Aaron Lun
| Snapshot Date: 2020-06-30 15:50:19 -0400 (Tue, 30 Jun 2020) |
| URL: https://git.bioconductor.org/packages/SingleR |
| Branch: RELEASE_3_11 |
| Last Commit: 4653a3c |
| Last Changed Date: 2020-05-24 18:13:10 -0400 (Sun, 24 May 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-07-01 14:18:46 -0400 (Wed, 01 Jul 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE SingleR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1674/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SingleR 1.2.4 Aaron Lun
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: SingleR |
| Version: 1.2.4 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SingleR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SingleR_1.2.4.tar.gz |
| StartedAt: 2020-07-01 06:35:17 -0400 (Wed, 01 Jul 2020) |
| EndedAt: 2020-07-01 06:51:30 -0400 (Wed, 01 Jul 2020) |
| EllapsedTime: 973.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: SingleR.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SingleR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SingleR_1.2.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SingleR.Rcheck’
* using R version 4.0.0 (2020-04-24)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SingleR/DESCRIPTION’ ... OK
* this is package ‘SingleR’ version ‘1.2.4’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
.github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SingleR’ 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
plotScoreDistribution 25.600 0.326 26.052
DatabaseImmuneCellExpressionData 12.950 0.750 13.992
BlueprintEncodeData 9.967 0.800 11.353
HumanPrimaryCellAtlasData 7.919 0.290 8.591
ImmGenData 7.275 0.224 7.864
MouseRNAseqData 6.307 0.171 6.720
MonacoImmuneData 6.102 0.133 6.523
NovershternHematopoieticData 5.921 0.168 6.336
* 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:
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 520 | SKIPPED: 0 | WARNINGS: 17 | FAILED: 8 ]
1. Failure: Ensembl coercion works for all datasets (@test-datasets.R#5)
2. Failure: Ensembl coercion works for all datasets (@test-datasets.R#7)
3. Failure: Ensembl coercion works for all datasets (@test-datasets.R#9)
4. Failure: Ensembl coercion works for all datasets (@test-datasets.R#11)
5. Failure: Ensembl coercion works for all datasets (@test-datasets.R#13)
6. Failure: Ensembl coercion works for all datasets (@test-datasets.R#15)
7. Failure: ontology mapping works for all datasets (@test-datasets.R#21)
8. Failure: ontology mapping works for all datasets (@test-datasets.R#23)
Error: testthat unit tests failed
In addition: Warning message:
call dbDisconnect() when finished working with a connection
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 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/SingleR.Rcheck/00check.log’
for details.
SingleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SingleR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘SingleR’ ... ** 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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/beachmat/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/beachmat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fine_tune_de.cpp -o fine_tune_de.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/beachmat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fine_tune_sd.cpp -o fine_tune_sd.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/beachmat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c recompute_scores.cpp -o recompute_scores.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 SingleR.so RcppExports.o fine_tune_de.o fine_tune_sd.o recompute_scores.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-SingleR/00new/SingleR/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 (SingleR)
SingleR.Rcheck/tests/testthat.Rout.fail
R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 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(SingleR)
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, 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, 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
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
> test_check("SingleR")
── 1. Failure: Ensembl coercion works for all datasets (@test-datasets.R#5) ───
`X <- BlueprintEncodeData(ensembl = TRUE)` threw an error.
Message: operation not supported on matrices of type character
Class: simpleError/error/condition
Backtrace:
1. testthat::expect_error(...)
6. SingleR::BlueprintEncodeData(ensembl = TRUE)
7. SingleR:::.create_se(...)
8. SingleR:::.rm_NAs(nrmcnts, rm.NA)
10. DelayedMatrixStats::rowAnyNAs(DelayedArray(mat))
11. DelayedMatrixStats:::.local(x, rows, cols, ...)
13. DelayedMatrixStats::rowAnys(...)
14. DelayedMatrixStats:::.local(...)
15. DelayedMatrixStats:::.DelayedMatrix_block_rowAnys(...)
16. DelayedArray:::.get_ans_type(x, must.be.numeric = TRUE)
── 2. Failure: Ensembl coercion works for all datasets (@test-datasets.R#7) ───
`X <- DatabaseImmuneCellExpressionData(ensembl = TRUE)` threw an error.
Message: invalid class "SummarizedExperiment" object:
nb of cols in 'assay' (259) must equal nb of rows in 'colData' (1561)
Class: simpleError/error/condition
Backtrace:
1. testthat::expect_error(...)
6. SingleR::DatabaseImmuneCellExpressionData(ensembl = TRUE)
7. SingleR:::.create_se(...)
10. SummarizedExperiment:::new_SummarizedExperiment(...)
11. methods::new(...)
13. methods::initialize(value, ...)
14. methods::validObject(.Object)
── 3. Failure: Ensembl coercion works for all datasets (@test-datasets.R#9) ───
`X <- HumanPrimaryCellAtlasData(ensembl = TRUE)` threw an error.
Message: failed to load resource
name: EH3090
title: Human Primary Cell Atlas logcounts
reason: 1 resources failed to download
Class: simpleError/error/condition
Backtrace:
1. testthat::expect_error(...)
6. SingleR::HumanPrimaryCellAtlasData(ensembl = TRUE)
7. SingleR:::.create_se(...)
9. hub[hub$rdatapath == file.path(host, ver, paste0(a, ".rds"))][[1]]
10. ExperimentHub:::.local(x, i, j = j, ...)
14. AnnotationHub:::.nextMethod(x, i, j, ..., force = force, verbose = verbose)
15. AnnotationHub:::.local(x, i, j = j, ...)
16. AnnotationHub:::.Hub_get1(x[i], force = force, verbose = verbose)
17. base::tryCatch(...)
18. base:::tryCatchList(expr, classes, parentenv, handlers)
19. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
20. value[[3L]](cond)
── 4. Failure: Ensembl coercion works for all datasets (@test-datasets.R#11) ──
`X <- ImmGenData(ensembl = TRUE)` threw an error.
Message: failed to load resource
name: EH3092
title: ImmGen logcounts
reason: 1 resources failed to download
Class: simpleError/error/condition
Backtrace:
1. testthat::expect_error(X <- ImmGenData(ensembl = TRUE), NA)
6. SingleR::ImmGenData(ensembl = TRUE)
7. SingleR:::.create_se(...)
9. hub[hub$rdatapath == file.path(host, ver, paste0(a, ".rds"))][[1]]
10. ExperimentHub:::.local(x, i, j = j, ...)
14. AnnotationHub:::.nextMethod(x, i, j, ..., force = force, verbose = verbose)
15. AnnotationHub:::.local(x, i, j = j, ...)
16. AnnotationHub:::.Hub_get1(x[i], force = force, verbose = verbose)
17. base::tryCatch(...)
18. base:::tryCatchList(expr, classes, parentenv, handlers)
19. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
20. value[[3L]](cond)
── 5. Failure: Ensembl coercion works for all datasets (@test-datasets.R#13) ──
`X <- MonacoImmuneData(ensembl = TRUE)` threw an error.
Message: failed to load resource
name: EH3100
title: Monaco Immune Cell RNA-seq logcounts
reason: unknown input format
Class: simpleError/error/condition
Backtrace:
1. testthat::expect_error(...)
6. SingleR::MonacoImmuneData(ensembl = TRUE)
7. SingleR:::.create_se(...)
9. hub[hub$rdatapath == file.path(host, ver, paste0(a, ".rds"))][[1]]
10. ExperimentHub:::.local(x, i, j = j, ...)
14. AnnotationHub:::.nextMethod(x, i, j, ..., force = force, verbose = verbose)
15. AnnotationHub:::.local(x, i, j = j, ...)
16. AnnotationHub:::.Hub_get1(x[i], force = force, verbose = verbose)
17. base::tryCatch(...)
18. base:::tryCatchList(expr, classes, parentenv, handlers)
19. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
20. value[[3L]](cond)
── 6. Failure: Ensembl coercion works for all datasets (@test-datasets.R#15) ──
`X <- MouseRNAseqData(ensembl = TRUE)` threw an error.
Message: failed to load resource
name: EH3095
title: Mouse bulk RNA-seq colData
reason: unknown input format
Class: simpleError/error/condition
Backtrace:
1. testthat::expect_error(...)
6. SingleR::MouseRNAseqData(ensembl = TRUE)
7. SingleR:::.create_se(...)
9. hub[hub$rdatapath == file.path(host, ver, "coldata.rds")][[1]]
10. ExperimentHub:::.local(x, i, j = j, ...)
14. AnnotationHub:::.nextMethod(x, i, j, ..., force = force, verbose = verbose)
15. AnnotationHub:::.local(x, i, j = j, ...)
16. AnnotationHub:::.Hub_get1(x[i], force = force, verbose = verbose)
17. base::tryCatch(...)
18. base:::tryCatchList(expr, classes, parentenv, handlers)
19. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
20. value[[3L]](cond)
── 7. Failure: ontology mapping works for all datasets (@test-datasets.R#21) ──
`X <- BlueprintEncodeData(cell.ont = "nonna")` threw an error.
Message: operation not supported on matrices of type character
Class: simpleError/error/condition
Backtrace:
1. testthat::expect_error(...)
6. SingleR::BlueprintEncodeData(cell.ont = "nonna")
7. SingleR:::.create_se(...)
8. SingleR:::.rm_NAs(nrmcnts, rm.NA)
10. DelayedMatrixStats::rowAnyNAs(DelayedArray(mat))
11. DelayedMatrixStats:::.local(x, rows, cols, ...)
13. DelayedMatrixStats::rowAnys(...)
14. DelayedMatrixStats:::.local(...)
15. DelayedMatrixStats:::.DelayedMatrix_block_rowAnys(...)
16. DelayedArray:::.get_ans_type(x, must.be.numeric = TRUE)
── 8. Failure: ontology mapping works for all datasets (@test-datasets.R#23) ──
`X <- DatabaseImmuneCellExpressionData(cell.ont = "nonna")` threw an error.
Message: invalid class "SummarizedExperiment" object:
nb of cols in 'assay' (259) must equal nb of rows in 'colData' (1561)
Class: simpleError/error/condition
Backtrace:
1. testthat::expect_error(...)
6. SingleR::DatabaseImmuneCellExpressionData(cell.ont = "nonna")
7. SingleR:::.create_se(...)
10. SummarizedExperiment:::new_SummarizedExperiment(...)
11. methods::new(...)
13. methods::initialize(value, ...)
14. methods::validObject(.Object)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 520 | SKIPPED: 0 | WARNINGS: 17 | FAILED: 8 ]
1. Failure: Ensembl coercion works for all datasets (@test-datasets.R#5)
2. Failure: Ensembl coercion works for all datasets (@test-datasets.R#7)
3. Failure: Ensembl coercion works for all datasets (@test-datasets.R#9)
4. Failure: Ensembl coercion works for all datasets (@test-datasets.R#11)
5. Failure: Ensembl coercion works for all datasets (@test-datasets.R#13)
6. Failure: Ensembl coercion works for all datasets (@test-datasets.R#15)
7. Failure: ontology mapping works for all datasets (@test-datasets.R#21)
8. Failure: ontology mapping works for all datasets (@test-datasets.R#23)
Error: testthat unit tests failed
In addition: Warning message:
call dbDisconnect() when finished working with a connection
Execution halted
SingleR.Rcheck/SingleR-Ex.timings
| name | user | system | elapsed | |
| BlueprintEncodeData | 9.967 | 0.800 | 11.353 | |
| DatabaseImmuneCellExpressionData | 12.950 | 0.750 | 13.992 | |
| HumanPrimaryCellAtlasData | 7.919 | 0.290 | 8.591 | |
| ImmGenData | 7.275 | 0.224 | 7.864 | |
| MonacoImmuneData | 6.102 | 0.133 | 6.523 | |
| MouseRNAseqData | 6.307 | 0.171 | 6.720 | |
| NovershternHematopoieticData | 5.921 | 0.168 | 6.336 | |
| SingleR | 1.873 | 0.042 | 1.924 | |
| aggregateReference | 2.066 | 0.048 | 2.126 | |
| classifySingleR | 0.446 | 0.011 | 0.459 | |
| combineCommonResults | 1.015 | 0.017 | 1.034 | |
| combineRecomputedResults | 0.955 | 0.023 | 0.978 | |
| getDeltaFromMedian | 0.886 | 0.012 | 0.900 | |
| matchReferences | 1.247 | 0.013 | 1.264 | |
| mockData | 0.041 | 0.001 | 0.042 | |
| plotScoreDistribution | 25.600 | 0.326 | 26.052 | |
| plotScoreHeatmap | 4.719 | 0.078 | 4.825 | |
| pruneScores | 0.924 | 0.013 | 0.944 | |
| trainSingleR | 1.904 | 0.023 | 1.933 | |