| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-26 06:18:05 -0000 (Fri, 26 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4254 |
| 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 | ||||
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To the developers/maintainers of the bluster package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bluster.git to reflect on this report. See Troubleshooting Build Report for more information. - 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 223/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bluster 1.11.0 (landing page) Aaron Lun
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: bluster |
| Version: 1.11.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:bluster.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings bluster_1.11.0.tar.gz |
| StartedAt: 2023-05-26 04:23:35 -0000 (Fri, 26 May 2023) |
| EndedAt: 2023-05-26 04:29:31 -0000 (Fri, 26 May 2023) |
| EllapsedTime: 355.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: bluster.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:bluster.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings bluster_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/bluster.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘bluster/DESCRIPTION’ ... OK
* this is package ‘bluster’ version ‘1.11.0’
* 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 ‘bluster’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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 ... 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
MbkmeansParam-class 7.316 0.242 7.576
* 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 ...
‘clusterRows.Rmd’ using ‘UTF-8’... OK
‘diagnostics.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/bluster.Rcheck/00check.log’
for details.
bluster.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL bluster ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘bluster’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c build_snn.cpp -o build_snn.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c sum_neighbor_weights.cpp -o sum_neighbor_weights.o g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o bluster.so RcppExports.o build_snn.o sum_neighbor_weights.o -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-bluster/00new/bluster/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 (bluster)
bluster.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(bluster)
> test_check("bluster")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2227 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2227 ]
>
> proc.time()
user system elapsed
49.880 0.841 50.793
bluster.Rcheck/bluster-Ex.timings
| name | user | system | elapsed | |
| AffinityParam-class | 1.191 | 0.052 | 1.246 | |
| AgnesParam-class | 0.028 | 0.000 | 0.029 | |
| ClaraParam-class | 0.019 | 0.004 | 0.023 | |
| DbscanParam-class | 0.124 | 0.000 | 0.124 | |
| DianaParam-class | 0.022 | 0.000 | 0.023 | |
| HclustParam-class | 0.005 | 0.008 | 0.013 | |
| KmeansParam-class | 0.01 | 0.00 | 0.01 | |
| MbkmeansParam-class | 7.316 | 0.242 | 7.576 | |
| NNGraphParam-class | 0.235 | 0.012 | 0.247 | |
| PamParam-class | 0.019 | 0.000 | 0.020 | |
| SomParam-class | 0.057 | 0.000 | 0.058 | |
| TwoStepParam-class | 0.363 | 0.004 | 0.367 | |
| approxSilhouette | 0.075 | 0.000 | 0.076 | |
| bootstrapStability | 1.029 | 0.036 | 1.068 | |
| clusterRMSD | 0.011 | 0.000 | 0.011 | |
| clusterRows | 1.100 | 0.012 | 1.114 | |
| clusterSweep | 0.631 | 0.020 | 0.653 | |
| compareClusterings | 0.206 | 0.012 | 0.218 | |
| defaultArguments | 0.004 | 0.000 | 0.003 | |
| linkClusters | 0.078 | 0.000 | 0.078 | |
| makeSNNGraph | 1.820 | 0.004 | 1.826 | |
| mergeCommunities | 0.035 | 0.016 | 0.052 | |
| neighborPurity | 0.156 | 0.016 | 0.173 | |
| nestedClusters | 0.049 | 0.000 | 0.048 | |
| pairwiseModularity | 1.231 | 0.024 | 1.256 | |
| pairwiseRand | 0.016 | 0.000 | 0.016 | |