Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:08 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for bluster on nebbiolo2


To the developers/maintainers of the bluster package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 205/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bluster 1.4.0  (landing page)
Aaron Lun
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/bluster
git_branch: RELEASE_3_14
git_last_commit: 6f4b821
git_last_commit_date: 2021-10-26 13:01:06 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: bluster
Version: 1.4.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:bluster.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings bluster_1.4.0.tar.gz
StartedAt: 2022-04-12 06:37:24 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 06:39:02 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 98.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: bluster.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:bluster.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings bluster_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/bluster.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bluster/DESCRIPTION’ ... OK
* this is package ‘bluster’ version ‘1.4.0’
* 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
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Failure (test-sweep.R:11:9): clusterSweep works correctly in simple cases ───
  out$clusters[, choice] not identical to clusterRows(x, param).
  132 string mismatches
  ── Failure (test-sweep.R:21:9): clusterSweep works correctly in simple cases ───
  out$clusters[, choice] not identical to clusterRows(x, param).
  Attributes: < Component "levels": Lengths (6, 5) differ (string compare on first 5) >
  148 string mismatches
  ── Failure (test-sweep.R:31:5): clusterSweep reports full objects correctly ────
  out[1:2] not identical to `ref`.
  Attributes: < Component "listData": Component "clusters": Attributes: < Component "listData": Component "cluster.fun.louvain": Attributes: < Component "levels": Lengths (7, 6) differ (string compare on first 6) > > >
  Attributes: < Component "listData": Component "clusters": Attributes: < Component "listData": Component "cluster.fun.louvain": 50 string mismatches > >
  
  [ FAIL 6 | WARN 1 | SKIP 0 | PASS 2222 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/bluster.Rcheck/00check.log’
for details.


Installation output

bluster.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL bluster
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘bluster’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c build_snn.cpp -o build_snn.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c sum_neighbor_weights.cpp -o sum_neighbor_weights.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o bluster.so RcppExports.o build_snn.o sum_neighbor_weights.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/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.fail


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(bluster)
> test_check("bluster")
[ FAIL 6 | WARN 1 | SKIP 0 | PASS 2222 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-nngraph-param.R:45:5): clusterRows works correctly ────────────
`out3` not identical to `out4`.
2 string mismatches
── Failure (test-sweep.R:11:9): clusterSweep works correctly in simple cases ───
out$clusters[, choice] not identical to clusterRows(x, param).
56 string mismatches
── Failure (test-sweep.R:11:9): clusterSweep works correctly in simple cases ───
out$clusters[, choice] not identical to clusterRows(x, param).
149 string mismatches
── Failure (test-sweep.R:11:9): clusterSweep works correctly in simple cases ───
out$clusters[, choice] not identical to clusterRows(x, param).
132 string mismatches
── Failure (test-sweep.R:21:9): clusterSweep works correctly in simple cases ───
out$clusters[, choice] not identical to clusterRows(x, param).
Attributes: < Component "levels": Lengths (6, 5) differ (string compare on first 5) >
148 string mismatches
── Failure (test-sweep.R:31:5): clusterSweep reports full objects correctly ────
out[1:2] not identical to `ref`.
Attributes: < Component "listData": Component "clusters": Attributes: < Component "listData": Component "cluster.fun.louvain": Attributes: < Component "levels": Lengths (7, 6) differ (string compare on first 6) > > >
Attributes: < Component "listData": Component "clusters": Attributes: < Component "listData": Component "cluster.fun.louvain": 50 string mismatches > >

[ FAIL 6 | WARN 1 | SKIP 0 | PASS 2222 ]
Error: Test failures
Execution halted

Example timings

bluster.Rcheck/bluster-Ex.timings

nameusersystemelapsed
AffinityParam-class0.7850.0360.820
AgnesParam-class0.0200.0000.019
ClaraParam-class0.020.000.02
DbscanParam-class0.0920.0000.091
DianaParam-class0.0180.0000.018
HclustParam-class0.0090.0000.009
KmeansParam-class0.0060.0000.007
MbkmeansParam-class4.2290.2084.438
NNGraphParam-class0.0540.0000.054
PamParam-class0.0200.0000.019
SomParam-class0.6210.0070.629
TwoStepParam-class0.3140.0000.315
approxSilhouette0.050.000.05
bootstrapStability0.1190.0320.151
clusterRMSD0.0060.0000.006
clusterRows0.4970.0120.509
clusterSweep0.3940.0080.403
compareClusterings0.1180.0000.119
defaultArguments0.0020.0000.002
linkClusters0.0430.0000.042
makeSNNGraph0.8600.0080.868
mergeCommunities0.0280.0000.028
neighborPurity0.0940.0000.093
nestedClusters0.0370.0000.037
pairwiseModularity0.7100.0110.723
pairwiseRand0.0110.0000.011