Jaehyun Joo
| Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/qmtools |
| git_branch: RELEASE_3_18 |
| git_last_commit: 48d7be4 |
| git_last_commit_date: 2023-10-24 11:41:06 -0400 (Tue, 24 Oct 2023) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:16 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 1624/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| qmtools 1.6.0 (landing page) Jaehyun Joo
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the qmtools 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: qmtools |
| Version: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qmtools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qmtools_1.6.0.tar.gz |
| StartedAt: 2024-04-18 00:01:19 -0400 (Thu, 18 Apr 2024) |
| EndedAt: 2024-04-18 00:05:28 -0400 (Thu, 18 Apr 2024) |
| EllapsedTime: 248.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qmtools.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qmtools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qmtools_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/qmtools.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qmtools/DESCRIPTION’ ... OK
* this is package ‘qmtools’ version ‘1.6.0’
* 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 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 ... 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 ... 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 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 6.848 0.077 6.984
plotCorr 5.741 0.120 5.878
* 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: OK
qmtools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL qmtools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘qmtools’ ... ** 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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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(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
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, 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: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
22.511 0.994 23.611
qmtools.Rcheck/qmtools-Ex.timings
| name | user | system | elapsed | |
| clusterFeatures | 0.242 | 0.016 | 0.259 | |
| compareSamples | 0.148 | 0.009 | 0.156 | |
| faahko_se | 0.021 | 0.005 | 0.025 | |
| imputeIntensity | 1.077 | 0.097 | 1.177 | |
| imputeKNN | 0.422 | 0.020 | 0.443 | |
| normalizeIntensity | 0.064 | 0.016 | 0.080 | |
| normalizePQN | 0.038 | 0.015 | 0.053 | |
| plotBox | 1.730 | 0.056 | 1.789 | |
| plotCorr | 5.741 | 0.120 | 5.878 | |
| plotMiss | 6.848 | 0.077 | 6.984 | |
| plotRTgroup | 0.292 | 0.016 | 0.310 | |
| plotReduced | 0.359 | 0.009 | 0.369 | |
| reduceFeatures | 0.053 | 0.006 | 0.060 | |
| reducePCA | 0.026 | 0.004 | 0.030 | |
| reducePLSDA | 0.030 | 0.004 | 0.035 | |
| reduceTSNE | 0.048 | 0.006 | 0.055 | |
| removeBlankRatio | 0.006 | 0.005 | 0.010 | |
| removeFeatures | 0.063 | 0.016 | 0.078 | |
| removeICC | 0.551 | 0.022 | 0.576 | |
| removeMiss | 0.034 | 0.020 | 0.054 | |
| removeRSD | 0.003 | 0.004 | 0.009 | |
| scaleCols | 0.030 | 0.016 | 0.046 | |
| scaleRows | 0.035 | 0.015 | 0.051 | |