Aaron Lun
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/BiocNeighbors |
| Branch: master |
| Last Commit: 47b839f |
| Last Changed Date: 2019-10-31 02:28:37 -0500 (Thu, 31 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:51:43 -0500 (Thu, 16 Jan 2020).
| Package 154/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BiocNeighbors 1.5.1 Aaron Lun
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: BiocNeighbors |
| Version: 1.5.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiocNeighbors_1.5.1.tar.gz |
| StartedAt: 2020-01-16 02:08:50 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 02:17:36 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 526.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BiocNeighbors.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiocNeighbors_1.5.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/BiocNeighbors.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocNeighbors/DESCRIPTION’ ... OK
* this is package ‘BiocNeighbors’ version ‘1.5.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BiocNeighbors’ can be installed ... WARNING
Found the following significant warnings:
kmknn.cpp:14:16: warning: field 'centers' will be initialized after field 'nearest' [-Wreorder]
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/BiocNeighbors.Rcheck/00install.out’ for details.
* 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 R 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 ... OK
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
rangeFind-methods 6.886 0.994 7.890
findNeighbors 6.776 0.053 6.836
findKNN 6.261 0.136 6.413
find-methods 4.851 0.135 5.021
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/BiocNeighbors.Rcheck/00check.log’
for details.
BiocNeighbors.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BiocNeighbors
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* 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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppAnnoy/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/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/4.0/Resources/library/00LOCK-BiocNeighbors/00new/BiocNeighbors/libs
** 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
** 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
* DONE (BiocNeighbors)
BiocNeighbors.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
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")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 2876 | SKIPPED: 0 | WARNINGS: 34 | FAILED: 0 ]
>
> proc.time()
user system elapsed
158.432 17.846 356.077
BiocNeighbors.Rcheck/BiocNeighbors-Ex.timings
| name | user | system | elapsed | |
| AnnoyIndex | 0.535 | 0.038 | 0.582 | |
| AnnoyParam | 0.013 | 0.001 | 0.015 | |
| BiocNeighbors-raw-index | 2.246 | 0.020 | 2.266 | |
| BiocNeighbors-ties | 0.012 | 0.001 | 0.011 | |
| HnswIndex | 1.153 | 0.014 | 1.234 | |
| HnswParam | 0.005 | 0.000 | 0.004 | |
| KmknnIndex | 0.504 | 0.031 | 0.537 | |
| KmknnParam | 0.006 | 0.000 | 0.006 | |
| VptreeIndex | 0.041 | 0.003 | 0.044 | |
| VptreeParam | 0.005 | 0.001 | 0.005 | |
| buildAnnoy | 0.464 | 0.031 | 0.504 | |
| buildHnsw | 1.091 | 0.013 | 1.105 | |
| buildIndex | 0.742 | 0.046 | 0.808 | |
| buildKmknn | 0.251 | 0.014 | 0.265 | |
| buildVptree | 0.034 | 0.004 | 0.038 | |
| find-methods | 4.851 | 0.135 | 5.021 | |
| findKNN | 6.261 | 0.136 | 6.413 | |
| findNeighbors | 6.776 | 0.053 | 6.836 | |
| query-methods | 2.459 | 0.142 | 2.648 | |
| queryKNN | 1.982 | 0.129 | 2.170 | |
| queryNeighbors | 1.205 | 0.016 | 1.222 | |
| rangeFind-methods | 6.886 | 0.994 | 7.890 | |
| rangeQuery-methods | 0.425 | 0.006 | 0.432 | |