Jaehyun Joo
| Snapshot Date: 2025-06-18 13:25 -0400 (Wed, 18 Jun 2025) |
| git_url: https://git.bioconductor.org/packages/qmtools |
| git_branch: devel |
| git_last_commit: e6f19a5 |
| git_last_commit_date: 2025-04-15 12:49:05 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-06-19 12:02 -0400 (Thu, 19 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4810 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4548 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4528 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4493 |
| 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 1638/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| qmtools 1.13.0 (landing page) Jaehyun Joo
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the qmtools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qmtools.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: qmtools |
| Version: 1.13.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:qmtools.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings qmtools_1.13.0.tar.gz |
| StartedAt: 2025-06-19 02:22:39 -0400 (Thu, 19 Jun 2025) |
| EndedAt: 2025-06-19 02:26:21 -0400 (Thu, 19 Jun 2025) |
| EllapsedTime: 222.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qmtools.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:qmtools.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings qmtools_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/qmtools.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘qmtools/DESCRIPTION’ ... OK
* this is package ‘qmtools’ version ‘1.13.0’
* 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 ‘qmtools’ 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 ... OK
* 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'compareSamples.Rd':
‘[limma:ebayes]{limma::eBayes}’ ‘[limma:toptable]{limma::topTable}’
Non-topic package-anchored link(s) in Rd file 'imputeIntensity.Rd':
‘[MsCoreUtils:imputation]{MsCoreUtils::impute_matrix}’
Non-topic package-anchored link(s) in Rd file 'normalizeIntensity.Rd':
‘[MsCoreUtils:normalize]{MsCoreUtils::normalize_matrix}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
clusterFeatures.Rd: SummarizedExperiment-class
compareSamples.Rd: SummarizedExperiment-class
faahko_se.Rd: SummarizedExperiment-class
imputeIntensity.Rd: SummarizedExperiment-class
imputeKNN.Rd: SummarizedExperiment-class
normalizeIntensity.Rd: SummarizedExperiment-class
normalizePQN.Rd: SummarizedExperiment-class
plotBox.Rd: SummarizedExperiment-class
plotCorr.Rd: SummarizedExperiment-class
plotMiss.Rd: SummarizedExperiment, SummarizedExperiment-class
plotRTgroup.Rd: SummarizedExperiment-class
reduceFeatures.Rd: SummarizedExperiment-class
reducePCA.Rd: SummarizedExperiment-class
reducePLSDA.Rd: SummarizedExperiment-class
reduceTSNE.Rd: SummarizedExperiment-class
removeBlankRatio.Rd: SummarizedExperiment-class
removeFeatures.Rd: SummarizedExperiment-class
removeICC.Rd: SummarizedExperiment-class
removeMiss.Rd: SummarizedExperiment-class
removeRSD.Rd: SummarizedExperiment-class
scaleCols.Rd: SummarizedExperiment-class
scaleRows.Rd: SummarizedExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
plotMiss 6.153 0.124 6.277
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.22-bioc/meat/qmtools.Rcheck/00check.log’
for details.
qmtools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL qmtools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘qmtools’ ... ** this is package ‘qmtools’ version ‘1.13.0’ ** using staged installation ** R ** data ** 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 (qmtools)
qmtools.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 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.
> library(testthat)
> library(qmtools)
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: 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
>
> test_check("qmtools")
Contrast: WT - KO
Contrast: WT - KO
Imputing along margin 1 (features/rows).
Imputing along margin 1 (features/rows).
Imputing along margin 1 (features/rows).
Imputing along margin 2 (samples/columns).
Imputing along margin 2 (samples/columns).
Imputing along margin 2 (samples/columns).
Imputing along margin 2 (samples/columns).
Imputing along margin 2 (samples/columns).
Imputing along margin 2 (samples/columns).
Imputing along margin 2 (samples/columns).
[1] 325618.6
Imputing along margin 2 (samples/columns).
[1] 325618.6
Imputing along margin 2 (samples/columns).
[1] 325618.6
Imputing along margin 1 (features/rows).
Missing value(s) in 'x'.
12% of values are missing.
Please consider missing value imputation.
Performing NIPALS PCA...
Missing value(s) in 'x'.
12% of values are missing.
Please consider missing value imputation.
Performing NIPALS PCA...
Calculating ICC...
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Calculating ICC...
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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 200 ]
>
> proc.time()
user system elapsed
18.279 0.920 19.197
qmtools.Rcheck/qmtools-Ex.timings
| name | user | system | elapsed | |
| clusterFeatures | 0.216 | 0.003 | 0.220 | |
| compareSamples | 0.167 | 0.001 | 0.167 | |
| faahko_se | 0.013 | 0.001 | 0.013 | |
| imputeIntensity | 1.445 | 0.029 | 1.473 | |
| imputeKNN | 0.319 | 0.007 | 0.325 | |
| normalizeIntensity | 0.051 | 0.000 | 0.051 | |
| normalizePQN | 0.030 | 0.000 | 0.029 | |
| plotBox | 0.923 | 0.088 | 1.011 | |
| plotCorr | 4.659 | 0.142 | 4.801 | |
| plotMiss | 6.153 | 0.124 | 6.277 | |
| plotRTgroup | 0.295 | 0.002 | 0.297 | |
| plotReduced | 0.324 | 0.000 | 0.323 | |
| reduceFeatures | 0.041 | 0.001 | 0.042 | |
| reducePCA | 0.018 | 0.000 | 0.019 | |
| reducePLSDA | 0.023 | 0.000 | 0.023 | |
| reduceTSNE | 0.035 | 0.000 | 0.034 | |
| removeBlankRatio | 0.006 | 0.000 | 0.005 | |
| removeFeatures | 0.042 | 0.002 | 0.044 | |
| removeICC | 0.532 | 0.003 | 0.534 | |
| removeMiss | 0.025 | 0.002 | 0.027 | |
| removeRSD | 0.003 | 0.001 | 0.003 | |
| scaleCols | 0.021 | 0.002 | 0.022 | |
| scaleRows | 0.026 | 0.001 | 0.027 | |