| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:04 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the ExperimentSubset package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ExperimentSubset.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 608/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ExperimentSubset 1.2.0 (landing page) Irzam Sarfraz
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ExperimentSubset |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ExperimentSubset.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ExperimentSubset_1.2.0.tar.gz |
| StartedAt: 2021-10-14 23:00:08 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 23:08:28 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 500.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ExperimentSubset.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ExperimentSubset.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ExperimentSubset_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ExperimentSubset.Rcheck' * using R version 4.1.1 (2021-08-10) * 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 '1.2.0' * 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:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ExperimentSubset_1.2.0.tar.gz && rm -rf ExperimentSubset.buildbin-libdir && mkdir ExperimentSubset.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ExperimentSubset.buildbin-libdir ExperimentSubset_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ExperimentSubset_1.2.0.zip && rm ExperimentSubset_1.2.0.tar.gz ExperimentSubset_1.2.0.zip
###
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install for i386
* installing *source* package 'ExperimentSubset' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in makePrototypeFromClassDef(properties, ClassDef, immediate, where) :
in constructing the prototype for class "SubsetSummarizedExperiment", slots in prototype and not in class: listData, elementType
Warning in makePrototypeFromClassDef(properties, ClassDef, immediate, where) :
in constructing the prototype for class "SubsetRangedSummarizedExperiment", slots in prototype and not in class: listData, elementType
Warning in makePrototypeFromClassDef(properties, ClassDef, immediate, where) :
in constructing the prototype for class "SubsetSingleCellExperiment", slots in prototype and not in class: listData, elementType
Warning in makePrototypeFromClassDef(properties, ClassDef, immediate, where) :
in constructing the prototype for class "SubsetTreeSummarizedExperiment", slots in prototype and not in class: listData, elementType
Warning in makePrototypeFromClassDef(properties, ClassDef, immediate, where) :
in constructing the prototype for class "SubsetSpatialExperiment", slots in prototype and not in class: listData, elementType
** help
*** installing help indices
converting help for package 'ExperimentSubset'
finding HTML links ... done
AssaySubset-class html
AssaySubset html
ExperimentSubset html
SubsetRangedSummarizedExperiment-class
html
SubsetSingleCellExperiment-class html
SubsetSpatialExperiment-class html
SubsetSummarizedExperiment-class html
SubsetTreeSummarizedExperiment-class html
createSubset html
getSubsetAssay html
reducedDimNames-set html
reducedDimNames html
reducedDims-set-ANY-method html
reducedDims-set html
setSubsetAssay html
subsetAssayCount html
subsetAssayNames html
subsetColData html
subsetColLinks html
subsetColnames html
subsetCount html
subsetDim html
subsetNames html
subsetParent html
subsetRowData html
subsetRowLinks html
subsetRownames html
subsetSpatialCoords html
subsetSpatialData 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_1.2.0.zip
* DONE (ExperimentSubset)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ExperimentSubset' successfully unpacked and MD5 sums checked
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ExperimentSubset.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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 objects are masked from 'package:base':
I, expand.grid, unname
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
Loading required package: SpatialExperiment
Loading required package: TreeSummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'ExperimentSubset'
The following objects are masked from 'package:SingleCellExperiment':
reducedDimNames, reducedDimNames<-, reducedDims<-
>
> test_check("ExperimentSubset")
class: SubsetSummarizedExperiment
dim: 2000 2000
metadata(0):
assays(2): counts logcounts
rownames(2000): C12orf73 RNU6-1256P ... FOXF1 PRR3
rowData names(0):
colnames(2000): CTGCTGTCAGGGTATG CAGTCCTTCGGTTAAC ... GATGCTATCAGCAACT
ATTTCTGGTGATGATA
colData names(0):
subsets(1): s1
subsetAssays(1): s1Main assay(s):
counts logcounts assay2
Subset(s):
Name Dim Parent Assays
1 s1 10, 2000 counts newS1
Main assay(s):
counts
Subset(s):
NULL
class: SubsetRangedSummarizedExperiment
dim: 64102 8
metadata(1): ''
assays(1): counts
rownames(64102): ENSG00000000003 ENSG00000000005 ... LRG_98 LRG_99
rowData names(0):
colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521
colData names(9): SampleName cell ... Sample BioSample
subsets(1): s2
subsetAssays(1): s2Main assay(s):
counts assay2
Subset(s):
Name Dim Parent Assays
1 s2 15, 8 counts newS2
Main assay(s):
counts logcounts
Subset(s):
Name Dim Parent Assays
1 subset1 10, 10 counts scaledSubset1
class: SubsetSingleCellExperiment
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):
mainExpName: NULL
altExpNames(0):
subsets(1): subset1
subsetAssays(2): subset1 scaledSubset1[ FAIL 0 | WARN 0 | SKIP 0 | PASS 127 ]
>
> proc.time()
user system elapsed
84.85 6.20 93.25
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ExperimentSubset.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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 objects are masked from 'package:base':
I, expand.grid, unname
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
Loading required package: SpatialExperiment
Loading required package: TreeSummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'ExperimentSubset'
The following objects are masked from 'package:SingleCellExperiment':
reducedDimNames, reducedDimNames<-, reducedDims<-
>
> test_check("ExperimentSubset")
class: SubsetSummarizedExperiment
dim: 2000 2000
metadata(0):
assays(2): counts logcounts
rownames(2000): C12orf73 RNU6-1256P ... FOXF1 PRR3
rowData names(0):
colnames(2000): CTGCTGTCAGGGTATG CAGTCCTTCGGTTAAC ... GATGCTATCAGCAACT
ATTTCTGGTGATGATA
colData names(0):
subsets(1): s1
subsetAssays(1): s1Main assay(s):
counts logcounts assay2
Subset(s):
Name Dim Parent Assays
1 s1 10, 2000 counts newS1
Main assay(s):
counts
Subset(s):
NULL
class: SubsetRangedSummarizedExperiment
dim: 64102 8
metadata(1): ''
assays(1): counts
rownames(64102): ENSG00000000003 ENSG00000000005 ... LRG_98 LRG_99
rowData names(0):
colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521
colData names(9): SampleName cell ... Sample BioSample
subsets(1): s2
subsetAssays(1): s2Main assay(s):
counts assay2
Subset(s):
Name Dim Parent Assays
1 s2 15, 8 counts newS2
Main assay(s):
counts logcounts
Subset(s):
Name Dim Parent Assays
1 subset1 10, 10 counts scaledSubset1
class: SubsetSingleCellExperiment
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):
mainExpName: NULL
altExpNames(0):
subsets(1): subset1
subsetAssays(2): subset1 scaledSubset1[ FAIL 0 | WARN 0 | SKIP 0 | PASS 127 ]
>
> proc.time()
user system elapsed
97.45 5.14 104.37
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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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