| Back to First build/check report with an "external build node" |
This page was generated on 2023-06-01 18:17:19 -0400 (Thu, 01 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| xps15 | Linux (Ubuntu 23.04) | x86_64 | 4.3.0 Patched (2023-05-23 r84466) -- "Already Tomorrow" | 544 |
| 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: Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 16/91 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||||
| BiocNeighbors 1.19.0 (landing page) Aaron Lun
| xps15 | Linux (Ubuntu 23.04) / x86_64 | OK | OK | WARNINGS | ||||||||
| Package: BiocNeighbors |
| Version: 1.19.0 |
| Command: /home/hpages/bbs-3.18-bioc/R/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/home/hpages/bbs-3.18-bioc-testing/Rlibs --timings BiocNeighbors_1.19.0.tar.gz |
| StartedAt: 2023-06-01 12:58:14 -0700 (Thu, 01 Jun 2023) |
| EndedAt: 2023-06-01 13:04:55 -0700 (Thu, 01 Jun 2023) |
| EllapsedTime: 400.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BiocNeighbors.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/hpages/bbs-3.18-bioc/R/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/home/hpages/bbs-3.18-bioc-testing/Rlibs --timings BiocNeighbors_1.19.0.tar.gz
###
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* using log directory ‘/home/hpages/bbs-3.18-bioc-testing/meat/BiocNeighbors.Rcheck’
* using R version 4.3.0 Patched (2023-05-23 r84466)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0
GNU Fortran (Ubuntu 12.2.0-17ubuntu1) 12.2.0
* running under: Ubuntu 23.04
* using session charset: UTF-8
* checking for file ‘BiocNeighbors/DESCRIPTION’ ... OK
* this is package ‘BiocNeighbors’ version ‘1.19.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BiocNeighbors’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 12.2.0-17ubuntu1) 12.2.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 14.1Mb
sub-directories of 1Mb or more:
libs 13.2Mb
* 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 loading without being on the library search path ... 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 ... WARNING
Note: information on .o files is not available
File ‘/home/hpages/bbs-3.18-bioc-testing/Rlibs/BiocNeighbors/libs/BiocNeighbors.so’:
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
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
findKNN-methods 6.657 0.011 6.669
findNeighbors-functions 6.097 0.460 6.559
findNeighbors-methods 6.281 0.016 6.299
findKNN-functions 5.488 0.012 5.500
* 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 ...
‘approx.Rmd’ using ‘UTF-8’... OK
‘exact.Rmd’ using ‘UTF-8’... OK
‘range.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 2 NOTEs
See
‘/home/hpages/bbs-3.18-bioc-testing/meat/BiocNeighbors.Rcheck/00check.log’
for details.
BiocNeighbors.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/hpages/bbs-3.18-bioc/R/bin/R CMD INSTALL BiocNeighbors ### ############################################################################## ############################################################################## * installing to library ‘/home/hpages/bbs-3.18-bioc-testing/Rlibs’ * installing *source* package ‘BiocNeighbors’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 12.2.0-17ubuntu1) 12.2.0’ using C++11 g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c annoy.cpp -o annoy.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c build_annoy.cpp -o build_annoy.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c build_hnsw.cpp -o build_hnsw.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c build_vptree.cpp -o build_vptree.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c distances.cpp -o distances.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c exhaustive.cpp -o exhaustive.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c find_annoy.cpp -o find_annoy.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c find_exhaustive.cpp -o find_exhaustive.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c find_hnsw.cpp -o find_hnsw.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c find_kmknn.cpp -o find_kmknn.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c find_mutual_nns.cpp -o find_mutual_nns.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c find_vptree.cpp -o find_vptree.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c hnsw.cpp -o hnsw.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c kmknn.cpp -o kmknn.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c query_annoy.cpp -o query_annoy.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c query_exhaustive.cpp -o query_exhaustive.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c query_hnsw.cpp -o query_hnsw.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c query_kmknn.cpp -o query_kmknn.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c query_vptree.cpp -o query_vptree.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/hpages/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c vptree.cpp -o vptree.o g++ -std=gnu++11 -shared -L/usr/local/lib -o BiocNeighbors.so 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 installing to /home/hpages/bbs-3.18-bioc-testing/Rlibs/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 version 4.3.0 Patched (2023-05-23 r84466) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
153.925 6.139 244.138
BiocNeighbors.Rcheck/BiocNeighbors-Ex.timings
| name | user | system | elapsed | |
| AnnoyIndex | 0.478 | 0.028 | 0.507 | |
| AnnoyParam | 0.018 | 0.000 | 0.018 | |
| BiocNeighbors-raw-index | 1.900 | 0.009 | 1.909 | |
| BiocNeighbors-ties | 0.012 | 0.000 | 0.011 | |
| ExhaustiveIndex | 0.015 | 0.000 | 0.015 | |
| ExhaustiveParam | 0.002 | 0.000 | 0.002 | |
| HnswIndex | 1.249 | 0.003 | 1.253 | |
| HnswParam | 0.007 | 0.000 | 0.008 | |
| KmknnIndex | 0.292 | 0.012 | 0.304 | |
| KmknnParam | 0.003 | 0.000 | 0.004 | |
| VptreeIndex | 0.030 | 0.004 | 0.034 | |
| VptreeParam | 0.002 | 0.000 | 0.002 | |
| buildAnnoy | 0.409 | 0.003 | 0.413 | |
| buildExhaustive | 0.008 | 0.000 | 0.008 | |
| buildHnsw | 1.242 | 0.000 | 1.242 | |
| buildIndex | 0.668 | 0.007 | 0.676 | |
| buildKmknn | 0.258 | 0.000 | 0.259 | |
| buildVptree | 0.017 | 0.000 | 0.017 | |
| findKNN-functions | 5.488 | 0.012 | 5.500 | |
| findKNN-methods | 6.657 | 0.011 | 6.669 | |
| findMutualNN | 0.038 | 0.000 | 0.037 | |
| findNeighbors-functions | 6.097 | 0.460 | 6.559 | |
| findNeighbors-methods | 6.281 | 0.016 | 6.299 | |
| queryKNN-functions | 2.498 | 0.032 | 2.529 | |
| queryKNN-methods | 1.899 | 0.036 | 1.935 | |
| queryNeighbors-functions | 0.533 | 0.012 | 0.545 | |
| queryNeighbors-methods | 1.129 | 0.024 | 1.153 | |