Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:30 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for iSEE on nebbiolo2


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 957/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iSEE 2.6.0  (landing page)
Kevin Rue-Albrecht
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/iSEE
git_branch: RELEASE_3_14
git_last_commit: 9c0e8e0
git_last_commit_date: 2021-10-26 12:42:43 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: iSEE
Version: 2.6.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:iSEE.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings iSEE_2.6.0.tar.gz
StartedAt: 2022-04-12 07:55:12 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 08:00:33 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 321.4 seconds
RetCode: 0
Status:   OK  
CheckDir: iSEE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:iSEE.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings iSEE_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/iSEE.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘2.6.0’
* 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 18.470  1.231  20.436
iSEE                       13.675  1.316  15.545
synchronizeAssays          12.578  1.432  14.545
* 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-3.14-bioc/meat/iSEE.Rcheck/00check.log’
for details.



Installation output

iSEE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL iSEE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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)

Tests output

iSEE.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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

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
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(): 2021-10-19
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 
 82.694   2.181  85.692 

Example timings

iSEE.Rcheck/iSEE-Ex.timings

nameusersystemelapsed
ColumnDataPlot-class2.6060.0602.665
ColumnDataTable-class0.6650.0560.721
ComplexHeatmapPlot-class1.0510.0401.091
ExperimentColorMap-class0.0170.0000.017
FeatureAssayPlot-class0.9790.0040.982
ReducedDimensionPlot-class1.4610.0001.461
RowDataPlot-class0.9870.0040.991
RowDataTable-class0.6690.0000.668
SampleAssayPlot-class0.9760.0000.977
aes-utils0.0000.0000.001
cache-utils0.0370.0000.037
checkColormapCompatibility18.470 1.23120.436
class-utils0.0020.0000.002
cleanDataset0.0920.0000.093
collapseBox0.0230.0080.031
createCustomPanels0.0710.0000.071
createLandingPage0.1100.0080.119
defaultTour0.0060.0000.006
filterDTColumn0.0020.0000.003
getPanelColor0.2560.0040.261
iSEE13.675 1.31615.545
iSEEOptions0.0010.0000.000
jitterPoints0.0580.0000.058
labs-utils0.0000.0000.001
lassoPoints0.0040.0000.005
manage_commands0.0010.0000.000
multiSelectionToFactor0.0010.0000.001
panelDefaults0.0010.0000.000
plot-utils0.010.000.01
registerAppOptions0.0110.0000.011
selectionColorMap0.0020.0000.002
setCachedCommonInfo0.0080.0000.009
subsetPointsByGrid0.4950.0520.548
synchronizeAssays12.578 1.43214.545