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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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

Package 1052/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iSEE 2.18.0  (landing page)
Kevin Rue-Albrecht
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/iSEE
git_branch: RELEASE_3_20
git_last_commit: 28d19ac
git_last_commit_date: 2024-10-29 10:26:27 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for iSEE on merida1

To the developers/maintainers of the iSEE package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: iSEE
Version: 2.18.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iSEE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iSEE_2.18.0.tar.gz
StartedAt: 2024-12-20 04:58:31 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 05:09:55 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 683.8 seconds
RetCode: 0
Status:   OK  
CheckDir: iSEE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iSEE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iSEE_2.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/iSEE.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iSEE/DESCRIPTION’ ... OK
* this is package ‘iSEE’ version ‘2.18.0’
* 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 code 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 whether startup messages can be suppressed ... 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 18.161  1.677  22.390
iSEE                       11.328  0.711  13.466
synchronizeAssays           8.942  0.862  11.093
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-bioc/meat/iSEE.Rcheck/00check.log’
for details.


Installation output

iSEE.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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, aperm, 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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

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
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 6 | SKIP 2 | PASS 1481 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_zzz.R:3:1'
• waiting for a fix to the SCE itself (1): 'test_clean.R:100:5'

[ FAIL 0 | WARN 6 | SKIP 2 | PASS 1481 ]
> 
> proc.time()
   user  system elapsed 
125.649   5.709 138.904 

Example timings

iSEE.Rcheck/iSEE-Ex.timings

nameusersystemelapsed
ColumnDataPlot-class3.6670.1103.941
ColumnDataTable-class0.7270.0860.856
ComplexHeatmapPlot-class1.1390.0391.280
ExperimentColorMap-class0.0310.0070.039
FeatureAssayPlot-class1.9000.0392.025
ReducedDimensionPlot-class1.5450.0351.650
RowDataPlot-class1.0150.0601.151
RowDataTable-class0.6600.0100.708
SampleAssayPlot-class1.0700.0251.185
aes-utils0.0000.0010.003
cache-utils0.1060.0020.110
checkColormapCompatibility18.161 1.67722.390
class-utils0.0050.0010.006
cleanDataset0.1270.0020.144
collapseBox0.0570.0020.064
createCustomPanels0.1630.0080.186
createLandingPage0.2710.0150.320
defaultTour0.0150.0040.020
filterDTColumn0.0060.0030.011
getPanelColor0.2410.0030.269
hidden-inputs0.0520.0010.061
iSEE11.328 0.71113.466
iSEEOptions0.0000.0000.001
jitterPoints0.1310.0240.185
labs-utils0.0000.0010.001
lassoPoints0.0110.0010.014
manage_commands0.0010.0010.001
multiSelectionToFactor0.0020.0010.002
panelDefaults0.0010.0010.003
plot-utils0.0250.0010.029
registerAppOptions0.0110.0020.017
selectionColorMap0.0040.0010.005
setCachedCommonInfo0.0090.0010.011
subsetPointsByGrid1.0110.0291.194
synchronizeAssays 8.942 0.86211.093