| 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).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (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 | ||||
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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. |
| Package 205/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bluster 1.4.0 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| 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 |
############################################################################## ############################################################################## ### ### 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.
bluster.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
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
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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
bluster.Rcheck/bluster-Ex.timings
| name | user | system | elapsed | |
| AffinityParam-class | 0.785 | 0.036 | 0.820 | |
| AgnesParam-class | 0.020 | 0.000 | 0.019 | |
| ClaraParam-class | 0.02 | 0.00 | 0.02 | |
| DbscanParam-class | 0.092 | 0.000 | 0.091 | |
| DianaParam-class | 0.018 | 0.000 | 0.018 | |
| HclustParam-class | 0.009 | 0.000 | 0.009 | |
| KmeansParam-class | 0.006 | 0.000 | 0.007 | |
| MbkmeansParam-class | 4.229 | 0.208 | 4.438 | |
| NNGraphParam-class | 0.054 | 0.000 | 0.054 | |
| PamParam-class | 0.020 | 0.000 | 0.019 | |
| SomParam-class | 0.621 | 0.007 | 0.629 | |
| TwoStepParam-class | 0.314 | 0.000 | 0.315 | |
| approxSilhouette | 0.05 | 0.00 | 0.05 | |
| bootstrapStability | 0.119 | 0.032 | 0.151 | |
| clusterRMSD | 0.006 | 0.000 | 0.006 | |
| clusterRows | 0.497 | 0.012 | 0.509 | |
| clusterSweep | 0.394 | 0.008 | 0.403 | |
| compareClusterings | 0.118 | 0.000 | 0.119 | |
| defaultArguments | 0.002 | 0.000 | 0.002 | |
| linkClusters | 0.043 | 0.000 | 0.042 | |
| makeSNNGraph | 0.860 | 0.008 | 0.868 | |
| mergeCommunities | 0.028 | 0.000 | 0.028 | |
| neighborPurity | 0.094 | 0.000 | 0.093 | |
| nestedClusters | 0.037 | 0.000 | 0.037 | |
| pairwiseModularity | 0.710 | 0.011 | 0.723 | |
| pairwiseRand | 0.011 | 0.000 | 0.011 | |