| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:20 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 | ||||
|
To the developers/maintainers of the BiocNeighbors package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 164/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocNeighbors 1.17.1 (landing page) Aaron Lun
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ||||||||
| Package: BiocNeighbors |
| Version: 1.17.1 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocNeighbors.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings BiocNeighbors_1.17.1.tar.gz |
| StartedAt: 2022-12-28 21:56:02 -0500 (Wed, 28 Dec 2022) |
| EndedAt: 2022-12-28 22:01:21 -0500 (Wed, 28 Dec 2022) |
| EllapsedTime: 319.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BiocNeighbors.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocNeighbors.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings BiocNeighbors_1.17.1.tar.gz
###
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##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/BiocNeighbors.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BiocNeighbors/DESCRIPTION' ... OK
* this is package 'BiocNeighbors' version '1.17.1'
* 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 whether package 'BiocNeighbors' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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 ... 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 'F:/biocbuild/bbs-3.17-bioc/R/library/BiocNeighbors/libs/x64/BiocNeighbors.dll':
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 5.15 0.54 5.7
* 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
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/BiocNeighbors.Rcheck/00check.log'
for details.
BiocNeighbors.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL BiocNeighbors ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'BiocNeighbors' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c annoy.cpp -o annoy.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c build_annoy.cpp -o build_annoy.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c distances.cpp -o distances.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c exhaustive.cpp -o exhaustive.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c find_annoy.cpp -o find_annoy.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hnsw.cpp -o hnsw.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kmknn.cpp -o kmknn.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c query_annoy.cpp -o query_annoy.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppHNSW/include' -I"c:/rtools42/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:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-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)
BiocNeighbors.Rcheck/tests/testthat.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
[ FAIL 0 | WARN 494 | SKIP 0 | PASS 3516 ]
[ FAIL 0 | WARN 494 | SKIP 0 | PASS 3516 ]
>
> proc.time()
user system elapsed
100.68 2.90 207.82
BiocNeighbors.Rcheck/BiocNeighbors-Ex.timings
| name | user | system | elapsed | |
| AnnoyIndex | 0.33 | 0.01 | 0.44 | |
| AnnoyParam | 0.01 | 0.00 | 0.01 | |
| BiocNeighbors-raw-index | 1.18 | 0.03 | 1.22 | |
| BiocNeighbors-ties | 0.02 | 0.00 | 0.01 | |
| ExhaustiveIndex | 0.02 | 0.00 | 0.02 | |
| ExhaustiveParam | 0 | 0 | 0 | |
| HnswIndex | 0.70 | 0.00 | 0.76 | |
| HnswParam | 0.01 | 0.00 | 0.02 | |
| KmknnIndex | 0.19 | 0.05 | 0.23 | |
| KmknnParam | 0 | 0 | 0 | |
| VptreeIndex | 0.03 | 0.00 | 0.03 | |
| VptreeParam | 0 | 0 | 0 | |
| buildAnnoy | 0.30 | 0.00 | 0.46 | |
| buildExhaustive | 0 | 0 | 0 | |
| buildHnsw | 0.70 | 0.00 | 0.71 | |
| buildIndex | 0.45 | 0.00 | 0.53 | |
| buildKmknn | 0.17 | 0.01 | 0.18 | |
| buildVptree | 0.04 | 0.00 | 0.04 | |
| findKNN-functions | 3.42 | 0.04 | 3.62 | |
| findKNN-methods | 4.50 | 0.03 | 4.75 | |
| findMutualNN | 0.03 | 0.00 | 0.03 | |
| findNeighbors-functions | 5.15 | 0.54 | 5.70 | |
| findNeighbors-methods | 4.16 | 0.02 | 4.18 | |
| queryKNN-functions | 2.09 | 0.02 | 2.22 | |
| queryKNN-methods | 1.44 | 0.03 | 1.64 | |
| queryNeighbors-functions | 0.5 | 0.0 | 0.5 | |
| queryNeighbors-methods | 0.78 | 0.01 | 0.79 | |