Davide Risso
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/SingleCellExperiment |
| Branch: RELEASE_3_10 |
| Last Commit: 11bd3ff |
| Last Changed Date: 2019-10-29 13:10:32 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:12:56 -0400 (Wed, 15 Apr 2020).
| Package 1604/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SingleCellExperiment 1.8.0 Davide Risso
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: SingleCellExperiment |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:SingleCellExperiment.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings SingleCellExperiment_1.8.0.tar.gz |
| StartedAt: 2020-04-15 04:58:36 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:01:56 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 200.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SingleCellExperiment.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:SingleCellExperiment.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings SingleCellExperiment_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/SingleCellExperiment.Rcheck’ * using R version 3.6.3 (2020-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SingleCellExperiment/DESCRIPTION’ ... OK * this is package ‘SingleCellExperiment’ version ‘1.8.0’ * 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 ‘SingleCellExperiment’ 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 ... NOTE Unexported objects imported by ':::' calls: ‘BiocGenerics:::replaceSlots’ ‘S4Vectors:::disableValidity’ ‘SummarizedExperiment:::.SummarizedExperiment.charbound’ See the note in ?`:::` about the use of this operator. * 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 files in ‘vignettes’ ... OK * checking examples ... WARNING Found the following significant warnings: Warning: 'isSpike<-' is deprecated. Warning: 'spikeNames' is deprecated. Warning: 'isSpike' is deprecated. Warning: 'isSpike' is deprecated. Warning: 'isSpike<-' is deprecated. Warning: 'spikeNames' is deprecated. Warning: 'isSpike' is deprecated. Warning: 'isSpike' is deprecated. Warning: 'spikeNames' is deprecated. Warning: 'isSpike' is deprecated. Warning: 'isSpike' is deprecated. Warning: 'isSpike<-' is deprecated. Warning: 'spikeNames' is deprecated. Warning: 'isSpike' is deprecated. Warning: 'spikeNames' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. * 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 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.10-bioc/meat/SingleCellExperiment.Rcheck/00check.log’ for details.
SingleCellExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL SingleCellExperiment ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘SingleCellExperiment’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SingleCellExperiment)
SingleCellExperiment.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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)
> library(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
> test_check("SingleCellExperiment")
class: SingleCellExperiment
dim: 200 100
metadata(0):
assays(2): counts logcounts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(0):
reducedDimNames(2): PCA TSNE
spikeNames(1): ERCC
altExpNames(2): Spike Protein
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 462 | SKIPPED: 0 | WARNINGS: 108 | FAILED: 0 ]
Warning messages:
1: 'isSpike<-' is deprecated.
Use 'isSpike<-' instead.
See help("Deprecated")
2: 'spikeNames' is deprecated.
See help("Deprecated")
3: 'isSpike' is deprecated.
See help("Deprecated")
>
> proc.time()
user system elapsed
23.404 0.340 24.454
SingleCellExperiment.Rcheck/SingleCellExperiment-Ex.timings
| name | user | system | elapsed | |
| LEM-combine | 0.084 | 0.000 | 0.088 | |
| LEM-getset | 0.132 | 0.032 | 0.165 | |
| LEM-misc | 0.016 | 0.000 | 0.015 | |
| LEM-subset | 0.540 | 0.004 | 0.545 | |
| LinearEmbeddingMatrix | 0.012 | 0.000 | 0.009 | |
| SCE-isSpike | 0.436 | 0.016 | 0.499 | |
| SCE-sizeFactors | 0.116 | 0.016 | 0.132 | |
| SingleCellExperiment | 0.184 | 0.020 | 0.204 | |
| altExps | 0.316 | 0.036 | 0.355 | |
| assays | 0.308 | 0.020 | 0.330 | |
| combine | 1.636 | 0.016 | 1.658 | |
| internals | 0.080 | 0.000 | 0.083 | |
| miscellaneous | 0.188 | 0.000 | 0.189 | |
| reducedDims | 0.340 | 0.004 | 0.347 | |
| splitAltExps | 0.208 | 0.000 | 0.208 | |
| swapAltExp | 0.276 | 0.000 | 0.276 | |