Joseph N. Paulson
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/metagenomeSeq |
| Branch: RELEASE_3_10 |
| Last Commit: 9c1b1a3 |
| Last Changed Date: 2020-02-02 23:10:36 -0400 (Sun, 02 Feb 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:38:39 -0400 (Wed, 15 Apr 2020).
| Package 1003/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| metagenomeSeq 1.28.2 Joseph N. Paulson
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: metagenomeSeq |
| Version: 1.28.2 |
| 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_1.28.2.tar.gz |
| StartedAt: 2020-04-15 03:41:45 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:47:11 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 326.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: metagenomeSeq.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### 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_1.28.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.28.2’
* 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 20.769 1.741 22.754
MRfulltable 1.419 0.060 7.455
* 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-3.10-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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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] '1.28.2'
> # 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
Loaded glmnet 3.0-2
Loading required package: RColorBrewer
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 15 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
>
> proc.time()
user system elapsed
129.321 10.011 140.581
metagenomeSeq.Rcheck/metagenomeSeq-Ex.timings
| name | user | system | elapsed | |
| MRcoefs | 1.751 | 0.136 | 1.899 | |
| MRcounts | 0.686 | 0.021 | 0.711 | |
| MRexperiment-class | 0 | 0 | 0 | |
| MRfulltable | 1.419 | 0.060 | 7.455 | |
| MRtable | 1.480 | 0.045 | 1.538 | |
| aggregateBySample | 0.201 | 0.015 | 0.216 | |
| aggregateByTaxonomy | 0.213 | 0.017 | 0.230 | |
| biom2MRexperiment | 0.396 | 0.011 | 0.412 | |
| calcNormFactors | 0.814 | 0.113 | 0.941 | |
| correctIndices | 0.181 | 0.037 | 0.219 | |
| correlationTest | 0.334 | 0.039 | 0.374 | |
| cumNorm | 0.551 | 0.087 | 0.642 | |
| cumNormMat | 0.766 | 0.110 | 0.887 | |
| cumNormStat | 0.600 | 0.077 | 0.689 | |
| cumNormStatFast | 0.398 | 0.027 | 0.430 | |
| expSummary | 0.129 | 0.010 | 0.141 | |
| exportMat | 2.241 | 1.924 | 4.213 | |
| exportStats | 0.767 | 0.074 | 0.846 | |
| extractMR | 3.415 | 0.939 | 4.394 | |
| filterData | 0.243 | 0.034 | 0.281 | |
| fitDO | 0.621 | 0.060 | 4.323 | |
| fitFeatureModel | 1.556 | 0.038 | 1.606 | |
| fitLogNormal | 2.164 | 0.290 | 2.473 | |
| fitMultipleTimeSeries | 2.023 | 0.094 | 2.130 | |
| fitPA | 0.773 | 0.061 | 4.211 | |
| fitSSTimeSeries | 0.478 | 0.040 | 0.522 | |
| fitTimeSeries | 0.460 | 0.032 | 0.495 | |
| fitZig | 1.924 | 0.335 | 2.277 | |
| libSize-set | 0.519 | 0.029 | 0.554 | |
| libSize | 0.487 | 0.003 | 0.497 | |
| loadBiom | 0.053 | 0.000 | 0.052 | |
| loadMeta | 0.024 | 0.002 | 0.025 | |
| loadMetaQ | 0.000 | 0.000 | 0.001 | |
| loadPhenoData | 0.022 | 0.000 | 0.022 | |
| makeLabels | 0.000 | 0.000 | 0.001 | |
| mergeMRexperiments | 2.163 | 0.345 | 2.538 | |
| newMRexperiment | 0.036 | 0.000 | 0.039 | |
| normFactors-set | 0.496 | 0.004 | 0.512 | |
| normFactors | 0.471 | 0.021 | 0.503 | |
| plotBubble | 0.396 | 0.056 | 3.902 | |
| plotClassTimeSeries | 1.270 | 0.146 | 1.426 | |
| plotCorr | 0.640 | 0.074 | 0.716 | |
| plotFeature | 0.201 | 0.021 | 0.229 | |
| plotGenus | 0.184 | 0.035 | 0.220 | |
| plotMRheatmap | 3.316 | 0.105 | 3.459 | |
| plotOTU | 0.218 | 0.017 | 0.237 | |
| plotOrd | 0.529 | 0.132 | 0.666 | |
| plotRare | 0.170 | 0.020 | 0.193 | |
| plotTimeSeries | 1.293 | 0.091 | 1.395 | |
| posteriorProbs | 1.986 | 0.365 | 2.371 | |
| returnAppropriateObj | 0.469 | 0.026 | 0.501 | |
| ssFit | 0.001 | 0.000 | 0.000 | |
| ssIntervalCandidate | 0.000 | 0.001 | 0.000 | |
| ssPerm | 0.000 | 0.000 | 0.001 | |
| ssPermAnalysis | 0 | 0 | 0 | |
| trapz | 0.000 | 0.001 | 0.001 | |
| ts2MRexperiment | 2.107 | 0.137 | 2.277 | |
| uniqueFeatures | 0.196 | 0.025 | 0.224 | |
| wrenchNorm | 20.769 | 1.741 | 22.754 | |
| zigControl | 0.001 | 0.000 | 0.000 | |