:1115:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1115 |     if (_verbose) showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ~~~~~~~~~~~~~
      |                                                                             |
      |                                                                             std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1115:39: note: format string is defined here
 1115 |     if (_verbose) showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                                     ~~^
      |                                       |
      |                                       long unsigned int
      |                                     %llu
annoy/annoylib.h: In instantiation of 'bool AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::load(const char*, bool, char**) [with S = int; T = float; Distance = Euclidean; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]':
annoy/annoylib.h:1032:14:   required from 'bool AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::save(const char*, bool, char**) [with S = int; T = float; Distance = Euclidean; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]'
build_annoy.cpp:17:13:   required from 'Rcpp::RObject build_annoy_internal(Rcpp::NumericMatrix, int, const std::string&) [with Distance = Euclidean; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericMatrix = Rcpp::Matrix<14>; std::string = std::__cxx11::basic_string<char>]'
build_annoy.cpp:27:47:   required from here
annoy/annoylib.h:1115:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1115 |     if (_verbose) showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ~~~~~~~~~~~~~
      |                                                                             |
      |                                                                             std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1115:39: note: format string is defined here
 1115 |     if (_verbose) showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                                     ~~^
      |                                       |
      |                                       long unsigned int
      |                                     %llu
annoy/annoylib.h: In instantiation of 'S AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::_make_tree(const std::vector<T>&, bool, Random&, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Manhattan; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]':
annoy/annoylib.h:1185:30:   required from 'void AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::thread_build(int, int, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Manhattan; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]'
annoy/annoylib.h:1407:24:   required from 'static void AnnoyIndexSingleThreadedBuildPolicy::build(AnnoyIndex<S, T, D, Random, AnnoyIndexSingleThreadedBuildPolicy>*, int, int) [with S = int; T = float; D = Manhattan; Random = Kiss64Random]'
annoy/annoylib.h:966:46:   required from 'bool AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::build(int, int, char**) [with S = int; T = float; Distance = Manhattan; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]'
build_annoy.cpp:16:14:   required from 'Rcpp::RObject build_annoy_internal(Rcpp::NumericMatrix, int, const std::string&) [with Distance = Manhattan; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericMatrix = Rcpp::Matrix<14>; std::string = std::__cxx11::basic_string<char>]'
build_annoy.cpp:25:47:   required from here
annoy/annoylib.h:1305:20: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1306 |           children_indices[0].size(), children_indices[1].size());
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                   |
      |                                   std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1305:55: note: format string is defined here
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                     ~~^
      |                                                       |
      |                                                       long int
      |                                                     %lld
annoy/annoylib.h:1305:20: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1306 |           children_indices[0].size(), children_indices[1].size());
      |                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                               |
      |                                                               std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1305:79: note: format string is defined here
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                                             ~~^
      |                                                                               |
      |                                                                               long int
      |                                                                             %lld
annoy/annoylib.h: In instantiation of 'S AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::_make_tree(const std::vector<T>&, bool, Random&, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Euclidean; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]':
annoy/annoylib.h:1185:30:   required from 'void AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::thread_build(int, int, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Euclidean; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]'
annoy/annoylib.h:1407:24:   required from 'static void AnnoyIndexSingleThreadedBuildPolicy::build(AnnoyIndex<S, T, D, Random, AnnoyIndexSingleThreadedBuildPolicy>*, int, int) [with S = int; T = float; D = Euclidean; Random = Kiss64Random]'
annoy/annoylib.h:966:46:   required from 'bool AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::build(int, int, char**) [with S = int; T = float; Distance = Euclidean; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]'
build_annoy.cpp:16:14:   required from 'Rcpp::RObject build_annoy_internal(Rcpp::NumericMatrix, int, const std::string&) [with Distance = Euclidean; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericMatrix = Rcpp::Matrix<14>; std::string = std::__cxx11::basic_string<char>]'
build_annoy.cpp:27:47:   required from here
annoy/annoylib.h:1305:20: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1306 |           children_indices[0].size(), children_indices[1].size());
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                   |
      |                                   std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1305:55: note: format string is defined here
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                     ~~^
      |                                                       |
      |                                                       long int
      |                                                     %lld
annoy/annoylib.h:1305:20: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1306 |           children_indices[0].size(), children_indices[1].size());
      |                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                               |
      |                                                               std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1305:79: note: format string is defined here
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                                             ~~^
      |                                                                               |
      |                                                                               long int
      |                                                                             %lld
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c build_hnsw.cpp -o build_hnsw.o
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c build_vptree.cpp -o build_vptree.o
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c distances.cpp -o distances.o
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c exhaustive.cpp -o exhaustive.o
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c find_annoy.cpp -o find_annoy.o
In file included from annoy/RcppAnnoy.h:24,
                 from annoy.h:8,
                 from find_annoy.cpp:1:
annoy/annoylib.h: In instantiation of 'bool AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::load(const char*, bool, char**) [with S = int; T = float; Distance = Euclidean; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]':
annoy/annoylib.h:1066:8:   required from here
annoy/annoylib.h:1115:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1115 |     if (_verbose) showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ~~~~~~~~~~~~~
      |                                                                             |
      |                                                                             std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1115:39: note: format string is defined here
 1115 |     if (_verbose) showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                                     ~~^
      |                                       |
      |                                       long unsigned int
      |                                     %llu
annoy/annoylib.h: In instantiation of 'bool AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::load(const char*, bool, char**) [with S = int; T = float; Distance = Manhattan; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]':
annoy/annoylib.h:1066:8:   required from here
annoy/annoylib.h:1115:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1115 |     if (_verbose) showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ~~~~~~~~~~~~~
      |                                                                             |
      |                                                                             std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1115:39: note: format string is defined here
 1115 |     if (_verbose) showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                                     ~~^
      |                                       |
      |                                       long unsigned int
      |                                     %llu
annoy/annoylib.h: In instantiation of 'S AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::_make_tree(const std::vector<T>&, bool, Random&, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Euclidean; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]':
annoy/annoylib.h:1185:30:   required from 'void AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::thread_build(int, int, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Euclidean; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]'
annoy/annoylib.h:1407:24:   required from 'static void AnnoyIndexSingleThreadedBuildPolicy::build(AnnoyIndex<S, T, D, Random, AnnoyIndexSingleThreadedBuildPolicy>*, int, int) [with S = int; T = float; D = Euclidean; Random = Kiss64Random]'
annoy/annoylib.h:966:46:   required from 'bool AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::build(int, int, char**) [with S = int; T = float; Distance = Euclidean; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]'
annoy/annoylib.h:951:8:   required from here
annoy/annoylib.h:1305:20: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1306 |           children_indices[0].size(), children_indices[1].size());
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                   |
      |                                   std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1305:55: note: format string is defined here
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                     ~~^
      |                                                       |
      |                                                       long int
      |                                                     %lld
annoy/annoylib.h:1305:20: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1306 |           children_indices[0].size(), children_indices[1].size());
      |                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                               |
      |                                                               std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1305:79: note: format string is defined here
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                                             ~~^
      |                                                                               |
      |                                                                               long int
      |                                                                             %lld
annoy/annoylib.h: In instantiation of 'S AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::_make_tree(const std::vector<T>&, bool, Random&, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Manhattan; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]':
annoy/annoylib.h:1185:30:   required from 'void AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::thread_build(int, int, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Manhattan; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]'
annoy/annoylib.h:1407:24:   required from 'static void AnnoyIndexSingleThreadedBuildPolicy::build(AnnoyIndex<S, T, D, Random, AnnoyIndexSingleThreadedBuildPolicy>*, int, int) [with S = int; T = float; D = Manhattan; Random = Kiss64Random]'
annoy/annoylib.h:966:46:   required from 'bool AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::build(int, int, char**) [with S = int; T = float; Distance = Manhattan; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]'
annoy/annoylib.h:951:8:   required from here
annoy/annoylib.h:1305:20: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1306 |           children_indices[0].size(), children_indices[1].size());
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                   |
      |                                   std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1305:55: note: format string is defined here
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                     ~~^
      |                                                       |
      |                                                       long int
      |                                                     %lld
annoy/annoylib.h:1305:20: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1306 |           children_indices[0].size(), children_indices[1].size());
      |                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                               |
      |                                                               std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1305:79: note: format string is defined here
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                                             ~~^
      |                                                                               |
      |                                                                               long int
      |                                                                             %lld
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c find_exhaustive.cpp -o find_exhaustive.o
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c find_hnsw.cpp -o find_hnsw.o
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c find_kmknn.cpp -o find_kmknn.o
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c find_mutual_nns.cpp -o find_mutual_nns.o
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c find_vptree.cpp -o find_vptree.o
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hnsw.cpp -o hnsw.o
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c kmknn.cpp -o kmknn.o
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c query_annoy.cpp -o query_annoy.o
In file included from annoy/RcppAnnoy.h:24,
                 from annoy.h:8,
                 from query_annoy.cpp:1:
annoy/annoylib.h: In instantiation of 'bool AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::load(const char*, bool, char**) [with S = int; T = float; Distance = Euclidean; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]':
annoy/annoylib.h:1066:8:   required from here
annoy/annoylib.h:1115:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1115 |     if (_verbose) showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ~~~~~~~~~~~~~
      |                                                                             |
      |                                                                             std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1115:39: note: format string is defined here
 1115 |     if (_verbose) showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                                     ~~^
      |                                       |
      |                                       long unsigned int
      |                                     %llu
annoy/annoylib.h: In instantiation of 'bool AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::load(const char*, bool, char**) [with S = int; T = float; Distance = Manhattan; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]':
annoy/annoylib.h:1066:8:   required from here
annoy/annoylib.h:1115:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1115 |     if (_verbose) showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ~~~~~~~~~~~~~
      |                                                                             |
      |                                                                             std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1115:39: note: format string is defined here
 1115 |     if (_verbose) showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                                     ~~^
      |                                       |
      |                                       long unsigned int
      |                                     %llu
annoy/annoylib.h: In instantiation of 'S AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::_make_tree(const std::vector<T>&, bool, Random&, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Euclidean; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]':
annoy/annoylib.h:1185:30:   required from 'void AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::thread_build(int, int, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Euclidean; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]'
annoy/annoylib.h:1407:24:   required from 'static void AnnoyIndexSingleThreadedBuildPolicy::build(AnnoyIndex<S, T, D, Random, AnnoyIndexSingleThreadedBuildPolicy>*, int, int) [with S = int; T = float; D = Euclidean; Random = Kiss64Random]'
annoy/annoylib.h:966:46:   required from 'bool AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::build(int, int, char**) [with S = int; T = float; Distance = Euclidean; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]'
annoy/annoylib.h:951:8:   required from here
annoy/annoylib.h:1305:20: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1306 |           children_indices[0].size(), children_indices[1].size());
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                   |
      |                                   std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1305:55: note: format string is defined here
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                     ~~^
      |                                                       |
      |                                                       long int
      |                                                     %lld
annoy/annoylib.h:1305:20: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1306 |           children_indices[0].size(), children_indices[1].size());
      |                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                               |
      |                                                               std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1305:79: note: format string is defined here
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                                             ~~^
      |                                                                               |
      |                                                                               long int
      |                                                                             %lld
annoy/annoylib.h: In instantiation of 'S AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::_make_tree(const std::vector<T>&, bool, Random&, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Manhattan; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]':
annoy/annoylib.h:1185:30:   required from 'void AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::thread_build(int, int, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Manhattan; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]'
annoy/annoylib.h:1407:24:   required from 'static void AnnoyIndexSingleThreadedBuildPolicy::build(AnnoyIndex<S, T, D, Random, AnnoyIndexSingleThreadedBuildPolicy>*, int, int) [with S = int; T = float; D = Manhattan; Random = Kiss64Random]'
annoy/annoylib.h:966:46:   required from 'bool AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::build(int, int, char**) [with S = int; T = float; Distance = Manhattan; Random = Kiss64Random; ThreadedBuildPolicy = AnnoyIndexSingleThreadedBuildPolicy]'
annoy/annoylib.h:951:8:   required from here
annoy/annoylib.h:1305:20: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1306 |           children_indices[0].size(), children_indices[1].size());
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                   |
      |                                   std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1305:55: note: format string is defined here
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                     ~~^
      |                                                       |
      |                                                       long int
      |                                                     %lld
annoy/annoylib.h:1305:20: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1306 |           children_indices[0].size(), children_indices[1].size());
      |                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                               |
      |                                                               std::vector<int>::size_type {aka long long unsigned int}
annoy/annoylib.h:81:57: note: in definition of macro 'showUpdate'
   81 |   #define showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                         ^~~~~~~~~~~
annoy/annoylib.h:1305:79: note: format string is defined here
 1305 |         showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                                             ~~^
      |                                                                               |
      |                                                                               long int
      |                                                                             %lld
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c query_exhaustive.cpp -o query_exhaustive.o
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c query_hnsw.cpp -o query_hnsw.o
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c query_kmknn.cpp -o query_kmknn.o
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c query_vptree.cpp -o query_vptree.o
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.cpp -o utils.o
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppHNSW/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c vptree.cpp -o vptree.o
g++ -shared -s -static-libgcc -o BiocNeighbors.dll tmp.def RcppExports.o annoy.o build_annoy.o build_hnsw.o build_vptree.o distances.o exhaustive.o find_annoy.o find_exhaustive.o find_hnsw.o find_kmknn.o find_mutual_nns.o find_vptree.o hnsw.o kmknn.o query_annoy.o query_exhaustive.o query_hnsw.o query_kmknn.o query_vptree.o utils.o vptree.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-BiocNeighbors/00new/BiocNeighbors/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocNeighbors)

Tests output

BiocNeighbors.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(BiocNeighbors)
> test_check("BiocNeighbors")
[ FAIL 0 | WARN 494 | SKIP 2 | PASS 3289 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• out of sync with RcppAnnoy, skipping tests (2): 'test-find-annoy.R:5:1',
  'test-query-annoy.R:5:1'

[ FAIL 0 | WARN 494 | SKIP 2 | PASS 3289 ]
> 
> proc.time()
   user  system elapsed 
  90.92    8.46  197.90

Example timings

BiocNeighbors.Rcheck/BiocNeighbors-Ex.timings

nameusersystemelapsed
AnnoyIndex0.300.010.33
AnnoyParam000
BiocNeighbors-raw-index1.020.011.03
BiocNeighbors-ties000
ExhaustiveIndex0.020.000.01
ExhaustiveParam000
HnswIndex0.640.000.64
HnswParam000
KmknnIndex0.200.020.22
KmknnParam0.020.000.01
VptreeIndex0.020.000.02
VptreeParam000
buildAnnoy0.250.020.28
buildExhaustive000
buildHnsw0.620.000.62
buildIndex0.400.020.43
buildKmknn0.190.000.19
buildVptree0.000.010.02
findKNN-functions5.810.024.54
findKNN-methods4.970.005.00
findMutualNN0.030.000.04
findNeighbors-functions5.570.456.01
findNeighbors-methods3.760.023.80
queryKNN-functions1.410.041.47
queryKNN-methods1.590.051.65
queryNeighbors-functions0.320.000.34
queryNeighbors-methods0.720.030.77