| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:07:42 -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 | ||||
|
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: /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_1.4.0.tar.gz |
| StartedAt: 2022-04-12 10:59:05 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 11:02:06 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 180.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: bluster.Rcheck |
| Warnings: NA |
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### Running command:
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### /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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/bluster.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MbkmeansParam-class 7.52 0.227 7.754
* 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$clusters[, choice] not identical to clusterRows(x, param).
Attributes: < Component "levels": Lengths (3, 4) differ (string compare on first 3) >
141 string mismatches
── Failure (test-sweep.R:21:9): clusterSweep works correctly in simple cases ───
out$clusters[, choice] not identical to clusterRows(x, param).
77 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 (5, 6) differ (string compare on first 5) > > >
Attributes: < Component "listData": Component "clusters": Attributes: < Component "listData": Component "cluster.fun.louvain": 126 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
‘/Users/biocbuild/bbs-3.14-bioc/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/4.1/Resources/library’ * installing *source* package ‘bluster’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c build_snn.cpp -o build_snn.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c sum_neighbor_weights.cpp -o sum_neighbor_weights.o clang++ -mmacosx-version-min=10.13 -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/usr/local/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/4.1/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.fail
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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$clusters[, choice] not identical to clusterRows(x, param).
Attributes: < Component "levels": Lengths (6, 7) differ (string compare on first 6) >
114 string mismatches
── Failure (test-sweep.R:11:9): clusterSweep works correctly in simple cases ───
out$clusters[, choice] not identical to clusterRows(x, param).
Attributes: < Component "levels": Lengths (6, 5) differ (string compare on first 5) >
185 string mismatches
── Failure (test-sweep.R:11:9): clusterSweep works correctly in simple cases ───
out$clusters[, choice] not identical to clusterRows(x, param).
Attributes: < Component "levels": Lengths (3, 4) differ (string compare on first 3) >
141 string mismatches
── Failure (test-sweep.R:21:9): clusterSweep works correctly in simple cases ───
out$clusters[, choice] not identical to clusterRows(x, param).
77 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 (5, 6) differ (string compare on first 5) > > >
Attributes: < Component "listData": Component "clusters": Attributes: < Component "listData": Component "cluster.fun.louvain": 126 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 | 1.163 | 0.089 | 1.255 | |
| AgnesParam-class | 0.033 | 0.003 | 0.034 | |
| ClaraParam-class | 0.032 | 0.004 | 0.036 | |
| DbscanParam-class | 0.197 | 0.004 | 0.201 | |
| DianaParam-class | 0.034 | 0.002 | 0.037 | |
| HclustParam-class | 0.015 | 0.003 | 0.018 | |
| KmeansParam-class | 0.014 | 0.005 | 0.020 | |
| MbkmeansParam-class | 7.520 | 0.227 | 7.754 | |
| NNGraphParam-class | 0.088 | 0.017 | 0.139 | |
| PamParam-class | 0.027 | 0.006 | 0.033 | |
| SomParam-class | 0.077 | 0.009 | 0.112 | |
| TwoStepParam-class | 0.466 | 0.003 | 0.470 | |
| approxSilhouette | 0.092 | 0.004 | 0.097 | |
| bootstrapStability | 0.757 | 0.011 | 0.769 | |
| clusterRMSD | 0.011 | 0.001 | 0.012 | |
| clusterRows | 0.652 | 0.036 | 0.689 | |
| clusterSweep | 0.749 | 0.015 | 0.765 | |
| compareClusterings | 0.227 | 0.007 | 0.236 | |
| defaultArguments | 0.004 | 0.001 | 0.005 | |
| linkClusters | 0.061 | 0.003 | 0.064 | |
| makeSNNGraph | 1.130 | 0.018 | 1.153 | |
| mergeCommunities | 0.077 | 0.005 | 0.082 | |
| neighborPurity | 0.170 | 0.004 | 0.173 | |
| nestedClusters | 0.071 | 0.004 | 0.073 | |
| pairwiseModularity | 0.917 | 0.022 | 0.939 | |
| pairwiseRand | 0.017 | 0.000 | 0.018 | |