Kevin Rue-Albrecht
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/iSEE |
| git_branch: RELEASE_3_13 |
| git_last_commit: 5c9f140 |
| git_last_commit_date: 2021-05-19 12:34:05 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:43 -0400 (Fri, 15 Oct 2021).
|
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 945/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| iSEE 2.4.0 (landing page) Kevin Rue-Albrecht
| 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: iSEE |
| Version: 2.4.0 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:iSEE.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings iSEE_2.4.0.tar.gz |
| StartedAt: 2021-10-14 10:18:50 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 10:24:33 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 343.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: iSEE.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:iSEE.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings iSEE_2.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/iSEE.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iSEE/DESCRIPTION’ ... OK
* this is package ‘iSEE’ version ‘2.4.0’
* 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 for sufficient/correct file permissions ... 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 17.674 0.896 19.369
iSEE 13.057 0.588 14.305
synchronizeAssays 11.070 0.428 12.157
* 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
‘/home/biocbuild/bbs-3.13-bioc/meat/iSEE.Rcheck/00check.log’
for details.
iSEE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL iSEE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘iSEE’ ... ** 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 (iSEE)
iSEE.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(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
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
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(): 2021-05-18
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
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)
══ 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
101.309 2.739 105.012
iSEE.Rcheck/iSEE-Ex.timings
| name | user | system | elapsed | |
| ColumnDataPlot-class | 2.769 | 0.215 | 2.986 | |
| ColumnDataTable-class | 0.799 | 0.004 | 0.803 | |
| ComplexHeatmapPlot-class | 1.215 | 0.195 | 1.411 | |
| ExperimentColorMap-class | 0.025 | 0.004 | 0.030 | |
| FeatureAssayPlot-class | 1.194 | 0.040 | 1.234 | |
| ReducedDimensionPlot-class | 2.187 | 0.448 | 2.635 | |
| RowDataPlot-class | 0.917 | 0.008 | 0.924 | |
| RowDataTable-class | 0.797 | 0.016 | 0.814 | |
| SampleAssayPlot-class | 0.973 | 0.004 | 0.976 | |
| aes-utils | 0.000 | 0.000 | 0.001 | |
| cache-utils | 0.024 | 0.006 | 0.032 | |
| checkColormapCompatibility | 17.674 | 0.896 | 19.369 | |
| class-utils | 0.002 | 0.000 | 0.002 | |
| cleanDataset | 0.093 | 0.003 | 0.096 | |
| collapseBox | 0.029 | 0.004 | 0.033 | |
| createCustomPanels | 0.089 | 0.003 | 0.093 | |
| createLandingPage | 0.136 | 0.005 | 0.141 | |
| defaultTour | 0.007 | 0.002 | 0.009 | |
| filterDTColumn | 0.000 | 0.004 | 0.004 | |
| getPanelColor | 0.287 | 0.020 | 0.307 | |
| iSEE | 13.057 | 0.588 | 14.305 | |
| iSEEOptions | 0 | 0 | 0 | |
| jitterPoints | 0.053 | 0.012 | 0.064 | |
| labs-utils | 0.000 | 0.000 | 0.001 | |
| lassoPoints | 0.004 | 0.002 | 0.006 | |
| manage_commands | 0.000 | 0.001 | 0.001 | |
| multiSelectionToFactor | 0.000 | 0.001 | 0.002 | |
| panelDefaults | 0.001 | 0.000 | 0.001 | |
| plot-utils | 0.01 | 0.00 | 0.01 | |
| registerAppOptions | 0.004 | 0.004 | 0.008 | |
| selectionColorMap | 0.002 | 0.000 | 0.001 | |
| setCachedCommonInfo | 0.006 | 0.000 | 0.007 | |
| subsetPointsByGrid | 0.437 | 0.004 | 0.440 | |
| synchronizeAssays | 11.070 | 0.428 | 12.157 | |