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 12:28:42 -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: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SingleCellExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings SingleCellExperiment_1.8.0.tar.gz |
| StartedAt: 2020-04-15 06:41:51 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:45:54 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 242.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SingleCellExperiment.Rcheck |
| Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SingleCellExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings SingleCellExperiment_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/SingleCellExperiment.Rcheck' * using R version 3.6.3 (2020-02-29) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * 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 whether package 'SingleCellExperiment' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp4EI3U0/R.INSTALL3ec451b6de/SingleCellExperiment/man/combine.Rd:27: file link 'rbind' in package 'base' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/SingleCellExperiment.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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... ** running examples for arch 'i386' ... 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. ** running examples for arch 'x64' ... 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 tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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: 3 WARNINGs, 1 NOTE See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/SingleCellExperiment.Rcheck/00check.log' for details.
SingleCellExperiment.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/SingleCellExperiment_1.8.0.tar.gz && rm -rf SingleCellExperiment.buildbin-libdir && mkdir SingleCellExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SingleCellExperiment.buildbin-libdir SingleCellExperiment_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL SingleCellExperiment_1.8.0.zip && rm SingleCellExperiment_1.8.0.tar.gz SingleCellExperiment_1.8.0.zip
###
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install for i386
* installing *source* package 'SingleCellExperiment' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SingleCellExperiment'
finding HTML links ... done
LEM-combine html
LEM-getset html
LEM-misc html
LEM-subset html
LinearEmbeddingMatrix html
SCE-isSpike html
SCE-sizeFactors html
SingleCellExperiment html
finding level-2 HTML links ... done
altExps html
assays html
combine html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp4EI3U0/R.INSTALL3ec451b6de/SingleCellExperiment/man/combine.Rd:27: file link 'rbind' in package 'base' does not exist and so has been treated as a topic
internals html
miscellaneous html
reducedDims html
splitAltExps html
swapAltExp html
updateObject html
** 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
install for x64
* installing *source* package 'SingleCellExperiment' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SingleCellExperiment' as SingleCellExperiment_1.8.0.zip
* DONE (SingleCellExperiment)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'SingleCellExperiment' successfully unpacked and MD5 sums checked
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SingleCellExperiment.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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
17.67 0.73 18.37
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SingleCellExperiment.Rcheck/tests_x64/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-w64-mingw32/x64 (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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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
25.20 0.53 25.71
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SingleCellExperiment.Rcheck/examples_i386/SingleCellExperiment-Ex.timings
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SingleCellExperiment.Rcheck/examples_x64/SingleCellExperiment-Ex.timings
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