| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:44:23 -0500 (Thu, 16 Jan 2020).
| Package 1519/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scater 1.15.16 Davis McCarthy
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | TIMEOUT | skipped | skipped | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: scater |
| Version: 1.15.16 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scater.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scater_1.15.16.tar.gz |
| StartedAt: 2020-01-16 08:35:32 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 08:46:19 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 646.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: scater.Rcheck |
| Warnings: NA |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scater.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scater_1.15.16.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/scater.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scater/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scater’ version ‘1.15.16’
* 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 ‘scater’ 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 ... ERROR
Running examples in ‘scater-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: perCellQCMetrics
> ### Title: Compute per-cell quality control metrics for a count matrix or a
> ### SingleCellExperiment.
> ### Aliases: perCellQCMetrics perCellQCMetrics,ANY-method
> ### perCellQCMetrics,SummarizedExperiment-method
> ### perCellQCMetrics,SingleCellExperiment-method
>
> ### ** Examples
>
> example_sce <- mockSCE()
> stats <- perCellQCMetrics(example_sce)
> stats
DataFrame with 200 rows and 10 columns
sum detected percent_top_50 percent_top_100 percent_top_200
<numeric> <integer> <numeric> <numeric> <numeric>
1 344015 1466 24.8957 39.2742 58.0658
2 334664 1480 22.6484 36.5665 56.1644
3 367199 1464 21.7430 35.0243 54.1143
4 349098 1487 22.5475 36.6029 56.0871
5 355320 1474 24.4706 38.7769 58.0564
... ... ... ... ... ...
196 364311 1466 24.6097 38.9450 57.8190
197 347147 1507 23.4108 36.9408 56.0705
198 348551 1487 24.5367 37.9921 56.1840
199 336934 1470 21.5927 34.8887 54.1002
200 347189 1488 23.4552 37.3808 55.8062
percent_top_500 altexps_Spikes_sum altexps_Spikes_detected
<numeric> <numeric> <integer>
1 85.9253 7557 77
2 85.4559 7866 73
3 84.3698 7957 82
4 84.9335 6741 80
5 85.5012 6123 76
... ... ... ...
196 85.1588 6207 75
197 84.2692 8745 85
198 84.4574 6794 83
199 83.6873 8525 79
200 85.3388 7524 85
altexps_Spikes_percent total
<numeric> <numeric>
1 2.14949 351572
2 2.29644 342530
3 2.12098 375156
4 1.89440 355839
5 1.69404 361443
... ... ...
196 1.67522 370518
197 2.45721 355892
198 1.91194 355345
199 2.46773 345459
200 2.12115 354713
>
> # With subsets.
> stats2 <- perCellQCMetrics(example_sce, subsets=list(Mito=1:10),
+ flatten=FALSE)
> stats2$subsets
DataFrame with 200 rows and 1 column
Error in dimnames(x) <- dn :
length of 'dimnames' [1] not equal to array extent
Calls: <Anonymous> ... .nextMethod -> .show_DataTable -> rownames<- -> rownames<-
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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-3.11-bioc/meat/scater.Rcheck/00check.log’
for details.
scater.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL scater ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘scater’ ... ** using staged installation ** libs clang++ -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' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/beachmat/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c combined_qc.cpp -o combined_qc.o clang++ -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' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c sum_counts.cpp -o sum_counts.o clang++ -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' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.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 scater.so RcppExports.o combined_qc.o sum_counts.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-scater/00new/scater/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 (scater)
scater.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-12-14 r77572) -- "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.
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(scater)
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, 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
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
Loading required package: ggplot2
>
> test_check("scater")
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══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 1746 | SKIPPED: 0 | WARNINGS: 11 | FAILED: 0 ]
>
> proc.time()
user system elapsed
314.873 17.812 331.532
scater.Rcheck/scater-Ex.timings
| name | user | system | elapsed | |
| accessors | 2.795 | 0.064 | 2.859 | |
| addPerCellQC | 1.268 | 0.162 | 1.435 | |
| annotateBMFeatures | 0.001 | 0.000 | 0.000 | |
| bootstraps | 0.422 | 0.003 | 0.425 | |
| calculateAverage | 0.429 | 0.002 | 0.431 | |
| calculateCPM | 0.343 | 0.007 | 0.349 | |
| calculateFPKM | 0.314 | 0.001 | 0.316 | |
| calculateTPM | 0.360 | 0.002 | 0.364 | |
| defunct | 0.001 | 0.000 | 0.002 | |
| getExplanatoryPCs | 1.040 | 0.011 | 1.053 | |
| getVarianceExplained | 0.656 | 0.077 | 0.734 | |
| isOutlier | 0.885 | 0.017 | 0.906 | |
| librarySizeFactors | 1.081 | 0.040 | 1.127 | |
| logNormCounts | 0.419 | 0.015 | 0.435 | |
| medianSizeFactors | 0.302 | 0.016 | 0.319 | |
| mockSCE | 0.388 | 0.011 | 0.399 | |
| multiplot | 2.768 | 0.255 | 3.024 | |
| nexprs | 0.422 | 0.006 | 0.428 | |
| normalizeCounts | 0.462 | 0.019 | 0.482 | |
| numDetectedAcrossCells | 0.393 | 0.022 | 0.415 | |
| numDetectedAcrossFeatures | 0.401 | 0.019 | 0.420 | |