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This page was generated on 2025-08-09 12:08 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 232/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bluster 1.19.0  (landing page)
Aaron Lun
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/bluster
git_branch: devel
git_last_commit: e860f35
git_last_commit_date: 2025-04-15 12:04:57 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for bluster on lconway

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.
- 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.

raw results


Summary

Package: bluster
Version: 1.19.0
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_1.19.0.tar.gz
StartedAt: 2025-08-08 19:39:16 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 19:45:01 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 345.1 seconds
RetCode: 0
Status:   OK  
CheckDir: bluster.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/bluster.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bluster/DESCRIPTION’ ... OK
* this is package ‘bluster’ version ‘1.19.0’
* package encoding: UTF-8
* 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 ... OK
* 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 code 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AgnesParam-class.Rd: agnes
  ClaraParam-class.Rd: clara
  DbscanParam-class.Rd: BiocNeighborParam-class
  DianaParam-class.Rd: diana
  DmmParam-class.Rd: BiocParallelParam-class
  NNGraphParam-class.Rd: BiocNeighborParam-class, communities,
    cluster_louvain, cluster_walktrap
  PamParam-class.Rd: pam
  approxSilhouette.Rd: DataFrame-class
  clusterSweep.Rd: BiocParallelParam-class, List-class, DataFrame-class
  linkClusters.Rd: graph
  makeSNNGraph.Rd: BiocNeighborParam-class, findKNN, graph, make_graph,
    cluster_walktrap, cluster_louvain
  mergeCommunities.Rd: graph, cut_at
  neighborPurity.Rd: BiocNeighborParam-class, findNeighbors,
    DataFrame-class
  nestedClusters.Rd: DataFrame-class
  pairwiseModularity.Rd: graph, modularity, as.undirected
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 5.208  0.253   6.156
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.22-bioc/meat/bluster.Rcheck/00check.log’
for details.


Installation output

bluster.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL bluster
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘bluster’ ...
** this is package ‘bluster’ version ‘1.19.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c build_snn.cpp -o build_snn.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c sum_neighbor_weights.cpp -o sum_neighbor_weights.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o bluster.so RcppExports.o build_snn.o sum_neighbor_weights.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/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)

Tests output

bluster.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 3 | SKIP 0 | PASS 2249 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 2249 ]
> 
> proc.time()
   user  system elapsed 
 53.623   4.515  85.562 

Example timings

bluster.Rcheck/bluster-Ex.timings

nameusersystemelapsed
AffinityParam-class1.6960.0901.999
AgnesParam-class0.0280.0020.030
ClaraParam-class0.0250.0040.029
DbscanParam-class0.0310.0040.040
DianaParam-class0.0240.0020.027
DmmParam-class1.2820.0521.373
HclustParam-class0.1160.0230.148
KmeansParam-class0.0110.0040.015
MbkmeansParam-class5.2080.2536.156
NNGraphParam-class0.0490.0110.063
PamParam-class0.0210.0040.025
SomParam-class0.0560.0110.074
TwoStepParam-class0.4380.0050.447
approxSilhouette0.0620.0030.068
bootstrapStability0.8110.0120.830
clusterRMSD0.0060.0010.007
clusterRows0.5200.0450.576
clusterSweep0.3780.0110.393
compareClusterings0.2210.0130.243
defaultArguments0.0040.0000.005
linkClusters0.0580.0080.067
makeSNNGraph0.8760.0280.911
mergeCommunities0.0260.0030.029
neighborPurity0.0770.0050.081
nestedClusters0.0390.0050.045
pairwiseModularity0.6490.0220.677
pairwiseRand0.0130.0010.014