Joseph N. Paulson
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/metagenomeSeq |
| Branch: RELEASE_3_9 |
| Last Commit: 8de127d |
| Last Changed Date: 2019-08-04 12:53:02 -0400 (Sun, 04 Aug 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:51:17 -0400 (Wed, 16 Oct 2019).
| Package 964/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| metagenomeSeq 1.26.3 Joseph N. Paulson
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: metagenomeSeq |
| Version: 1.26.3 |
| 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_1.26.3.tar.gz |
| StartedAt: 2019-10-16 04:26:50 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:33:50 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 420.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: metagenomeSeq.Rcheck |
| Warnings: 2 |
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### Running 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_1.26.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.26.3’
* 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 ... WARNING
Missing link or links in documentation object 'MRihw-fitFeatureModelResults.Rd':
‘fitFeatureModelResults’ ‘fitZigResults’
Missing link or links in documentation object 'MRihw-fitZigResults.Rd':
‘fitFeatureModelResults’ ‘fitZigResults’
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 ... WARNING
Documented arguments not in \usage in documentation object 'MRcoefs':
‘IHWcov’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
wrenchNorm 26.419 4.325 30.745
exportMat 3.517 4.363 7.883
extractMR 4.209 1.959 6.170
MRfulltable 2.004 0.145 9.343
fitPA 0.720 0.128 5.335
fitDO 0.595 0.104 5.767
* 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: 2 WARNINGs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/metagenomeSeq.Rcheck/00check.log’
for details.
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’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘MRihw’ with signature ‘"fitFeatureModelResults"’: no definition for class “fitFeatureModelResults” in method for ‘MRihw’ with signature ‘"fitZigResults"’: no definition for class “fitZigResults” ** 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 (metagenomeSeq)
metagenomeSeq.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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] '1.26.3'
> # 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, 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, 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 2.0-18
Loading required package: RColorBrewer
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 15 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
>
> proc.time()
user system elapsed
155.790 19.987 175.735
metagenomeSeq.Rcheck/metagenomeSeq-Ex.timings
| name | user | system | elapsed | |
| MRcoefs | 2.329 | 0.289 | 2.617 | |
| MRcounts | 0.799 | 0.058 | 0.857 | |
| MRexperiment-class | 0.001 | 0.000 | 0.000 | |
| MRfulltable | 2.004 | 0.145 | 9.343 | |
| MRtable | 1.908 | 0.102 | 2.010 | |
| aggregateBySample | 0.275 | 0.035 | 0.309 | |
| aggregateByTaxonomy | 0.230 | 0.035 | 0.265 | |
| biom2MRexperiment | 0.446 | 0.028 | 0.474 | |
| calcNormFactors | 0.927 | 0.205 | 1.132 | |
| correctIndices | 0.203 | 0.067 | 0.269 | |
| correlationTest | 0.342 | 0.059 | 0.402 | |
| cumNorm | 0.589 | 0.140 | 0.729 | |
| cumNormMat | 0.860 | 0.222 | 1.083 | |
| cumNormStat | 0.652 | 0.170 | 0.821 | |
| cumNormStatFast | 0.396 | 0.048 | 0.444 | |
| expSummary | 0.125 | 0.020 | 0.145 | |
| exportMat | 3.517 | 4.363 | 7.883 | |
| exportStats | 0.757 | 0.120 | 0.877 | |
| extractMR | 4.209 | 1.959 | 6.170 | |
| filterData | 0.300 | 0.057 | 0.357 | |
| fitDO | 0.595 | 0.104 | 5.767 | |
| fitFeatureModel | 1.921 | 0.090 | 2.011 | |
| fitLogNormal | 2.787 | 0.620 | 3.408 | |
| fitMultipleTimeSeries | 2.643 | 0.363 | 3.006 | |
| fitPA | 0.720 | 0.128 | 5.335 | |
| fitSSTimeSeries | 0.692 | 0.098 | 0.790 | |
| fitTimeSeries | 0.664 | 0.098 | 0.762 | |
| fitZig | 2.653 | 0.641 | 3.296 | |
| libSize-set | 0.551 | 0.046 | 0.598 | |
| libSize | 0.533 | 0.025 | 0.557 | |
| loadBiom | 0.075 | 0.001 | 0.075 | |
| loadMeta | 0.034 | 0.001 | 0.038 | |
| loadMetaQ | 0.000 | 0.000 | 0.001 | |
| loadPhenoData | 0.043 | 0.001 | 0.044 | |
| makeLabels | 0.001 | 0.000 | 0.001 | |
| mergeMRexperiments | 2.802 | 0.722 | 3.524 | |
| newMRexperiment | 0.058 | 0.001 | 0.059 | |
| normFactors-set | 0.545 | 0.010 | 0.554 | |
| normFactors | 0.504 | 0.010 | 0.514 | |
| plotBubble | 0.378 | 0.113 | 4.922 | |
| plotClassTimeSeries | 1.637 | 0.387 | 2.024 | |
| plotCorr | 0.920 | 0.170 | 1.091 | |
| plotFeature | 0.244 | 0.038 | 0.283 | |
| plotGenus | 0.251 | 0.068 | 0.318 | |
| plotMRheatmap | 4.376 | 0.295 | 4.673 | |
| plotOTU | 0.244 | 0.034 | 0.279 | |
| plotOrd | 0.333 | 0.093 | 0.426 | |
| plotRare | 0.197 | 0.033 | 0.232 | |
| plotTimeSeries | 1.479 | 0.271 | 1.752 | |
| posteriorProbs | 2.513 | 0.759 | 3.272 | |
| returnAppropriateObj | 0.505 | 0.053 | 0.558 | |
| ssFit | 0 | 0 | 0 | |
| ssIntervalCandidate | 0.000 | 0.001 | 0.000 | |
| ssPerm | 0.000 | 0.000 | 0.001 | |
| ssPermAnalysis | 0.000 | 0.001 | 0.001 | |
| trapz | 0.001 | 0.000 | 0.002 | |
| ts2MRexperiment | 2.758 | 0.521 | 3.279 | |
| uniqueFeatures | 0.209 | 0.046 | 0.254 | |
| wrenchNorm | 26.419 | 4.325 | 30.745 | |
| zigControl | 0.001 | 0.000 | 0.000 | |