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Installation issue, directly related to RcppAnnoy 0.0.15 vs the previous 0.0.14 #10

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lcolladotor opened this issue Feb 27, 2020 · 8 comments · Fixed by eddelbuettel/rcppannoy#58
Closed

Installation issue, directly related to RcppAnnoy 0.0.15 vs the previous 0.0.14 #10

lcolladotor opened this issue Feb 27, 2020 · 8 comments · Fixed by eddelbuettel/rcppannoy#58

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@lcolladotor
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Hi,

I noticed that RcppAnnoy just changed from 0.0.14 to 0.0.15 and as this is used by BiocNeighbors while compiling, there's now an installation issue that was absent before. I have no idea how RcppAnnoy works but maybe you do. Maybe this involves an update on BiocNeighbors or fixing something in RcppAnnoy.

Best,
Leo

Remote (shinyapps.io)

Below is the installation log from shinyapps.io where I saw the error (30 min ago, 2 hours ago this was not the case). That is, when trying to update https://jhubiostatistics.shinyapps.io/spatialLIBD/.

[2020-02-27T17:47:39.611226257+0000] Building R package: RcppAnnoy (0.0.15)
/mnt/packages/build /mnt
* installing to library ‘/opt/R/3.6.2/lib/R/library’
* installing *source* package ‘RcppAnnoy’ ...
** package ‘RcppAnnoy’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"/opt/R/3.6.2/lib/R/include" -DNDEBUG -I../inst/include/ -I"/opt/R/3.6.2/lib/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c annoy.cpp -o annoy.o
gcc -I"/opt/R/3.6.2/lib/R/include" -DNDEBUG -I../inst/include/ -I"/opt/R/3.6.2/lib/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c init.c -o init.o
In file included from annoy.cpp:39:0:
../inst/include/annoylib.h:118:17: note: #pragma message: Just for your information: using no AVX instructions
 #pragma message "Just for your information: using no AVX instructions"
                 ^
g++ -std=gnu++11 -shared -L/opt/R/3.6.2/lib/R/lib -L/usr/local/lib -o RcppAnnoy.so annoy.o init.o -L/opt/R/3.6.2/lib/R/lib -lR
installing to /opt/R/3.6.2/lib/R/library/00LOCK-RcppAnnoy/00new/RcppAnnoy/libs
** R
** demo
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* creating tarball
packaged installation of ‘RcppAnnoy’ as ‘RcppAnnoy_0.0.15_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (RcppAnnoy)
/mnt
[2020-02-27T17:47:54.216922453+0000] Building R package: BiocNeighbors (1.4.1)
/mnt/packages/build /mnt
* installing to library ‘/opt/R/3.6.2/lib/R/library’
* installing *source* package ‘BiocNeighbors’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/opt/R/3.6.2/lib/R/include" -DNDEBUG  -I"/opt/R/3.6.2/lib/R/library/Rcpp/include" -I"/opt/R/3.6.2/lib/R/library/RcppAnnoy/include" -I"/opt/R/3.6.2/lib/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/opt/R/3.6.2/lib/R/include" -DNDEBUG  -I"/opt/R/3.6.2/lib/R/library/Rcpp/include" -I"/opt/R/3.6.2/lib/R/library/RcppAnnoy/include" -I"/opt/R/3.6.2/lib/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -c annoy.cpp -o annoy.o
g++ -std=gnu++11 -I"/opt/R/3.6.2/lib/R/include" -DNDEBUG  -I"/opt/R/3.6.2/lib/R/library/Rcpp/include" -I"/opt/R/3.6.2/lib/R/library/RcppAnnoy/include" -I"/opt/R/3.6.2/lib/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -c build_annoy.cpp -o build_annoy.o
g++ -std=gnu++11 -I"/opt/R/3.6.2/lib/R/include" -DNDEBUG  -I"/opt/R/3.6.2/lib/R/library/Rcpp/include" -I"/opt/R/3.6.2/lib/R/library/RcppAnnoy/include" -I"/opt/R/3.6.2/lib/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -c build_hnsw.cpp -o build_hnsw.o
In file included from annoy.h:17:0,
                 from annoy.cpp:1:
/opt/R/3.6.2/lib/R/library/RcppAnnoy/include/annoylib.h:118:17: note: #pragma message: Just for your information: using no AVX instructions
 #pragma message "Just for your information: using no AVX instructions"
                 ^
In file included from annoy.h:17:0,
                 from build_annoy.cpp:1:
/opt/R/3.6.2/lib/R/library/RcppAnnoy/include/annoylib.h:118:17: note: #pragma message: Just for your information: using no AVX instructions
 #pragma message "Just for your information: using no AVX instructions"
                 ^
g++ -std=gnu++11 -I"/opt/R/3.6.2/lib/R/include" -DNDEBUG  -I"/opt/R/3.6.2/lib/R/library/Rcpp/include" -I"/opt/R/3.6.2/lib/R/library/RcppAnnoy/include" -I"/opt/R/3.6.2/lib/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -c build_vptree.cpp -o build_vptree.o
g++ -std=gnu++11 -I"/opt/R/3.6.2/lib/R/include" -DNDEBUG  -I"/opt/R/3.6.2/lib/R/library/Rcpp/include" -I"/opt/R/3.6.2/lib/R/library/RcppAnnoy/include" -I"/opt/R/3.6.2/lib/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -c distances.cpp -o distances.o
g++ -std=gnu++11 -I"/opt/R/3.6.2/lib/R/include" -DNDEBUG  -I"/opt/R/3.6.2/lib/R/library/Rcpp/include" -I"/opt/R/3.6.2/lib/R/library/RcppAnnoy/include" -I"/opt/R/3.6.2/lib/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -c find_annoy.cpp -o find_annoy.o
g++ -std=gnu++11 -I"/opt/R/3.6.2/lib/R/include" -DNDEBUG  -I"/opt/R/3.6.2/lib/R/library/Rcpp/include" -I"/opt/R/3.6.2/lib/R/library/RcppAnnoy/include" -I"/opt/R/3.6.2/lib/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -c find_hnsw.cpp -o find_hnsw.o
In file included from annoy.h:17:0,
                 from find_annoy.cpp:1:
/opt/R/3.6.2/lib/R/library/RcppAnnoy/include/annoylib.h:118:17: note: #pragma message: Just for your information: using no AVX instructions
 #pragma message "Just for your information: using no AVX instructions"
                 ^
g++ -std=gnu++11 -I"/opt/R/3.6.2/lib/R/include" -DNDEBUG  -I"/opt/R/3.6.2/lib/R/library/Rcpp/include" -I"/opt/R/3.6.2/lib/R/library/RcppAnnoy/include" -I"/opt/R/3.6.2/lib/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -c find_kmknn.cpp -o find_kmknn.o
g++ -std=gnu++11 -I"/opt/R/3.6.2/lib/R/include" -DNDEBUG  -I"/opt/R/3.6.2/lib/R/library/Rcpp/include" -I"/opt/R/3.6.2/lib/R/library/RcppAnnoy/include" -I"/opt/R/3.6.2/lib/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -c find_vptree.cpp -o find_vptree.o
g++ -std=gnu++11 -I"/opt/R/3.6.2/lib/R/include" -DNDEBUG  -I"/opt/R/3.6.2/lib/R/library/Rcpp/include" -I"/opt/R/3.6.2/lib/R/library/RcppAnnoy/include" -I"/opt/R/3.6.2/lib/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -c hnsw.cpp -o hnsw.o
g++ -std=gnu++11 -I"/opt/R/3.6.2/lib/R/include" -DNDEBUG  -I"/opt/R/3.6.2/lib/R/library/Rcpp/include" -I"/opt/R/3.6.2/lib/R/library/RcppAnnoy/include" -I"/opt/R/3.6.2/lib/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -c kmknn.cpp -o kmknn.o
g++ -std=gnu++11 -I"/opt/R/3.6.2/lib/R/include" -DNDEBUG  -I"/opt/R/3.6.2/lib/R/library/Rcpp/include" -I"/opt/R/3.6.2/lib/R/library/RcppAnnoy/include" -I"/opt/R/3.6.2/lib/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -c query_annoy.cpp -o query_annoy.o
g++ -std=gnu++11 -I"/opt/R/3.6.2/lib/R/include" -DNDEBUG  -I"/opt/R/3.6.2/lib/R/library/Rcpp/include" -I"/opt/R/3.6.2/lib/R/library/RcppAnnoy/include" -I"/opt/R/3.6.2/lib/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -c query_hnsw.cpp -o query_hnsw.o
g++ -std=gnu++11 -I"/opt/R/3.6.2/lib/R/include" -DNDEBUG  -I"/opt/R/3.6.2/lib/R/library/Rcpp/include" -I"/opt/R/3.6.2/lib/R/library/RcppAnnoy/include" -I"/opt/R/3.6.2/lib/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -c query_kmknn.cpp -o query_kmknn.o
In file included from annoy.h:17:0,
                 from query_annoy.cpp:1:
/opt/R/3.6.2/lib/R/library/RcppAnnoy/include/annoylib.h:118:17: note: #pragma message: Just for your information: using no AVX instructions
 #pragma message "Just for your information: using no AVX instructions"
                 ^
g++ -std=gnu++11 -I"/opt/R/3.6.2/lib/R/include" -DNDEBUG  -I"/opt/R/3.6.2/lib/R/library/Rcpp/include" -I"/opt/R/3.6.2/lib/R/library/RcppAnnoy/include" -I"/opt/R/3.6.2/lib/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -c query_vptree.cpp -o query_vptree.o
g++ -std=gnu++11 -I"/opt/R/3.6.2/lib/R/include" -DNDEBUG  -I"/opt/R/3.6.2/lib/R/library/Rcpp/include" -I"/opt/R/3.6.2/lib/R/library/RcppAnnoy/include" -I"/opt/R/3.6.2/lib/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -c utils.cpp -o utils.o
g++ -std=gnu++11 -I"/opt/R/3.6.2/lib/R/include" -DNDEBUG  -I"/opt/R/3.6.2/lib/R/library/Rcpp/include" -I"/opt/R/3.6.2/lib/R/library/RcppAnnoy/include" -I"/opt/R/3.6.2/lib/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -c vptree.cpp -o vptree.o
g++ -std=gnu++11 -shared -L/opt/R/3.6.2/lib/R/lib -L/usr/local/lib -o BiocNeighbors.so RcppExports.o annoy.o build_annoy.o build_hnsw.o build_vptree.o distances.o find_annoy.o find_hnsw.o find_kmknn.o find_vptree.o hnsw.o kmknn.o query_annoy.o query_hnsw.o query_kmknn.o query_vptree.o utils.o vptree.o -L/opt/R/3.6.2/lib/R/lib -lR
build_annoy.o: In function `set_error_from_errno(char**, char const*)':
/usr/include/c++/5/sstream:548: multiple definition of `set_error_from_errno(char**, char const*)'
annoy.o:/opt/R/3.6.2/lib/R/library/RcppAnnoy/include/annoylib.h:84: first defined here
build_annoy.o: In function `set_error_from_string(char**, char const*)':
/opt/R/3.6.2/lib/R/library/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h:505: multiple definition of `set_error_from_string(char**, char const*)'
annoy.o:/opt/R/3.6.2/lib/R/library/RcppAnnoy/include/annoylib.h:92: first defined here
find_annoy.o: In function `set_error_from_errno(char**, char const*)':
/opt/R/3.6.2/lib/R/library/RcppAnnoy/include/annoylib.h:84: multiple definition of `set_error_from_errno(char**, char const*)'
annoy.o:/opt/R/3.6.2/lib/R/library/RcppAnnoy/include/annoylib.h:84: first defined here
find_annoy.o: In function `set_error_from_string(char**, char const*)':
/opt/R/3.6.2/lib/R/library/RcppAnnoy/include/annoylib.h:92: multiple definition of `set_error_from_string(char**, char const*)'
annoy.o:/opt/R/3.6.2/lib/R/library/RcppAnnoy/include/annoylib.h:92: first defined here
query_annoy.o: In function `set_error_from_errno(char**, char const*)':
/usr/include/c++/5/sstream:548: multiple definition of `set_error_from_errno(char**, char const*)'
annoy.o:/opt/R/3.6.2/lib/R/library/RcppAnnoy/include/annoylib.h:84: first defined here
query_annoy.o: In function `set_error_from_string(char**, char const*)':
/opt/R/3.6.2/lib/R/library/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h:505: multiple definition of `set_error_from_string(char**, char const*)'
annoy.o:/opt/R/3.6.2/lib/R/library/RcppAnnoy/include/annoylib.h:92: first defined here
collect2: error: ld returned 1 exit status
/opt/R/3.6.2/lib/R/share/make/shlib.mk:6: recipe for target 'BiocNeighbors.so' failed
make: *** [BiocNeighbors.so] Error 1
ERROR: compilation failed for package ‘BiocNeighbors’
* removing ‘/opt/R/3.6.2/lib/R/library/BiocNeighbors’
################################# End Task Log ################################# 
Error: Unhandled Exception: Child Task 696897222 failed: Error building image: Error building BiocNeighbors (1.4.1). Build exited with non-zero status: 1
Execution halted

Reproduce locally (macOS)

I see at http://bioconductor.org/checkResults/release/bioc-LATEST/BiocNeighbors/ that the latest BioC build report hasn't picked this up yet. In any case, I can also reproduce this locally on my macOS:

## The binary works great =)
> BiocManager::install('BiocNeighbors')
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.2 (2019-12-12)
Installing package(s) 'BiocNeighbors'
trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/macosx/el-capitan/contrib/3.6/BiocNeighbors_1.4.1.tgz'
Content type 'application/x-gzip' length 1279902 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
## the source fails
> BiocManager::install('BiocNeighbors', type = 'source')
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.2 (2019-12-12)
Installing package(s) 'BiocNeighbors'
trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz'
Content type 'application/x-gzip' length 902569 bytes (881 KB)
==================================================
downloaded 881 KB

Loading required package: colorout
* installing *source* package ‘BiocNeighbors’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c annoy.cpp -o annoy.o
In file included from annoy.cpp:1:
In file included from ./annoy.h:17:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include/annoylib.h:118:9: warning: Just for your information:
      using no AVX instructions [-W#pragma-messages]
#pragma message "Just for your information: using no AVX instructions"
        ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c build_annoy.cpp -o build_annoy.o
In file included from build_annoy.cpp:1:
In file included from ./annoy.h:17:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include/annoylib.h:118:9: warning: Just for your information:
      using no AVX instructions [-W#pragma-messages]
#pragma message "Just for your information: using no AVX instructions"
        ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c build_hnsw.cpp -o build_hnsw.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c build_vptree.cpp -o build_vptree.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c distances.cpp -o distances.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c find_annoy.cpp -o find_annoy.o
In file included from find_annoy.cpp:1:
In file included from ./annoy.h:17:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include/annoylib.h:118:9: warning: Just for your information:
      using no AVX instructions [-W#pragma-messages]
#pragma message "Just for your information: using no AVX instructions"
        ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c find_hnsw.cpp -o find_hnsw.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c find_kmknn.cpp -o find_kmknn.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c find_vptree.cpp -o find_vptree.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c hnsw.cpp -o hnsw.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c kmknn.cpp -o kmknn.o
kmknn.cpp:14:16: warning: field 'centers' will be initialized after field 'nearest' [-Wreorder]
    exprs(ex), centers(cen), nearest(warn_ties)
               ^
kmknn.cpp:218:16: note: in instantiation of member function 'Kmknn<BNManhattan>::Kmknn' requested here
template class Kmknn<BNManhattan>;
               ^
kmknn.cpp:14:16: warning: field 'centers' will be initialized after field 'nearest' [-Wreorder]
    exprs(ex), centers(cen), nearest(warn_ties)
               ^
kmknn.cpp:219:16: note: in instantiation of member function 'Kmknn<BNEuclidean>::Kmknn' requested here
template class Kmknn<BNEuclidean>;
               ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c query_annoy.cpp -o query_annoy.o
In file included from query_annoy.cpp:1:
In file included from ./annoy.h:17:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include/annoylib.h:118:9: warning: Just for your information:
      using no AVX instructions [-W#pragma-messages]
#pragma message "Just for your information: using no AVX instructions"
        ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c query_hnsw.cpp -o query_hnsw.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c query_kmknn.cpp -o query_kmknn.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c query_vptree.cpp -o query_vptree.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c utils.cpp -o utils.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c vptree.cpp -o vptree.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/clang6/lib -o BiocNeighbors.so RcppExports.o annoy.o build_annoy.o build_hnsw.o build_vptree.o distances.o find_annoy.o find_hnsw.o find_kmknn.o find_vptree.o hnsw.o kmknn.o query_annoy.o query_hnsw.o query_kmknn.o query_vptree.o utils.o vptree.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
duplicate symbol 'set_error_from_errno(char**, char const*)' in:
    annoy.o
    build_annoy.o
duplicate symbol 'set_error_from_string(char**, char const*)' in:
    annoy.o
    build_annoy.o
duplicate symbol 'set_error_from_errno(char**, char const*)' in:
    annoy.o
    find_annoy.o
duplicate symbol 'set_error_from_string(char**, char const*)' in:
    annoy.o
    find_annoy.o
duplicate symbol 'set_error_from_errno(char**, char const*)' in:
    annoy.o
    query_annoy.o
duplicate symbol 'set_error_from_string(char**, char const*)' in:
    annoy.o
    query_annoy.o
ld: 6 duplicate symbols for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [BiocNeighbors.so] Error 1
ERROR: compilation failed for package ‘BiocNeighbors’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BiocNeighbors’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BiocNeighbors’

Install RcppAnnoy 0.0.14

## Thanks to https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages
> packageurl <- "https://cran.r-project.org/src/contrib/Archive/RcppAnnoy/RcppAnnoy_0.0.14.tar.gz"
> install.packages(packageurl, repos=NULL, type="source")
trying URL 'https://cran.r-project.org/src/contrib/Archive/RcppAnnoy/RcppAnnoy_0.0.14.tar.gz'
Content type 'application/x-gzip' length 439993 bytes (429 KB)
==================================================
downloaded 429 KB

Loading required package: colorout
* installing *source* package ‘RcppAnnoy’ ...
** package ‘RcppAnnoy’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c annoy.cpp -o annoy.o
In file included from annoy.cpp:39:
../inst/include/annoylib.h:84:9: warning: Using no AVX instructions [-W#pragma-messages]
#pragma message "Using no AVX instructions"
        ^
1 warning generated.
/usr/local/clang6/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c init.c -o init.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/clang6/lib -o RcppAnnoy.so annoy.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-RcppAnnoy/00new/RcppAnnoy/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
Loading required package: colorout
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Loading required package: colorout
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Loading required package: colorout
** testing if installed package keeps a record of temporary installation path
* DONE (RcppAnnoy)

then try again to install BiocNeighbors from source:

> BiocManager::install('BiocNeighbors', type = 'source')
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.2 (2019-12-12)
Installing package(s) 'BiocNeighbors'
trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz'
Content type 'application/x-gzip' length 902569 bytes (881 KB)
==================================================
downloaded 881 KB

Loading required package: colorout
* installing *source* package ‘BiocNeighbors’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c annoy.cpp -o annoy.o
In file included from annoy.cpp:1:
In file included from ./annoy.h:17:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include/annoylib.h:84:9: warning: Using no AVX instructions
      [-W#pragma-messages]
#pragma message "Using no AVX instructions"
        ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c build_annoy.cpp -o build_annoy.o
In file included from build_annoy.cpp:1:
In file included from ./annoy.h:17:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include/annoylib.h:84:9: warning: Using no AVX instructions
      [-W#pragma-messages]
#pragma message "Using no AVX instructions"
        ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c build_hnsw.cpp -o build_hnsw.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c build_vptree.cpp -o build_vptree.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c distances.cpp -o distances.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c find_annoy.cpp -o find_annoy.o
In file included from find_annoy.cpp:1:
In file included from ./annoy.h:17:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include/annoylib.h:84:9: warning: Using no AVX instructions
      [-W#pragma-messages]
#pragma message "Using no AVX instructions"
        ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c find_hnsw.cpp -o find_hnsw.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c find_kmknn.cpp -o find_kmknn.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c find_vptree.cpp -o find_vptree.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c hnsw.cpp -o hnsw.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c kmknn.cpp -o kmknn.o
kmknn.cpp:14:16: warning: field 'centers' will be initialized after field 'nearest' [-Wreorder]
    exprs(ex), centers(cen), nearest(warn_ties)
               ^
kmknn.cpp:218:16: note: in instantiation of member function 'Kmknn<BNManhattan>::Kmknn' requested here
template class Kmknn<BNManhattan>;
               ^
kmknn.cpp:14:16: warning: field 'centers' will be initialized after field 'nearest' [-Wreorder]
    exprs(ex), centers(cen), nearest(warn_ties)
               ^
kmknn.cpp:219:16: note: in instantiation of member function 'Kmknn<BNEuclidean>::Kmknn' requested here
template class Kmknn<BNEuclidean>;
               ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c query_annoy.cpp -o query_annoy.o
In file included from query_annoy.cpp:1:
In file included from ./annoy.h:17:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include/annoylib.h:84:9: warning: Using no AVX instructions
      [-W#pragma-messages]
#pragma message "Using no AVX instructions"
        ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c query_hnsw.cpp -o query_hnsw.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c query_kmknn.cpp -o query_kmknn.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c query_vptree.cpp -o query_vptree.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c utils.cpp -o utils.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c vptree.cpp -o vptree.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/clang6/lib -o BiocNeighbors.so RcppExports.o annoy.o build_annoy.o build_hnsw.o build_vptree.o distances.o find_annoy.o find_hnsw.o find_kmknn.o find_vptree.o hnsw.o kmknn.o query_annoy.o query_hnsw.o query_kmknn.o query_vptree.o utils.o vptree.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-BiocNeighbors/00new/BiocNeighbors/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Loading required package: colorout
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Loading required package: colorout
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Loading required package: colorout
** testing if installed package keeps a record of temporary installation path
* DONE (BiocNeighbors)

R session information (macOS)

> options(width = 120)
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 3.6.2 (2019-12-12)
 os       macOS Catalina 10.15.2
 system   x86_64, darwin15.6.0
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/New_York
 date     2020-02-27

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
 package     * version date       lib source
 assertthat    0.2.1   2019-03-21 [1] CRAN (R 3.6.0)
 backports     1.1.5   2019-10-02 [1] CRAN (R 3.6.0)
 BiocManager   1.30.10 2019-11-16 [1] CRAN (R 3.6.1)
 callr         3.4.2   2020-02-12 [1] CRAN (R 3.6.0)
 cli           2.0.1   2020-01-08 [1] CRAN (R 3.6.0)
 colorout    * 1.2-1   2019-05-07 [1] Github (jalvesaq/colorout@7ea9440)
 crayon        1.3.4   2017-09-16 [1] CRAN (R 3.6.0)
 desc          1.2.0   2018-05-01 [1] CRAN (R 3.6.0)
 devtools    * 2.2.1   2019-09-24 [1] CRAN (R 3.6.1)
 digest        0.6.25  2020-02-23 [1] CRAN (R 3.6.0)
 ellipsis      0.3.0   2019-09-20 [1] CRAN (R 3.6.0)
 fansi         0.4.1   2020-01-08 [1] CRAN (R 3.6.0)
 fs            1.3.1   2019-05-06 [1] CRAN (R 3.6.0)
 glue          1.3.1   2019-03-12 [1] CRAN (R 3.6.0)
 magrittr      1.5     2014-11-22 [1] CRAN (R 3.6.0)
 memoise       1.1.0   2017-04-21 [1] CRAN (R 3.6.0)
 pkgbuild      1.0.6   2019-10-09 [1] CRAN (R 3.6.0)
 pkgload       1.0.2   2018-10-29 [1] CRAN (R 3.6.0)
 prettyunits   1.1.1   2020-01-24 [1] CRAN (R 3.6.2)
 processx      3.4.2   2020-02-09 [1] CRAN (R 3.6.0)
 ps            1.3.2   2020-02-13 [1] CRAN (R 3.6.0)
 R6            2.4.1   2019-11-12 [1] CRAN (R 3.6.1)
 Rcpp          1.0.3   2019-11-08 [1] CRAN (R 3.6.0)
 remotes       2.1.1   2020-02-15 [1] CRAN (R 3.6.0)
 rlang         0.4.4   2020-01-28 [1] CRAN (R 3.6.0)
 rprojroot     1.3-2   2018-01-03 [1] CRAN (R 3.6.0)
 sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 3.6.0)
 testthat    * 2.3.1   2019-12-01 [1] CRAN (R 3.6.0)
 usethis     * 1.5.1   2019-07-04 [1] CRAN (R 3.6.0)
 withr         2.1.2   2018-03-15 [1] CRAN (R 3.6.0)

[1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library

R session information (shinyapps)

Here's the full session information from the last successful build at shinyapps.io. Note that spatialLIBD doesn't actually load RcppAnnoy (it's on the suggests for BiocNeighbor). So we can't see the version number there.

─ Session info ───────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.2 (2019-12-12)
 os       Ubuntu 16.04.6 LTS          
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Etc/UTC                     
 date     2020-02-27                  

─ Packages ───────────────────────────────────────────────────────────────────
 ! package                * version  date       lib source        
   AnnotationDbi            1.48.0   2019-10-29 [1] Bioconductor  
   AnnotationHub            2.18.0   2019-10-29 [1] Bioconductor  
   assertthat               0.2.1    2019-03-21 [1] CRAN (R 3.6.2)
   attempt                  0.3.0    2019-04-08 [1] CRAN (R 3.6.2)
   backports                1.1.5    2019-10-02 [1] CRAN (R 3.6.2)
   beeswarm                 0.2.3    2016-04-25 [1] CRAN (R 3.6.2)
   Biobase                * 2.46.0   2019-10-29 [1] Bioconductor  
   BiocFileCache            1.10.2   2019-11-08 [1] Bioconductor  
   BiocGenerics           * 0.32.0   2019-10-29 [1] Bioconductor  
   BiocManager              1.30.10  2019-11-16 [1] CRAN (R 3.6.2)
   BiocNeighbors            1.4.1    2019-11-01 [1] Bioconductor  
   BiocParallel           * 1.20.1   2019-12-21 [1] Bioconductor  
   BiocSingular             1.2.2    2020-02-14 [1] Bioconductor  
   BiocVersion              3.10.1   2019-06-06 [1] Bioconductor  
   bit                      1.1-15.2 2020-02-10 [1] CRAN (R 3.6.2)
   bit64                    0.9-7    2017-05-08 [1] CRAN (R 3.6.2)
   bitops                   1.0-6    2013-08-17 [1] CRAN (R 3.6.2)
   blob                     1.2.1    2020-01-20 [1] CRAN (R 3.6.2)
   callr                    3.4.2    2020-02-12 [1] CRAN (R 3.6.2)
   cli                      2.0.1    2020-01-08 [1] CRAN (R 3.6.2)
   colorspace               1.4-1    2019-03-18 [1] CRAN (R 3.6.2)
   cowplot                  1.0.0    2019-07-11 [1] CRAN (R 3.6.2)
   crayon                   1.3.4    2017-09-16 [1] CRAN (R 3.6.2)
   crosstalk                1.0.0    2016-12-21 [1] CRAN (R 3.6.2)
   curl                     4.3      2019-12-02 [1] CRAN (R 3.6.2)
   data.table               1.12.8   2019-12-09 [1] CRAN (R 3.6.2)
   DBI                      1.1.0    2019-12-15 [1] CRAN (R 3.6.2)
   dbplyr                   1.4.2    2019-06-17 [1] CRAN (R 3.6.2)
   DelayedArray           * 0.12.2   2020-01-06 [1] Bioconductor  
   DelayedMatrixStats       1.8.0    2019-10-29 [1] Bioconductor  
   desc                     1.2.0    2018-05-01 [1] CRAN (R 3.6.2)
   digest                   0.6.25   2020-02-23 [1] CRAN (R 3.6.2)
   dotCall64                1.0-0    2018-07-30 [1] CRAN (R 3.6.2)
   dplyr                    0.8.4    2020-01-31 [1] CRAN (R 3.6.2)
   DT                       0.12     2020-02-05 [1] CRAN (R 3.6.2)
   ExperimentHub            1.12.0   2019-10-29 [1] Bioconductor  
   fansi                    0.4.1    2020-01-08 [1] CRAN (R 3.6.2)
   fastmap                  1.0.1    2019-10-08 [1] CRAN (R 3.6.2)
   fields                   10.3     2020-02-04 [1] CRAN (R 3.6.2)
   fs                       1.3.1    2019-05-06 [1] CRAN (R 3.6.2)
   GenomeInfoDb           * 1.22.0   2019-10-29 [1] Bioconductor  
   GenomeInfoDbData         1.2.2    2020-01-03 [1] Bioconductor  
   GenomicRanges          * 1.38.0   2019-10-29 [1] Bioconductor  
   ggbeeswarm               0.6.0    2017-08-07 [1] CRAN (R 3.6.2)
   ggplot2                  3.2.1    2019-08-10 [1] CRAN (R 3.6.2)
   glue                     1.3.1    2019-03-12 [1] CRAN (R 3.6.2)
   golem                    0.1      2019-08-05 [1] CRAN (R 3.6.2)
   gridExtra                2.3      2017-09-09 [1] CRAN (R 3.6.2)
   gtable                   0.3.0    2019-03-25 [1] CRAN (R 3.6.2)
   here                     0.1      2017-05-28 [1] CRAN (R 3.6.2)
   htmltools                0.4.0    2019-10-04 [1] CRAN (R 3.6.2)
   htmlwidgets              1.5.1    2019-10-08 [1] CRAN (R 3.6.2)
   httpuv                   1.5.2    2019-09-11 [1] CRAN (R 3.6.2)
   httr                     1.4.1    2019-08-05 [1] CRAN (R 3.6.2)
   interactiveDisplayBase   1.24.0   2019-10-29 [1] Bioconductor  
   IRanges                * 2.20.2   2020-01-13 [1] Bioconductor  
   irlba                    2.3.3    2019-02-05 [1] CRAN (R 3.6.2)
   jsonlite                 1.6.1    2020-02-02 [1] CRAN (R 3.6.2)
   later                    1.0.0    2019-10-04 [1] CRAN (R 3.6.2)
   lattice                  0.20-38  2018-11-04 [1] CRAN (R 3.6.2)
   lazyeval                 0.2.2    2019-03-15 [1] CRAN (R 3.6.2)
   lifecycle                0.1.0    2019-08-01 [1] CRAN (R 3.6.2)
   magrittr                 1.5      2014-11-22 [1] CRAN (R 3.6.2)
   maps                     3.3.0    2018-04-03 [1] CRAN (R 3.6.2)
   markdown                 1.1      2019-08-07 [1] CRAN (R 3.6.2)
   Matrix                   1.2-18   2019-11-27 [1] CRAN (R 3.6.2)
   matrixStats            * 0.55.0   2019-09-07 [1] CRAN (R 3.6.2)
   memoise                  1.1.0    2017-04-21 [1] CRAN (R 3.6.2)
   mime                     0.9      2020-02-04 [1] CRAN (R 3.6.2)
   munsell                  0.5.0    2018-06-12 [1] CRAN (R 3.6.2)
   pillar                   1.4.3    2019-12-20 [1] CRAN (R 3.6.2)
   pkgbuild                 1.0.6    2019-10-09 [1] CRAN (R 3.6.2)
   pkgconfig                2.0.3    2019-09-22 [1] CRAN (R 3.6.2)
   pkgload                  1.0.2    2018-10-29 [1] CRAN (R 3.6.2)
   plotly                   4.9.2    2020-02-12 [1] CRAN (R 3.6.2)
   png                      0.1-7    2013-12-03 [1] CRAN (R 3.6.2)
   Polychrome               1.2.4    2020-02-03 [1] CRAN (R 3.6.2)
   prettyunits              1.1.1    2020-01-24 [1] CRAN (R 3.6.2)
   processx                 3.4.2    2020-02-09 [1] CRAN (R 3.6.2)
   promises                 1.1.0    2019-10-04 [1] CRAN (R 3.6.2)
   ps                       1.3.2    2020-02-13 [1] CRAN (R 3.6.2)
   purrr                    0.3.3    2019-10-18 [1] CRAN (R 3.6.2)
   R6                       2.4.1    2019-11-12 [1] CRAN (R 3.6.2)
   rappdirs                 0.3.1    2016-03-28 [1] CRAN (R 3.6.2)
   RColorBrewer             1.1-2    2014-12-07 [1] CRAN (R 3.6.2)
   Rcpp                     1.0.3    2019-11-08 [1] CRAN (R 3.6.2)
   RCurl                    1.98-1.1 2020-01-19 [1] CRAN (R 3.6.2)
   rlang                    0.4.4    2020-01-28 [1] CRAN (R 3.6.2)
   roxygen2                 7.0.2    2019-12-02 [1] CRAN (R 3.6.2)
   rprojroot                1.3-2    2018-01-03 [1] CRAN (R 3.6.2)
   RSQLite                  2.2.0    2020-01-07 [1] CRAN (R 3.6.2)
   rstudioapi               0.11     2020-02-07 [1] CRAN (R 3.6.2)
   rsvd                     1.0.3    2020-02-17 [1] CRAN (R 3.6.2)
   S4Vectors              * 0.24.3   2020-01-18 [1] Bioconductor  
   scales                   1.1.0    2019-11-18 [1] CRAN (R 3.6.2)
   scater                   1.14.6   2019-12-16 [1] Bioconductor  
   scatterplot3d            0.3-41   2018-03-14 [1] CRAN (R 3.6.2)
   sessioninfo              1.1.1    2018-11-05 [1] CRAN (R 3.6.2)
   shiny                  * 1.4.0    2019-10-10 [1] CRAN (R 3.6.2)
   shinyWidgets             0.5.0    2019-11-18 [1] CRAN (R 3.6.2)
   SingleCellExperiment   * 1.8.0    2019-10-29 [1] Bioconductor  
   spam                     2.5-1    2019-12-12 [1] CRAN (R 3.6.2)
 R spatialLIBD            * 0.99.3   <NA>       [?] <NA>          
   stringi                  1.4.6    2020-02-17 [1] CRAN (R 3.6.2)
   stringr                  1.4.0    2019-02-10 [1] CRAN (R 3.6.2)
   SummarizedExperiment   * 1.16.1   2019-12-19 [1] Bioconductor  
   testthat               * 2.3.1    2019-12-01 [1] CRAN (R 3.6.2)
   tibble                   2.1.3    2019-06-06 [1] CRAN (R 3.6.2)
   tidyr                    1.0.2    2020-01-24 [1] CRAN (R 3.6.2)
   tidyselect               1.0.0    2020-01-27 [1] CRAN (R 3.6.2)
   usethis                  1.5.1    2019-07-04 [1] CRAN (R 3.6.2)
   vctrs                    0.2.3    2020-02-20 [1] CRAN (R 3.6.2)
   vipor                    0.4.5    2017-03-22 [1] CRAN (R 3.6.2)
   viridis                  0.5.1    2018-03-29 [1] CRAN (R 3.6.2)
   viridisLite              0.3.0    2018-02-01 [1] CRAN (R 3.6.2)
   withr                    2.1.2    2018-03-15 [1] CRAN (R 3.6.2)
   xfun                     0.12     2020-01-13 [1] CRAN (R 3.6.2)
   xml2                     1.2.2    2019-08-09 [1] CRAN (R 3.6.2)
   xtable                   1.8-4    2019-04-21 [1] CRAN (R 3.6.2)
   XVector                  0.26.0   2019-10-29 [1] Bioconductor  
   yaml                     2.2.1    2020-02-01 [1] CRAN (R 3.6.2)
   yesno                    0.1.0    2018-04-14 [1] CRAN (R 3.6.2)
   zlibbioc                 1.32.0   2019-10-29 [1] Bioconductor  

[1] /opt/R/3.6.2/lib/R/library

 R ── Package was removed from disk.
lcolladotor added a commit to LieberInstitute/spatialLIBD that referenced this issue Feb 27, 2020
@lcolladotor
Hm... can we set the specific version of RcppAnnoy on the DESCRIPTION…
25f0f8c 
… file? Related to knncolle/BiocNeighbors#10
@lcolladotor lcolladotor mentioned this issue Feb 27, 2020
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@eddelbuettel
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That is ... pretty long and detailed. One issue is

build_annoy.o: In function `set_error_from_errno(char**, char const*)':
/usr/include/c++/5/sstream:548: multiple definition of `set_error_from_errno(char**, char const*)'
annoy.o:/opt/R/3.6.2/lib/R/library/RcppAnnoy/include/annoylib.h:84: first defined here
build_annoy.o: In function `set_error_from_string(char**, char const*)':
/opt/R/3.6.2/lib/R/library/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h:505: multiple definition of `set_error_from_string(char**, char const*)'
annoy.o:/opt/R/3.6.2/lib/R/library/RcppAnnoy/include/annoylib.h:92: first defined here
find_annoy.o: In function `set_error_from_errno(char**, char const*)':

which comes from sourcing the same header multiple times and not having the functions inline. Something we can change.

@lcolladotor lcolladotor mentioned this issue Feb 28, 2020
Closed
@mjsteinbaugh
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I'm seeing an error on Debian in my Docker image also:

/usr/bin/ld: build_annoy.o: in function `AnnoyIndex<int, float, Euclidean, Kiss64Random>::unbuild(char**)':
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h:972: multiple definition of `set_e
rror_from_errno(char**, char const*)'; annoy.o:/usr/local/lib/R/site-library/RcppAnnoy/include/annoylib.h:84: fi
rst defined here
/usr/bin/ld: build_annoy.o: in function `set_error_from_string(char**, char const*)':
/usr/include/c++/8/streambuf:473: multiple definition of `set_error_from_string(char**, char const*)'; annoy.o:/
usr/local/lib/R/site-library/RcppAnnoy/include/annoylib.h:92: first defined here
/usr/bin/ld: find_annoy.o: in function `AnnoyIndex<int, float, Euclidean, Kiss64Random>::unbuild(char**)':
/usr/include/c++/8/bits/stl_vector.h:806: multiple definition of `set_error_from_errno(char**, char const*)'; an
noy.o:/usr/local/lib/R/site-library/RcppAnnoy/include/annoylib.h:84: first defined here
/usr/bin/ld: find_annoy.o: in function `set_error_from_string(char**, char const*)':
/usr/include/c++/8/bits/stl_vector.h:1076: multiple definition of `set_error_from_string(char**, char const*)';
annoy.o:/usr/local/lib/R/site-library/RcppAnnoy/include/annoylib.h:92: first defined here
/usr/bin/ld: query_annoy.o: in function `AnnoyIndex<int, float, Euclidean, Kiss64Random>::unbuild(char**)':
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h:972: multiple definition of `set_e
rror_from_errno(char**, char const*)'; annoy.o:/usr/local/lib/R/site-library/RcppAnnoy/include/annoylib.h:84: fi
rst defined here
/usr/bin/ld: query_annoy.o: in function `set_error_from_string(char**, char const*)':
/usr/include/c++/8/streambuf:473: multiple definition of `set_error_from_string(char**, char const*)'; annoy.o:/
usr/local/lib/R/site-library/RcppAnnoy/include/annoylib.h:92: first defined here
collect2: error: ld returned 1 exit status
make: *** [/usr/local/lib/R/share/make/shlib.mk:6: BiocNeighbors.so] Error 1
ERROR: compilation failed for package ‘BiocNeighbors’
* removing ‘/usr/local/lib/R/site-library/BiocNeighbors’

@LTLA LTLA mentioned this issue Feb 28, 2020
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@LTLA
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LTLA commented Feb 28, 2020 •
edited
Loading

I was wondering when the ripple effects of jlmelville/uwot#50 would eventually reach BiocNeighbors. I must say that this entire affair has been rather... Annoy-ing.

(Ho ho ho. I've been wanting to say that since this entire business started.)

Seems to be an easy enough fix at the RcppAnnoy level. If we get the patch onto CRAN in a timely manner, no change should be needed in BiocNeighbors or its downstream packages.

Otherwise I guess I could divert all the Annoy code to point to, say, HNSW. I'd rather not, though maybe I'll have to do it if things like eddelbuettel/rcppannoy#56 are blocking updates to CRAN.

If you urgently need a new installation, just pull RcppAnnoy from https://github.com/LTLA/RcppAnnoy and override the CRAN version for the time being.

@eddelbuettel
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Just to confirm: you tested my (off-the cuff) suggestion to make the functions inline, and the problem went away? Your PR (which I already accepted / merged) didn't really say so ...

@mjsteinbaugh
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mjsteinbaugh commented Feb 28, 2020 •
edited
Loading

Thanks @eddelbuettel and @LTLA. In case anyone else comes across this issue, reinstalling RcppAnnoy v0.0.14 keeps BiocNeighbors working in the meantime:

utils::install.packages(
    pkgs = paste(
        "https://cran.r-project.org",
        "src",
        "contrib",
        "Archive",
        "RcppAnnoy",
        "RcppAnnoy_0.0.14.tar.gz",
        sep = "/"
    ),
    repos = NULL,
    type = "source"
)

@LTLA
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LTLA commented Feb 28, 2020

@eddelbuettel Yes, that's right. I was also hoping that the "Fixes" keyword would close this issue, but apparently GitHub isn't that smart.

@LTLA LTLA closed this as completed Feb 28, 2020
@eddelbuettel
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I am away at a workshop but I plan to create a 0.0.15.1 version that you can get from a drat repo. Maybe take a day or two for me to get to it...

@eddelbuettel
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0.0.16 is now in incoming at CRAN and should fix it for good.

lcolladotor added a commit to LieberInstitute/spatialLIBD that referenced this issue Apr 22, 2020
@lcolladotor
Hm... can we set the specific version of RcppAnnoy on the DESCRIPTION…
3c3a855 
… file? Related to knncolle/BiocNeighbors#10

Former-commit-id: 1c1485d79a76d72cbf7c3ea4e68be9b34e7f8e08 [formerly 25f0f8c]
Former-commit-id: 2f8e6f6fab07f537d28965cf8187bb1b895c8fe2
lcolladotor added a commit to LieberInstitute/spatialLIBD that referenced this issue Apr 22, 2020
@lcolladotor
Hm... can we set the specific version of RcppAnnoy on the DESCRIPTION…
cc460ad 
… file? Related to knncolle/BiocNeighbors#10

Former-commit-id: 1c1485d79a76d72cbf7c3ea4e68be9b34e7f8e08 [formerly 25f0f8c]
Former-commit-id: 2f8e6f6fab07f537d28965cf8187bb1b895c8fe2
Former-commit-id: 3c3a855
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Inlined set_error_* functions for multiple include's. LTLA/rcppannoy
4 participants
@eddelbuettel @mjsteinbaugh @lcolladotor @LTLA