Laurent Gatto
| Snapshot Date: 2026-04-19 13:40 -0400 (Sun, 19 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/QFeatures |
| git_branch: devel |
| git_last_commit: a7049ad |
| git_last_commit_date: 2026-04-19 13:09:50 -0400 (Sun, 19 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-20 11:36 -0400 (Mon, 20 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4961 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4690 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 1704/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| QFeatures 1.21.3 (landing page) Laurent Gatto
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
| See other builds for QFeatures in R Universe. | ||||||||||||||
|
To the developers/maintainers of the QFeatures package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/QFeatures.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. |
| Package: QFeatures |
| Version: 1.21.3 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:QFeatures.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings QFeatures_1.21.3.tar.gz |
| StartedAt: 2026-04-20 03:26:33 -0400 (Mon, 20 Apr 2026) |
| EndedAt: 2026-04-20 03:35:45 -0400 (Mon, 20 Apr 2026) |
| EllapsedTime: 552.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: QFeatures.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:QFeatures.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings QFeatures_1.21.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/QFeatures.Rcheck’
* using R version 4.6.0 alpha (2026-04-05 r89794)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-20 07:26:33 UTC
* checking for file ‘QFeatures/DESCRIPTION’ ... OK
* this is package ‘QFeatures’ version ‘1.21.3’
* 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 ‘QFeatures’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘BiocGenerics:::replaceSlots’
‘MultiAssayExperiment:::.sampleMapFromData’
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 ... NOTE
.formatDimethylReportData: no visible global function definition for
‘everything’
.splitSE: no visible global function definition for ‘txtProgressBar’
.splitSE: no visible global function definition for ‘setNames’
.splitSE : <anonymous>: no visible global function definition for
‘setTxtProgressBar’
aggregateFeatures,QFeatures: no visible global function definition for
‘txtProgressBar’
aggregateFeatures,QFeatures: no visible global function definition for
‘setTxtProgressBar’
Undefined global functions or variables:
everything setNames setTxtProgressBar txtProgressBar
Consider adding
importFrom("stats", "setNames")
importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'QFeatures-aggregate.Rd':
‘[ProtGenerics:protgenerics]{ProtGenerics::adjacencyMatrix()}’
Non-topic package-anchored link(s) in Rd file 'QFeatures-processing.Rd':
‘[MsCoreUtils:normalize]{MsCoreUtils::normalizeMethods()}’
‘[MsCoreUtils:normalize]{MsCoreUtils::normalize_matrix()}’
Non-topic package-anchored link(s) in Rd file 'impute.Rd':
‘[MsCoreUtils:imputation]{MsCoreUtils::impute_matrix()}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
readQFeaturesFromDIANN 177.617 8.705 187.673
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/QFeatures.Rcheck/00check.log’
for details.
QFeatures.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL QFeatures ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘QFeatures’ ... ** this is package ‘QFeatures’ version ‘1.21.3’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘sweep’ in package ‘QFeatures’ ** help *** installing help indices *** copying figures ** 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 (QFeatures)
QFeatures.Rcheck/tests/testthat.Rout
R version 4.6.0 alpha (2026-04-05 r89794)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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.
> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
>
> library("testthat")
> library("QFeatures")
Loading required package: MultiAssayExperiment
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: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Seqinfo
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
Attaching package: 'QFeatures'
The following object is masked from 'package:base':
sweep
>
> test_check("QFeatures")
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[from:NA|fcol:NA|hits:0]
AssayLinks of length 0
names(0):
An empty instance of class QFeatures (type: bulk)
An instance of class QFeatures (type: bulk) with 1 set:
[1] psms: SummarizedExperiment with 10 rows and 2 columns
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[ FAIL 0 | WARN 2 | SKIP 0 | PASS 835 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 835 ]
>
> proc.time()
user system elapsed
68.296 1.469 69.761
QFeatures.Rcheck/QFeatures-Ex.timings
| name | user | system | elapsed | |
| AssayLinks | 0.594 | 0.002 | 0.596 | |
| QFeatures-aggregate | 1.693 | 0.033 | 1.725 | |
| QFeatures-class | 1.24 | 0.00 | 1.24 | |
| QFeatures-filtering | 2.784 | 0.043 | 2.828 | |
| QFeatures-longForm | 0.479 | 0.010 | 0.489 | |
| QFeatures-missing-data | 0.256 | 0.014 | 0.269 | |
| QFeatures-processing | 0.001 | 0.000 | 0.000 | |
| QFeatures-subsetBy | 1.588 | 0.033 | 1.621 | |
| countUniqueFeatures | 0.124 | 0.003 | 0.127 | |
| createPrecursorId | 0.324 | 0.006 | 0.330 | |
| display | 0.001 | 0.000 | 0.000 | |
| feat3 | 0.058 | 0.000 | 0.058 | |
| feat4 | 0.003 | 0.001 | 0.004 | |
| impute | 1.118 | 0.105 | 1.226 | |
| joinAssays | 0.303 | 0.011 | 0.314 | |
| readQFeatures | 0.790 | 0.005 | 0.795 | |
| readQFeaturesFromDIANN | 177.617 | 8.705 | 187.673 | |
| reduceDataFrame | 2.528 | 0.017 | 2.546 | |
| unfoldDataFrame | 0.100 | 0.001 | 0.102 | |