Kevin Rue-Albrecht
| Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024) |
| git_url: https://git.bioconductor.org/packages/iSEE |
| git_branch: RELEASE_3_19 |
| git_last_commit: ef6667f |
| git_last_commit_date: 2024-04-30 11:04:45 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:36 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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 1062/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| iSEE 2.16.0 (landing page) Kevin Rue-Albrecht
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the iSEE package: - 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. |
| Package: iSEE |
| Version: 2.16.0 |
| 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_2.16.0.tar.gz |
| StartedAt: 2024-05-06 22:27:42 -0400 (Mon, 06 May 2024) |
| EndedAt: 2024-05-06 22:29:41 -0400 (Mon, 06 May 2024) |
| EllapsedTime: 119.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: iSEE.Rcheck |
| Warnings: 0 |
##############################################################################
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### 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_2.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/iSEE.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iSEE/DESCRIPTION’ ... OK
* this is package ‘iSEE’ version ‘2.16.0’
* 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 ... NOTE
License stub is invalid DCF.
* 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 ... NOTE
checkRd: (-1) registerAppOptions.Rd:46-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) registerAppOptions.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) registerAppOptions.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) registerAppOptions.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) registerAppOptions.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) registerAppOptions.Rd:57: Lost braces in \itemize; meant \describe ?
* 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 4.785 0.257 5.078
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/iSEE.Rcheck/00check.log’
for details.
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-arm64/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)
iSEE.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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':
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, 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':
expand.grid, I, 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 5 | SKIP 2 | PASS 1479 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_zzz.R:3:1'
• waiting for a fix to the SCE itself (1): 'test_clean.R:85:5'
[ FAIL 0 | WARN 5 | SKIP 2 | PASS 1479 ]
>
> proc.time()
user system elapsed
21.538 0.984 23.163
iSEE.Rcheck/iSEE-Ex.timings
| name | user | system | elapsed | |
| ColumnDataPlot-class | 0.934 | 0.026 | 0.959 | |
| ColumnDataTable-class | 0.161 | 0.002 | 0.163 | |
| ComplexHeatmapPlot-class | 0.255 | 0.006 | 0.261 | |
| ExperimentColorMap-class | 0.007 | 0.001 | 0.008 | |
| FeatureAssayPlot-class | 0.227 | 0.006 | 0.233 | |
| ReducedDimensionPlot-class | 0.666 | 0.006 | 0.673 | |
| RowDataPlot-class | 0.203 | 0.004 | 0.208 | |
| RowDataTable-class | 0.165 | 0.008 | 0.174 | |
| SampleAssayPlot-class | 0.218 | 0.010 | 0.229 | |
| aes-utils | 0 | 0 | 0 | |
| cache-utils | 0.013 | 0.000 | 0.013 | |
| checkColormapCompatibility | 4.785 | 0.257 | 5.078 | |
| class-utils | 0.001 | 0.000 | 0.001 | |
| cleanDataset | 0.015 | 0.001 | 0.016 | |
| collapseBox | 0.011 | 0.001 | 0.012 | |
| createCustomPanels | 0.024 | 0.002 | 0.026 | |
| createLandingPage | 0.042 | 0.005 | 0.045 | |
| defaultTour | 0.004 | 0.000 | 0.004 | |
| filterDTColumn | 0.001 | 0.001 | 0.002 | |
| getPanelColor | 0.058 | 0.003 | 0.060 | |
| iSEE | 2.941 | 0.152 | 3.098 | |
| iSEEOptions | 0 | 0 | 0 | |
| jitterPoints | 0.020 | 0.003 | 0.023 | |
| labs-utils | 0 | 0 | 0 | |
| lassoPoints | 0.002 | 0.000 | 0.001 | |
| manage_commands | 0.000 | 0.001 | 0.000 | |
| multiSelectionToFactor | 0.001 | 0.000 | 0.000 | |
| panelDefaults | 0.000 | 0.000 | 0.001 | |
| plot-utils | 0.003 | 0.000 | 0.003 | |
| registerAppOptions | 0.002 | 0.000 | 0.001 | |
| selectionColorMap | 0.001 | 0.000 | 0.000 | |
| setCachedCommonInfo | 0.001 | 0.000 | 0.001 | |
| subsetPointsByGrid | 0.181 | 0.004 | 0.185 | |
| synchronizeAssays | 3.053 | 0.159 | 3.215 | |