Aaron Lun
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/bluster |
| git_branch: RELEASE_3_17 |
| git_last_commit: 3234042 |
| git_last_commit_date: 2023-04-25 11:20:36 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:59 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 | ||||
| Package 227/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bluster 1.10.0 (landing page) Aaron Lun
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the bluster package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: bluster |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bluster.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bluster_1.10.0.tar.gz |
| StartedAt: 2023-10-17 06:22:48 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 06:26:24 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 215.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: bluster.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bluster.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bluster_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/bluster.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bluster/DESCRIPTION’ ... OK
* this is package ‘bluster’ version ‘1.10.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 5.64 0.233 9.005
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/bluster.Rcheck/00check.log’
for details.
bluster.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL bluster ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘bluster’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c build_snn.cpp -o build_snn.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sum_neighbor_weights.cpp -o sum_neighbor_weights.o clang++ -arch arm64 -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/opt/R/arm64/lib -o bluster.so RcppExports.o build_snn.o sum_neighbor_weights.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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
38.946 1.264 61.816
bluster.Rcheck/bluster-Ex.timings
| name | user | system | elapsed | |
| AffinityParam-class | 0.902 | 0.034 | 1.428 | |
| AgnesParam-class | 0.029 | 0.002 | 0.049 | |
| ClaraParam-class | 0.023 | 0.002 | 0.037 | |
| DbscanParam-class | 0.111 | 0.004 | 0.180 | |
| DianaParam-class | 0.024 | 0.002 | 0.041 | |
| HclustParam-class | 0.012 | 0.002 | 0.021 | |
| KmeansParam-class | 0.010 | 0.003 | 0.021 | |
| MbkmeansParam-class | 5.640 | 0.233 | 9.005 | |
| NNGraphParam-class | 0.096 | 0.012 | 0.163 | |
| PamParam-class | 0.021 | 0.003 | 0.039 | |
| SomParam-class | 0.054 | 0.007 | 0.095 | |
| TwoStepParam-class | 0.357 | 0.005 | 0.550 | |
| approxSilhouette | 0.070 | 0.008 | 0.115 | |
| bootstrapStability | 0.193 | 0.006 | 0.304 | |
| clusterRMSD | 0.008 | 0.000 | 0.012 | |
| clusterRows | 0.752 | 0.025 | 1.200 | |
| clusterSweep | 0.584 | 0.019 | 0.917 | |
| compareClusterings | 0.157 | 0.009 | 0.260 | |
| defaultArguments | 0.003 | 0.000 | 0.005 | |
| linkClusters | 0.088 | 0.004 | 0.140 | |
| makeSNNGraph | 1.358 | 0.019 | 2.121 | |
| mergeCommunities | 0.039 | 0.001 | 0.059 | |
| neighborPurity | 0.147 | 0.004 | 0.232 | |
| nestedClusters | 0.043 | 0.003 | 0.070 | |
| pairwiseModularity | 1.516 | 0.020 | 2.382 | |
| pairwiseRand | 0.013 | 0.001 | 0.019 | |