| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:46:22 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:clusterExperiment.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings clusterExperiment_2.3.1.tar.gz |
| StartedAt: 2019-04-08 23:30:59 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:43:51 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 771.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: clusterExperiment.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:clusterExperiment.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings clusterExperiment_2.3.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/clusterExperiment.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ... WARNING
Found the following significant warnings:
subsampleLoop.cpp:89:32: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
subsampleLoop.cpp:90:32: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
subsampleLoop.cpp:122:25: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/biocbuild/bbs-3.9-bioc/meat/clusterExperiment.Rcheck/00install.out’ for details.
* 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 27.805 0.051 27.883
plotClusters 7.564 0.016 7.582
clusterMany 5.905 0.032 5.963
plotClustersWorkflow 5.282 0.016 5.298
assignUnassigned 5.187 0.080 5.286
* 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, 2 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/clusterExperiment.Rcheck/00check.log’
for details.
clusterExperiment.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL clusterExperiment
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘clusterExperiment’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c search_pairs.cpp -o search_pairs.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c subsampleLoop.cpp -o subsampleLoop.o
subsampleLoop.cpp: In function ‘Rcpp::IntegerMatrix subsampleLoop(Rcpp::List, int)’:
subsampleLoop.cpp:89:32: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
LogicalVector clusterj = j <= indexClusterEnds & j >= indexClusterStarts;
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
subsampleLoop.cpp:90:32: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
LogicalVector clusterk = k <= indexClusterEnds & k >= indexClusterStarts;
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
subsampleLoop.cpp:122:25: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
if((it->second).first>0 | (it->second).second==NA_INTEGER){
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o clusterExperiment.so RcppExports.o search_pairs.o subsampleLoop.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/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-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)
> 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 | 0.4 | 0.0 | 0.4 | |
| ClusterFunction-class | 0.014 | 0.000 | 0.014 | |
| addClusterings | 0.909 | 0.096 | 1.043 | |
| assignUnassigned | 5.187 | 0.080 | 5.286 | |
| builtInClusteringFunctions | 0.001 | 0.000 | 0.001 | |
| clusterContrasts | 3.903 | 0.020 | 3.925 | |
| clusterMany | 5.905 | 0.032 | 5.963 | |
| clusterSingle | 0.151 | 0.008 | 0.159 | |
| getBestFeatures | 2.886 | 0.004 | 2.891 | |
| getClusterManyParams | 4.306 | 0.008 | 4.313 | |
| mainClustering | 0.746 | 0.004 | 0.750 | |
| makeConsensus | 1.776 | 0.000 | 1.775 | |
| makeDendrogram | 1.587 | 0.000 | 1.588 | |
| mergeClusters | 2.706 | 0.000 | 2.706 | |
| numericalAsCharacter | 0 | 0 | 0 | |
| plotBarplot | 3.477 | 0.004 | 3.480 | |
| plotClusters | 7.564 | 0.016 | 7.582 | |
| plotClustersTable | 3.613 | 0.000 | 3.613 | |
| plotClustersWorkflow | 5.282 | 0.016 | 5.298 | |
| plotContrastHeatmap | 3.478 | 0.012 | 3.490 | |
| plotDendrogram | 2.752 | 0.008 | 2.761 | |
| plotFeatureBoxplot | 2 | 0 | 2 | |
| plotFeatureScatter | 1.705 | 0.008 | 1.721 | |
| plotHeatmap | 27.805 | 0.051 | 27.883 | |
| plotReducedDims | 2.127 | 0.008 | 2.135 | |
| plottingFunctions | 2.682 | 0.012 | 2.694 | |
| reduceFunctions | 0.321 | 0.000 | 0.320 | |
| rsecFluidigm | 0 | 0 | 0 | |
| seqCluster | 0 | 0 | 0 | |
| simData | 0.000 | 0.000 | 0.001 | |
| subsampleClustering | 0.000 | 0.000 | 0.001 | |
| transformData | 0.124 | 0.000 | 0.125 | |
| workflowClusters | 3.487 | 0.004 | 3.493 | |