Irzam Sarfraz
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/ExperimentSubset |
| Branch: RELEASE_3_12 |
| Last Commit: ae54a23 |
| Last Changed Date: 2020-10-27 12:02:48 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:31:04 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the ExperimentSubset package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 580/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ExperimentSubset 1.0.0 (landing page) Irzam Sarfraz
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ExperimentSubset |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ExperimentSubset.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ExperimentSubset_1.0.0.tar.gz |
| StartedAt: 2021-05-06 02:42:52 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 02:53:17 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 624.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ExperimentSubset.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ExperimentSubset.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ExperimentSubset_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ExperimentSubset.Rcheck' * using R version 4.0.5 (2021-03-31) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ExperimentSubset/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ExperimentSubset' version '1.0.0' * 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 ... OK * checking for portable file names ... OK * checking whether package 'ExperimentSubset' 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 * 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 ... 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * 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: OK
ExperimentSubset.Rcheck/00install.out
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### Running command:
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### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/ExperimentSubset_1.0.0.tar.gz && rm -rf ExperimentSubset.buildbin-libdir && mkdir ExperimentSubset.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ExperimentSubset.buildbin-libdir ExperimentSubset_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ExperimentSubset_1.0.0.zip && rm ExperimentSubset_1.0.0.tar.gz ExperimentSubset_1.0.0.zip
###
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install for i386
* installing *source* package 'ExperimentSubset' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'rownames' in package 'ExperimentSubset'
Creating a new generic function for 'rownames<-' in package 'ExperimentSubset'
Creating a new generic function for 'colnames' in package 'ExperimentSubset'
Creating a new generic function for 'colnames<-' in package 'ExperimentSubset'
** help
*** installing help indices
converting help for package 'ExperimentSubset'
finding HTML links ... done
AssaySubset-class html
AssaySubset html
ExperimentSubset-class html
ExperimentSubset html
altExp-set html
altExp html
altExpNames-set html
altExpNames html
altExps-set html
altExps html
assay-ExperimentSubset-character-method
html
assay-set-ExperimentSubset-character-method
html
colData-ExperimentSubset-method html
colData-set-ExperimentSubset-DataFrame-method
html
colnames-set html
colnames html
createSubset html
dim-ExperimentSubset-method html
metadata-set-ANY-method html
metadata-set html
metadata html
reducedDim-set-ANY-method html
reducedDim-set html
reducedDim html
reducedDimNames-set html
reducedDimNames html
reducedDims-set-ANY-method html
reducedDims-set html
reducedDims html
rowData-ExperimentSubset-method html
rowData-set-ExperimentSubset-method html
rownames-set html
rownames html
show html
storeSubset html
subsetAssayCount html
subsetAssayNames html
subsetColData html
subsetCount html
subsetDim html
subsetNames html
subsetParent html
subsetRowData html
subsetSummary 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 'ExperimentSubset' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ExperimentSubset' as ExperimentSubset_1.0.0.zip
* DONE (ExperimentSubset)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ExperimentSubset' successfully unpacked and MD5 sums checked
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ExperimentSubset.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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(ExperimentSubset)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
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.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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: SingleCellExperiment
Attaching package: 'ExperimentSubset'
The following objects are masked from 'package:SingleCellExperiment':
altExp, altExp<-, altExpNames, altExpNames<-, altExps, altExps<-,
reducedDim, reducedDim<-, reducedDimNames, reducedDimNames<-,
reducedDims, reducedDims<-
The following object is masked from 'package:SummarizedExperiment':
metadata<-
The following objects are masked from 'package:IRanges':
colnames, colnames<-, rownames, rownames<-
The following objects are masked from 'package:S4Vectors':
colnames, colnames<-, metadata, metadata<-, rownames, rownames<-
The following objects are masked from 'package:BiocGenerics':
colnames, colnames<-, rownames, rownames<-
The following objects are masked from 'package:base':
colnames, colnames<-, rownames, rownames<-
>
> test_check("ExperimentSubset")
Main assay(s):
counts logcounts
Subset(s):
Name Dim Parent Assays
1 subset1 10, 10 counts scaledSubset1
class: ExperimentSubset
root class: SingleCellExperiment
dim: 2000 2000
metadata(0):
assays(2): counts logcounts
rownames(2000): C12orf73 RNU6-1256P ... FOXF1 PRR3
rowData names(1): gene
colnames(2000): CTGCTGTCAGGGTATG CAGTCCTTCGGTTAAC ... GATGCTATCAGCAACT
ATTTCTGGTGATGATA
colData names(11): nGene nUMI ... ident doublet_true_labels
reducedDimNames(0):
altExpNames(0):
subsets(1): subset1
subsetAssays(2): subset1 scaledSubset1[ FAIL 0 | WARN 0 | SKIP 0 | PASS 87 ]
>
> proc.time()
user system elapsed
173.75 13.12 209.98
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ExperimentSubset.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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(ExperimentSubset)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
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.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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: SingleCellExperiment
Attaching package: 'ExperimentSubset'
The following objects are masked from 'package:SingleCellExperiment':
altExp, altExp<-, altExpNames, altExpNames<-, altExps, altExps<-,
reducedDim, reducedDim<-, reducedDimNames, reducedDimNames<-,
reducedDims, reducedDims<-
The following object is masked from 'package:SummarizedExperiment':
metadata<-
The following objects are masked from 'package:IRanges':
colnames, colnames<-, rownames, rownames<-
The following objects are masked from 'package:S4Vectors':
colnames, colnames<-, metadata, metadata<-, rownames, rownames<-
The following objects are masked from 'package:BiocGenerics':
colnames, colnames<-, rownames, rownames<-
The following objects are masked from 'package:base':
colnames, colnames<-, rownames, rownames<-
>
> test_check("ExperimentSubset")
Main assay(s):
counts logcounts
Subset(s):
Name Dim Parent Assays
1 subset1 10, 10 counts scaledSubset1
class: ExperimentSubset
root class: SingleCellExperiment
dim: 2000 2000
metadata(0):
assays(2): counts logcounts
rownames(2000): C12orf73 RNU6-1256P ... FOXF1 PRR3
rowData names(1): gene
colnames(2000): CTGCTGTCAGGGTATG CAGTCCTTCGGTTAAC ... GATGCTATCAGCAACT
ATTTCTGGTGATGATA
colData names(11): nGene nUMI ... ident doublet_true_labels
reducedDimNames(0):
altExpNames(0):
subsets(1): subset1
subsetAssays(2): subset1 scaledSubset1[ FAIL 0 | WARN 0 | SKIP 0 | PASS 87 ]
>
> proc.time()
user system elapsed
163.17 9.89 174.03
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ExperimentSubset.Rcheck/examples_i386/ExperimentSubset-Ex.timings
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ExperimentSubset.Rcheck/examples_x64/ExperimentSubset-Ex.timings
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