Jaehyun Joo
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/qmtools |
| git_branch: RELEASE_3_16 |
| git_last_commit: e3660f9 |
| git_last_commit_date: 2022-11-01 11:26:50 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:21 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the qmtools package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1562/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| qmtools 1.2.0 (landing page) Jaehyun Joo
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: qmtools |
| Version: 1.2.0 |
| 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_1.2.0.tar.gz |
| StartedAt: 2023-04-10 22:02:01 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 22:04:42 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 161.3 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_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/qmtools.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘qmtools/DESCRIPTION’ ... OK * this is package ‘qmtools’ version ‘1.2.0’ * 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 * 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/4.2/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 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")
[1] 325618.6
[1] 325618.6
[1] 325618.6
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...
|
| | 0%
|
|= | 2%
|
|=== | 4%
|
|==== | 6%
|
|====== | 8%
|
|======= | 10%
|
|========= | 12%
|
|========== | 14%
|
|=========== | 16%
|
|============= | 18%
|
|============== | 20%
|
|================ | 22%
|
|================= | 24%
|
|=================== | 27%
|
|==================== | 29%
|
|===================== | 31%
|
|======================= | 33%
|
|======================== | 35%
|
|========================== | 37%
|
|=========================== | 39%
|
|============================= | 41%
|
|============================== | 43%
|
|=============================== | 45%
|
|================================= | 47%
|
|================================== | 49%
|
|==================================== | 51%
|
|===================================== | 53%
|
|======================================= | 55%
|
|======================================== | 57%
|
|========================================= | 59%
|
|=========================================== | 61%
|
|============================================ | 63%
|
|============================================== | 65%
|
|=============================================== | 67%
|
|================================================= | 69%
|
|================================================== | 71%
|
|=================================================== | 73%
|
|===================================================== | 76%
|
|====================================================== | 78%
|
|======================================================== | 80%
|
|========================================================= | 82%
|
|=========================================================== | 84%
|
|============================================================ | 86%
|
|============================================================= | 88%
|
|=============================================================== | 90%
|
|================================================================ | 92%
|
|================================================================== | 94%
|
|=================================================================== | 96%
|
|===================================================================== | 98%
|
|======================================================================| 100%
Calculating ICC...
|
| | 0%
|
|= | 2%
|
|=== | 4%
|
|==== | 6%
|
|====== | 8%
|
|======= | 10%
|
|========= | 12%
|
|========== | 14%
|
|=========== | 16%
|
|============= | 18%
|
|============== | 20%
|
|================ | 22%
|
|================= | 24%
|
|=================== | 27%
|
|==================== | 29%
|
|===================== | 31%
|
|======================= | 33%
|
|======================== | 35%
|
|========================== | 37%
|
|=========================== | 39%
|
|============================= | 41%
|
|============================== | 43%
|
|=============================== | 45%
|
|================================= | 47%
|
|================================== | 49%
|
|==================================== | 51%
|
|===================================== | 53%
|
|======================================= | 55%
|
|======================================== | 57%
|
|========================================= | 59%
|
|=========================================== | 61%
|
|============================================ | 63%
|
|============================================== | 65%
|
|=============================================== | 67%
|
|================================================= | 69%
|
|================================================== | 71%
|
|=================================================== | 73%
|
|===================================================== | 76%
|
|====================================================== | 78%
|
|======================================================== | 80%
|
|========================================================= | 82%
|
|=========================================================== | 84%
|
|============================================================ | 86%
|
|============================================================= | 88%
|
|=============================================================== | 90%
|
|================================================================ | 92%
|
|================================================================== | 94%
|
|=================================================================== | 96%
|
|===================================================================== | 98%
|
|======================================================================| 100%
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 190 ]
>
> proc.time()
user system elapsed
15.153 0.669 15.846
qmtools.Rcheck/qmtools-Ex.timings
| name | user | system | elapsed | |
| clusterFeatures | 0.178 | 0.013 | 0.192 | |
| faahko_se | 0.012 | 0.002 | 0.013 | |
| imputeIntensity | 1.331 | 0.059 | 1.395 | |
| imputeKNN | 0.292 | 0.022 | 0.316 | |
| normalizeIntensity | 0.046 | 0.016 | 0.061 | |
| normalizePQN | 0.033 | 0.018 | 0.051 | |
| plotBox | 0.728 | 0.035 | 0.765 | |
| plotCorr | 2.041 | 0.083 | 2.128 | |
| plotMiss | 3.980 | 0.062 | 4.052 | |
| plotRTgroup | 0.282 | 0.016 | 0.299 | |
| plotReduced | 0.315 | 0.005 | 0.321 | |
| reduceFeatures | 0.038 | 0.004 | 0.042 | |
| reducePCA | 0.016 | 0.002 | 0.019 | |
| reducePLSDA | 0.019 | 0.002 | 0.021 | |
| reduceTSNE | 0.032 | 0.004 | 0.036 | |
| removeBlankRatio | 0.006 | 0.004 | 0.010 | |
| removeFeatures | 0.047 | 0.013 | 0.061 | |
| removeICC | 0.571 | 0.020 | 0.592 | |
| removeMiss | 0.024 | 0.021 | 0.046 | |
| removeRSD | 0.004 | 0.005 | 0.008 | |
| scaleCols | 0.022 | 0.015 | 0.038 | |
| scaleRows | 0.023 | 0.013 | 0.037 | |