Kevin Rue-Albrecht
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/iSEE |
| git_branch: master |
| git_last_commit: c6bb93a |
| git_last_commit_date: 2021-10-26 12:42:43 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:50 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the iSEE package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iSEE.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 960/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| iSEE 2.7.0 (landing page) Kevin Rue-Albrecht
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: iSEE |
| Version: 2.7.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:iSEE.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings iSEE_2.7.0.tar.gz |
| StartedAt: 2022-03-17 19:23:40 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:28:07 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 266.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: iSEE.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:iSEE.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings iSEE_2.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/iSEE.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'iSEE/DESCRIPTION' ... OK
* this is package 'iSEE' version '2.7.0'
* 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 'iSEE' 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 object imported by a ':::' call: 'S4Vectors:::selectSome'
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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
checkColormapCompatibility 10.71 1.76 13.91
iSEE 9.11 0.77 10.86
synchronizeAssays 8.69 0.73 10.47
* 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 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/iSEE.Rcheck/00check.log'
for details.
iSEE.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL iSEE
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'iSEE' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'iSEE'
finding HTML links ... done
ColumnDataPlot-class html
finding level-2 HTML links ... done
ColumnDataTable-class html
ColumnDotPlot-class html
ColumnTable-class html
ComplexHeatmapPlot-class html
DotPlot-class html
ExperimentColorMap-class html
FeatureAssayPlot-class html
Panel-class html
ReducedDimensionPlot-class html
RowDataPlot-class html
RowDataTable-class html
RowDotPlot-class html
RowTable-class html
SampleAssayPlot-class html
Table-class html
addCustomLabelsCommands html
addLabelCentersCommands html
addMultiSelectionCommands html
addTourStep html
aes-utils html
cache-utils html
checkColormapCompatibility html
class-utils html
cleanDataset html
collapseBox html
conditional-utils html
createCustomDimnamesModalObservers html
createCustomPanels html
createLandingPage html
createProtectedParameterObservers html
defaultTour html
documentation-generics html
extractAssaySubmatrix html
filterDTColumn html
getEncodedName html
getPanelColor html
iSEE-pkg html
iSEE html
iSEEOptions html
interface-generics html
interface-wrappers html
jitterPoints html
labs-utils html
lassoPoints html
manage_commands html
metadata-plot-generics html
multi-select-generics html
multiSelectionToFactor html
observer-generics html
output-generics html
panelDefaults html
plot-generics html
plot-utils html
processMultiSelections html
registerAppOptions html
replaceMissingWithFirst html
requestUpdate html
retrieveOutput html
selectionColorMap html
setCachedCommonInfo html
setup-generics html
single-select-generics html
specific-tours html
subsetPointsByGrid html
synchronizeAssays html
table-generics html
track-utils html
validate-utils html
visual-parameters-generics 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
* DONE (iSEE)
Making 'packages.html' ... done
iSEE.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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(iSEE)
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
Attaching package: 'BiocGenerics'
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
>
> test_check("iSEE")
Loading required package: scRNAseq
Loading required package: scater
Loading required package: scuttle
Loading required package: ggplot2
snapshotDate(): 2022-03-16
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
Warning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, :
You're computing too large a percentage of total singular values, use a standard svd instead.
Class: ExperimentColorMap
assays(5): counts tophat_counts cufflinks_fpkm cufflinks_fpkm rsem_tpm
colData(1): passes_qc_checks_s
rowData(0):
all_discrete(0):
all_continuous(0):
global_discrete(1)
global_continuous(1)
[ FAIL 0 | WARN 4 | SKIP 2 | PASS 1453 ]
== Skipped tests ===============================================================
* empty test (1)
* waiting for a fix to the SCE itself (1)
[ FAIL 0 | WARN 4 | SKIP 2 | PASS 1453 ]
>
> proc.time()
user system elapsed
42.96 3.17 47.53
iSEE.Rcheck/iSEE-Ex.timings
| name | user | system | elapsed | |
| ColumnDataPlot-class | 2.56 | 0.07 | 2.71 | |
| ColumnDataTable-class | 0.57 | 0.03 | 0.61 | |
| ComplexHeatmapPlot-class | 0.91 | 0.02 | 0.92 | |
| ExperimentColorMap-class | 0.01 | 0.01 | 0.04 | |
| FeatureAssayPlot-class | 1.25 | 0.05 | 1.29 | |
| ReducedDimensionPlot-class | 0.96 | 0.03 | 0.99 | |
| RowDataPlot-class | 1.29 | 0.10 | 1.45 | |
| RowDataTable-class | 0.41 | 0.03 | 0.44 | |
| SampleAssayPlot-class | 0.87 | 0.00 | 0.87 | |
| aes-utils | 0 | 0 | 0 | |
| cache-utils | 0.07 | 0.00 | 0.06 | |
| checkColormapCompatibility | 10.71 | 1.76 | 13.91 | |
| class-utils | 0 | 0 | 0 | |
| cleanDataset | 0.05 | 0.00 | 0.05 | |
| collapseBox | 0.02 | 0.00 | 0.01 | |
| createCustomPanels | 0.06 | 0.02 | 0.08 | |
| createLandingPage | 0.08 | 0.03 | 0.11 | |
| defaultTour | 0 | 0 | 0 | |
| filterDTColumn | 0 | 0 | 0 | |
| getPanelColor | 0.14 | 0.00 | 0.14 | |
| iSEE | 9.11 | 0.77 | 10.86 | |
| iSEEOptions | 0 | 0 | 0 | |
| jitterPoints | 0.06 | 0.01 | 0.08 | |
| labs-utils | 0 | 0 | 0 | |
| lassoPoints | 0.02 | 0.00 | 0.01 | |
| manage_commands | 0 | 0 | 0 | |
| multiSelectionToFactor | 0 | 0 | 0 | |
| panelDefaults | 0 | 0 | 0 | |
| plot-utils | 0.01 | 0.00 | 0.02 | |
| registerAppOptions | 0 | 0 | 0 | |
| selectionColorMap | 0 | 0 | 0 | |
| setCachedCommonInfo | 0 | 0 | 0 | |
| subsetPointsByGrid | 0.42 | 0.02 | 0.43 | |
| synchronizeAssays | 8.69 | 0.73 | 10.47 | |