| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 13:16:31 -0400 (Tue, 09 Apr 2019).
| Package 287/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| clusterExperiment 2.3.1 Elizabeth Purdom
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: clusterExperiment |
| Version: 2.3.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:clusterExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings clusterExperiment_2.3.1.tar.gz |
| StartedAt: 2019-04-09 00:46:27 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:06:02 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 1174.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: clusterExperiment.Rcheck |
| Warnings: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:clusterExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings clusterExperiment_2.3.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/clusterExperiment.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clusterExperiment/DESCRIPTION’ ... OK
* this is package ‘clusterExperiment’ version ‘2.3.1’
* 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 ‘clusterExperiment’ 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 ... NOTE
Foreign function calls to a different package:
.C(ape::node_depth, ...)
.C(ape::node_depth_edgelength, ...)
.C(ape::node_height, ...)
.C(ape::node_height_clado, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* 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 contents of ‘data’ directory ... WARNING
Output for data("rsecFluidigm", package = "clusterExperiment"):
Search path was changed
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotHeatmap 42.344 1.012 43.711
plotClusters 9.588 0.434 10.027
assignUnassigned 8.395 0.308 8.703
clusterMany 7.036 0.286 7.323
plotClustersWorkflow 6.369 0.215 6.585
clusterContrasts 6.251 0.231 6.489
plotBarplot 5.834 0.188 6.023
plottingFunctions 5.671 0.217 6.153
mergeClusters 5.478 0.164 5.643
getClusterManyParams 5.410 0.229 5.640
plotClustersTable 4.963 0.131 5.098
workflowClusters 4.640 0.178 5.078
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat_a-c.R’
ERROR
Running the tests in ‘tests/testthat_a-c.R’ failed.
Last 13 lines of output:
[1] "hierarchical01"
[1] "tight"
══ testthat results ═══════════════════════════════════════════════════════════
OK: 773 SKIPPED: 1 FAILED: 8
1. Failure: RSEC works wih non default assays (@test-assays.R#85)
2. Failure: RSEC works wih non default assays (@test-assays.R#99)
3. Failure: RSEC works independent of assay order (@test-assays.R#131)
4. Failure: RSEC works independent of assay order (@test-assays.R#138)
5. Failure: RSEC works independent of assay order (@test-assays.R#147)
6. Failure: RSEC works independent of assay order (@test-assays.R#154)
7. Failure: RSEC works independent of assay order (@test-assays.R#179)
8. Failure: RSEC works independent of assay order (@test-assays.R#186)
Error: testthat unit tests failed
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 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/clusterExperiment.Rcheck/00check.log’
for details.
clusterExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL clusterExperiment ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘clusterExperiment’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c search_pairs.cpp -o search_pairs.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c subsampleLoop.cpp -o subsampleLoop.o clang++ -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 clusterExperiment.so RcppExports.o search_pairs.o subsampleLoop.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-clusterExperiment/00new/clusterExperiment/libs ** R ** data ** byte-compile and prepare package for lazy loading Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors' Also defined by ‘RNeXML’ Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors' Also defined by ‘RNeXML’ Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors' Also defined by ‘RNeXML’ Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors' Also defined by ‘RNeXML’ Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors' Also defined by ‘RNeXML’ ** 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 (clusterExperiment)
clusterExperiment.Rcheck/tests/testthat_a-c.Rout.fail
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)
> test_check("clusterExperiment",filter = "^[A-Ca-c]")
Loading required package: clusterExperiment
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
── 1. Failure: RSEC works wih non default assays (@test-assays.R#85) ──────────
`... <- NULL` produced unexpected messages.
Expected match: Merging will be done on
Actual values:
* Note: makeDendrogram encountered following error and therefore clusters were not merged:
Error in .makeClusterDendro(x, cluster, type = "mat", ...) :
all samples have clusterIds<0
── 2. Failure: RSEC works wih non default assays (@test-assays.R#99) ──────────
`... <- NULL` produced unexpected messages.
Expected match: Merging will be done on
Actual values:
* Note: makeDendrogram encountered following error and therefore clusters were not merged:
Error in .makeClusterDendro(x, cluster, type = "mat", ...) :
all samples have clusterIds<0
── 3. Failure: RSEC works independent of assay order (@test-assays.R#131) ─────
`... <- NULL` produced unexpected messages.
Expected match: Merging will be done on
Actual values:
* Note: makeDendrogram encountered following error and therefore clusters were not merged:
Error in .makeClusterDendro(x, cluster, type = "mat", ...) :
all samples have clusterIds<0
── 4. Failure: RSEC works independent of assay order (@test-assays.R#138) ─────
`... <- NULL` produced unexpected messages.
Expected match: Merging will be done on
Actual values:
* Note: makeDendrogram encountered following error and therefore clusters were not merged:
Error in .makeClusterDendro(x, cluster, type = "mat", ...) :
all samples have clusterIds<0
── 5. Failure: RSEC works independent of assay order (@test-assays.R#147) ─────
`... <- NULL` produced unexpected messages.
Expected match: Merging will be done on
Actual values:
* Note: makeDendrogram encountered following error and therefore clusters were not merged:
Error in .makeClusterDendro(x, cluster, type = "mat", ...) :
all samples have clusterIds<0
── 6. Failure: RSEC works independent of assay order (@test-assays.R#154) ─────
`... <- NULL` produced unexpected messages.
Expected match: Merging will be done on
Actual values:
* Note: makeDendrogram encountered following error and therefore clusters were not merged:
Error in .makeClusterDendro(x, cluster, type = "mat", ...) :
all samples have clusterIds<0
── 7. Failure: RSEC works independent of assay order (@test-assays.R#179) ─────
`... <- NULL` produced unexpected messages.
Expected match: Merging will be done on
Actual values:
* Note: Not all of the methods requested in 'reduceMethod' have been calculated. Will calculate all the methods requested (any pre-existing values -- filtering statistics or dimensionality reductions -- with these names will be recalculated and overwritten): var.
* Note: makeDendrogram encountered following error and therefore clusters were not merged:
Error in .makeClusterDendro(x, cluster, type = "mat", ...) :
all samples have clusterIds<0
── 8. Failure: RSEC works independent of assay order (@test-assays.R#186) ─────
`... <- NULL` produced unexpected messages.
Expected match: Merging will be done on
Actual values:
* Note: Not all of the methods requested in 'reduceMethod' have been calculated. Will calculate all the methods requested (any pre-existing values -- filtering statistics or dimensionality reductions -- with these names will be recalculated and overwritten): var.
* Note: makeDendrogram encountered following error and therefore clusters were not merged:
Error in .makeClusterDendro(x, cluster, type = "mat", ...) :
all samples have clusterIds<0
[1] "pam"
[1] "clara"
[1] "kmeans"
[1] "hierarchicalK"
[1] "spectral"
[1] "hierarchical01"
[1] "tight"
══ testthat results ═══════════════════════════════════════════════════════════
OK: 773 SKIPPED: 1 FAILED: 8
1. Failure: RSEC works wih non default assays (@test-assays.R#85)
2. Failure: RSEC works wih non default assays (@test-assays.R#99)
3. Failure: RSEC works independent of assay order (@test-assays.R#131)
4. Failure: RSEC works independent of assay order (@test-assays.R#138)
5. Failure: RSEC works independent of assay order (@test-assays.R#147)
6. Failure: RSEC works independent of assay order (@test-assays.R#154)
7. Failure: RSEC works independent of assay order (@test-assays.R#179)
8. Failure: RSEC works independent of assay order (@test-assays.R#186)
Error: testthat unit tests failed
Execution halted
clusterExperiment.Rcheck/clusterExperiment-Ex.timings
| name | user | system | elapsed | |
| ClusterExperiment-class | 0.475 | 0.002 | 0.478 | |
| ClusterFunction-class | 0.020 | 0.001 | 0.020 | |
| addClusterings | 1.321 | 0.216 | 1.537 | |
| assignUnassigned | 8.395 | 0.308 | 8.703 | |
| builtInClusteringFunctions | 0.001 | 0.001 | 0.001 | |
| clusterContrasts | 6.251 | 0.231 | 6.489 | |
| clusterMany | 7.036 | 0.286 | 7.323 | |
| clusterSingle | 0.325 | 0.013 | 0.338 | |
| getBestFeatures | 3.912 | 0.151 | 4.064 | |
| getClusterManyParams | 5.410 | 0.229 | 5.640 | |
| mainClustering | 1.433 | 0.164 | 1.598 | |
| makeConsensus | 4.517 | 0.170 | 4.690 | |
| makeDendrogram | 1.875 | 0.111 | 1.987 | |
| mergeClusters | 5.478 | 0.164 | 5.643 | |
| numericalAsCharacter | 0.001 | 0.001 | 0.001 | |
| plotBarplot | 5.834 | 0.188 | 6.023 | |
| plotClusters | 9.588 | 0.434 | 10.027 | |
| plotClustersTable | 4.963 | 0.131 | 5.098 | |
| plotClustersWorkflow | 6.369 | 0.215 | 6.585 | |
| plotContrastHeatmap | 4.341 | 0.115 | 4.456 | |
| plotDendrogram | 3.426 | 0.087 | 3.525 | |
| plotFeatureBoxplot | 2.442 | 0.086 | 2.531 | |
| plotFeatureScatter | 3.553 | 0.165 | 3.719 | |
| plotHeatmap | 42.344 | 1.012 | 43.711 | |
| plotReducedDims | 2.573 | 0.098 | 3.092 | |
| plottingFunctions | 5.671 | 0.217 | 6.153 | |
| reduceFunctions | 0.347 | 0.021 | 0.368 | |
| rsecFluidigm | 0.001 | 0.002 | 0.003 | |
| seqCluster | 0.000 | 0.001 | 0.001 | |
| simData | 0.000 | 0.001 | 0.002 | |
| subsampleClustering | 0.000 | 0.000 | 0.001 | |
| transformData | 0.142 | 0.000 | 0.143 | |
| workflowClusters | 4.640 | 0.178 | 5.078 | |