Joseph N. Paulson
| Snapshot Date: 2019-03-17 17:01:51 -0400 (Sun, 17 Mar 2019) |
| URL: https://git.bioconductor.org/packages/metagenomeSeq |
| Branch: master |
| Last Commit: 237560f |
| Last Changed Date: 2019-02-27 10:35:57 -0400 (Wed, 27 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-03-18 11:46:04 -0400 (Mon, 18 Mar 2019).
| Package 937/1676 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||
| metagenomeSeq 1.25.3 Joseph N. Paulson
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | |||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] |
| Package: metagenomeSeq |
| Version: 1.25.3 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings metagenomeSeq_1.25.3.tar.gz |
| StartedAt: 2019-03-18 02:56:56 -0400 (Mon, 18 Mar 2019) |
| EndedAt: 2019-03-18 03:02:59 -0400 (Mon, 18 Mar 2019) |
| EllapsedTime: 363.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: metagenomeSeq.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings metagenomeSeq_1.25.3.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/metagenomeSeq.Rcheck’
* using R Under development (unstable) (2019-01-22 r76000)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK
* this is package ‘metagenomeSeq’ version ‘1.25.3’
* 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 ‘metagenomeSeq’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
exportMat 3.043 3.671 6.712
plotMRheatmap 5.496 0.278 5.777
extractMR 3.428 1.722 5.151
fitDO 0.880 0.099 5.476
* 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
metagenomeSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL metagenomeSeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘metagenomeSeq’ ... ** 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 * DONE (metagenomeSeq)
metagenomeSeq.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-01-22 r76000) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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")
> packageVersion("metagenomeSeq")
[1] '1.25.3'
> # As suggested for opt-out option on testing by users,
> # recommended by CRAN: http://adv-r.had.co.nz/Testing.html
> # Previously, best practice was to put all test files in inst/tests
> # and ensure that R CMD check ran them by putting the following code in tests/test-all.R:
> # >library(testthat)
> # >library(yourpackage)
> # >test_package("yourpackage")
> # Now, recommended practice is to put your tests in tests/testthat,
> # and ensure R CMD check runs them by putting the following code in tests/test-all.R:
> # >library(testthat)
> # >test_check("yourpackage")
> # The advantage of this new structure is that the user has control over whether or not tests are installed using the –install-tests parameter to
> # R CMD install, or INSTALL_opts = c(“–install-tests”) argument to install.packages(). I’m not sure why you wouldn’t want to install the tests,
> # but now you have the flexibility as requested by CRAN maintainers.
> test_check("metagenomeSeq")
Loading required package: metagenomeSeq
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, append,
as.data.frame, basename, cbind, colMeans, colSums, 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, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16
Loading required package: RColorBrewer
══ testthat results ═══════════════════════════════════════════════════════════
OK: 21 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
157.440 20.096 177.506
metagenomeSeq.Rcheck/metagenomeSeq-Ex.timings
| name | user | system | elapsed | |
| MRcoefs | 2.102 | 0.246 | 2.350 | |
| MRcounts | 0.780 | 0.054 | 0.833 | |
| MRexperiment-class | 0 | 0 | 0 | |
| MRfulltable | 1.718 | 0.112 | 1.830 | |
| MRtable | 1.490 | 0.094 | 1.583 | |
| aggregateBySample | 0.264 | 0.029 | 0.292 | |
| aggregateByTaxonomy | 0.228 | 0.036 | 0.265 | |
| biom2MRexperiment | 0.443 | 0.026 | 0.470 | |
| calcNormFactors | 0.590 | 0.181 | 0.772 | |
| correctIndices | 0.150 | 0.041 | 0.192 | |
| correlationTest | 0.557 | 0.068 | 0.624 | |
| cumNorm | 0.682 | 0.164 | 0.847 | |
| cumNormMat | 0.703 | 0.191 | 0.895 | |
| cumNormStat | 0.680 | 0.102 | 0.782 | |
| cumNormStatFast | 0.282 | 0.038 | 0.320 | |
| expSummary | 0.133 | 0.039 | 0.172 | |
| exportMat | 3.043 | 3.671 | 6.712 | |
| exportStats | 0.666 | 0.160 | 0.825 | |
| extractMR | 3.428 | 1.722 | 5.151 | |
| filterData | 0.205 | 0.036 | 0.240 | |
| fitDO | 0.880 | 0.099 | 5.476 | |
| fitFeatureModel | 1.837 | 0.219 | 2.056 | |
| fitLogNormal | 2.753 | 0.660 | 3.413 | |
| fitMultipleTimeSeries | 2.508 | 0.299 | 2.807 | |
| fitPA | 0.644 | 0.119 | 4.956 | |
| fitSSTimeSeries | 1.500 | 0.214 | 1.715 | |
| fitTimeSeries | 1.334 | 0.154 | 1.488 | |
| fitZig | 2.389 | 0.604 | 2.992 | |
| libSize-set | 0.502 | 0.045 | 0.546 | |
| libSize | 0.510 | 0.013 | 0.523 | |
| loadBiom | 0.077 | 0.002 | 0.078 | |
| loadMeta | 0.035 | 0.002 | 0.037 | |
| loadMetaQ | 0.000 | 0.000 | 0.001 | |
| loadPhenoData | 0.040 | 0.001 | 0.041 | |
| makeLabels | 0.000 | 0.000 | 0.001 | |
| mergeMRexperiments | 2.244 | 0.668 | 2.911 | |
| newMRexperiment | 0.047 | 0.000 | 0.047 | |
| normFactors-set | 0.484 | 0.014 | 0.498 | |
| normFactors | 0.466 | 0.013 | 0.479 | |
| plotBubble | 0.425 | 0.136 | 4.587 | |
| plotClassTimeSeries | 1.439 | 0.355 | 1.794 | |
| plotCorr | 0.901 | 0.186 | 1.088 | |
| plotFeature | 0.215 | 0.044 | 0.260 | |
| plotGenus | 0.224 | 0.059 | 0.284 | |
| plotMRheatmap | 5.496 | 0.278 | 5.777 | |
| plotOTU | 0.205 | 0.032 | 0.237 | |
| plotOrd | 0.369 | 0.094 | 0.463 | |
| plotRare | 0.209 | 0.041 | 0.250 | |
| plotTimeSeries | 1.323 | 0.155 | 1.479 | |
| posteriorProbs | 2.780 | 0.910 | 3.692 | |
| returnAppropriateObj | 0.555 | 0.059 | 0.614 | |
| ssFit | 0 | 0 | 0 | |
| ssIntervalCandidate | 0.001 | 0.000 | 0.001 | |
| ssPerm | 0.001 | 0.000 | 0.001 | |
| ssPermAnalysis | 0 | 0 | 0 | |
| trapz | 0.001 | 0.001 | 0.002 | |
| ts2MRexperiment | 2.755 | 0.358 | 3.115 | |
| uniqueFeatures | 0.200 | 0.045 | 0.246 | |
| zigControl | 0.000 | 0.000 | 0.001 | |