Charlotte Soneson
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/iSEE |
| Branch: RELEASE_3_11 |
| Last Commit: 0d82c2a |
| Last Changed Date: 2020-04-27 15:14:42 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:54:59 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE iSEE PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 895/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| iSEE 2.0.0 Charlotte Soneson
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: iSEE |
| Version: 2.0.0 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:iSEE.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings iSEE_2.0.0.tar.gz |
| StartedAt: 2020-10-17 02:28:09 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 02:33:47 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 337.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: iSEE.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:iSEE.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings iSEE_2.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/iSEE.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘2.0.0’
* 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 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 ... WARNING
Found the following significant warnings:
Warning: 'redDimPlotDefaults' is deprecated.
Warning: 'featAssayPlotDefaults' is deprecated.
Warning: 'colDataPlotDefaults' is deprecated.
Warning: 'rowStatTableDefaults' is deprecated.
Warning: 'colStatTableDefaults' is deprecated.
Warning: 'rowDataPlotDefaults' is deprecated.
Warning: 'sampAssayPlotDefaults' is deprecated.
Warning: 'heatMapPlotDefaults' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
iSEE 14.170 0.448 15.061
checkColormapCompatibility 12.189 0.244 13.087
synchronizeAssays 11.519 0.348 12.315
* 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 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.11-bioc/meat/iSEE.Rcheck/00check.log’
for details.
iSEE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL iSEE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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: 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
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
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
Loading required package: SingleCellExperiment
>
> test_check("iSEE")
Loading required package: scRNAseq
Loading required package: scater
Loading required package: ggplot2
snapshotDate(): 2020-04-27
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)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 1094 | SKIPPED: 4 | WARNINGS: 28 | FAILED: 0 ]
>
> proc.time()
user system elapsed
89.122 1.292 91.020
iSEE.Rcheck/iSEE-Ex.timings
| name | user | system | elapsed | |
| ColumnDataPlot-class | 2.505 | 0.032 | 2.673 | |
| ColumnDataTable-class | 0.539 | 0.004 | 0.543 | |
| ComplexHeatmapPlot-class | 1.43 | 0.02 | 1.45 | |
| ExperimentColorMap-class | 0.032 | 0.000 | 0.032 | |
| FeatureAssayPlot-class | 0.733 | 0.020 | 0.753 | |
| ReducedDimensionPlot-class | 1.138 | 0.008 | 1.147 | |
| RowDataPlot-class | 0.503 | 0.000 | 0.503 | |
| RowDataTable-class | 0.27 | 0.00 | 0.27 | |
| SampleAssayPlot-class | 0.436 | 0.000 | 0.436 | |
| aes-utils | 0 | 0 | 0 | |
| checkColormapCompatibility | 12.189 | 0.244 | 13.087 | |
| class-utils | 0.002 | 0.000 | 0.002 | |
| collapseBox | 0.026 | 0.000 | 0.027 | |
| createCustomPanels | 0.062 | 0.004 | 0.066 | |
| createLandingPage | 0.121 | 0.000 | 0.134 | |
| dataframe-utils | 0.048 | 0.000 | 0.048 | |
| defaults | 1.430 | 0.103 | 1.548 | |
| filterDTColumn | 0.003 | 0.000 | 0.004 | |
| getPanelColor | 0.009 | 0.000 | 0.008 | |
| iSEE | 14.170 | 0.448 | 15.061 | |
| iSEEOptions | 0 | 0 | 0 | |
| jitterPoints | 0.103 | 0.000 | 0.103 | |
| labs-utils | 0.001 | 0.000 | 0.000 | |
| lassoPoints | 0.009 | 0.000 | 0.010 | |
| manage_commands | 0.001 | 0.000 | 0.000 | |
| plot-utils | 0.012 | 0.000 | 0.012 | |
| setCachedCommonInfo | 0.007 | 0.000 | 0.008 | |
| subsetPointsByGrid | 0.886 | 0.008 | 0.894 | |
| synchronizeAssays | 11.519 | 0.348 | 12.315 | |