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CHECK report for iSEE on merida1

This page was generated on 2021-05-06 12:35:24 -0400 (Thu, 06 May 2021).

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 914/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iSEE 2.2.4  (landing page)
Kevin Rue-Albrecht
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/iSEE
Branch: RELEASE_3_12
Last Commit: b5d95ef
Last Changed Date: 2021-02-01 06:00:45 -0400 (Mon, 01 Feb 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: iSEE
Version: 2.2.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:iSEE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings iSEE_2.2.4.tar.gz
StartedAt: 2021-05-06 02:56:52 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:04:05 -0400 (Thu, 06 May 2021)
EllapsedTime: 432.9 seconds
RetCode: 0
Status:   OK  
CheckDir: iSEE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:iSEE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings iSEE_2.2.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/iSEE.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iSEE/DESCRIPTION’ ... OK
* this is package ‘iSEE’ version ‘2.2.4’
* 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 19.429  1.185  23.091
iSEE                       14.331  0.279  15.315
synchronizeAssays          13.889  0.196  14.641
* 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
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/iSEE.Rcheck/00check.log’
for details.



Installation output

iSEE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL iSEE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 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")'.


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: ggplot2
snapshotDate(): 2020-10-27
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)
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (2)

[ FAIL 0 | WARN 9 | SKIP 2 | PASS 1135 ]
> 
> proc.time()
   user  system elapsed 
117.594   2.545 123.302 

Example timings

iSEE.Rcheck/iSEE-Ex.timings

nameusersystemelapsed
ColumnDataPlot-class2.7430.0702.833
ColumnDataTable-class0.4770.0110.490
ComplexHeatmapPlot-class0.8410.0440.889
ExperimentColorMap-class0.0290.0030.033
FeatureAssayPlot-class0.8060.0140.851
ReducedDimensionPlot-class1.7200.0151.738
RowDataPlot-class0.7860.0440.830
RowDataTable-class0.4610.0380.499
SampleAssayPlot-class0.7650.0190.784
aes-utils0.0000.0010.000
cache-utils0.0520.0010.053
checkColormapCompatibility19.429 1.18523.091
class-utils0.0030.0010.003
collapseBox0.0430.0010.044
createCustomPanels0.0990.0030.102
createLandingPage0.1140.0040.120
defaultTour0.0230.0030.025
filterDTColumn0.0030.0010.004
getPanelColor0.0110.0000.011
iSEE14.331 0.27915.315
iSEEOptions0.0010.0000.001
jitterPoints0.0700.0110.081
labs-utils0.0010.0000.001
lassoPoints0.0060.0010.007
manage_commands000
plot-utils0.0080.0000.009
setCachedCommonInfo0.0060.0010.006
subsetPointsByGrid0.5940.0120.607
synchronizeAssays13.889 0.19614.641