Felix G.M. Ernst
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/mia |
| git_branch: master |
| git_last_commit: 2aa5b09 |
| git_last_commit_date: 2022-02-06 08:40:41 -0400 (Sun, 06 Feb 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:01 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 mia package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mia.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1142/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mia 1.3.18 (landing page) Felix G.M. Ernst
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: mia |
| Version: 1.3.18 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mia.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings mia_1.3.18.tar.gz |
| StartedAt: 2022-03-17 19:34:04 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:41:23 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 439.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: mia.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mia.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings mia_1.3.18.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/mia.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mia/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mia' version '1.3.18'
* 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 whether package 'mia' 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
taxonomy-methods 20.79 2.83 23.61
agglomerate-methods 12.36 0.77 13.19
estimateDiversity 7.75 1.78 9.53
makeTreeSummarizedExperimentFromDADA2 8.64 0.41 9.05
getExperimentCrossCorrelation 7.53 1.46 10.53
calculateJSD 4.55 1.89 6.44
splitByRanks 5.78 0.25 6.03
getPrevalence 5.17 0.18 5.36
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
Time difference of 8.12 secs
Initializing error rates to maximum possible estimate.
selfConsist step 1 .
selfConsist step 2
selfConsist step 3
selfConsist step 4
Convergence after 4 rounds.
Initializing error rates to maximum possible estimate.
selfConsist step 1 .
selfConsist step 2
selfConsist step 3
selfConsist step 4
Convergence after 4 rounds.
* 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: 1 ERROR
See
'D:/biocbuild/bbs-3.15-bioc/meat/mia.Rcheck/00check.log'
for details.
mia.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL mia
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'mia' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'mia'
finding HTML links ... done
agglomerate-methods html
calculateDMN html
calculateDistance html
calculateJSD html
calculateOverlap html
calculateUnifrac html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-mia/00new/mia/help/calculateUniFrac.html
estimateDivergence html
finding level-2 HTML links ... done
estimateDiversity html
estimateDominance html
estimateEvenness html
estimateRichness html
getAbundance html
getExperimentCrossCorrelation html
getPrevalence html
isContaminant html
loadFromMetaphlan html
loadFromMothur html
loadFromQIIME2 html
makePhyloseqFromTreeSummarizedExperiment
html
makeSummarizedExperimentFromBiom html
makeTreeSummarizedExperimentFromDADA2 html
makeTreeSummarizedExperimentFromPhyloseq
html
meltAssay html
merge-methods html
mia-datasets html
mia-package html
perSampleDominantTaxa html
relabundance html
runCCA html
runDPCoA html
runNMDS html
splitByRanks html
subsampleCounts html
subsetSamples html
summaries html
taxonomy-methods html
transformCounts html
** 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 (mia)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'doppelgangR' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'hipathia' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'MuData' is missing or broken
done
mia.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(mia)
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, 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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
Loading required package: SingleCellExperiment
Loading required package: TreeSummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: MultiAssayExperiment
>
> test_check("mia")
================================================================================
Time difference of 8.12 secs
Initializing error rates to maximum possible estimate.
selfConsist step 1 .
selfConsist step 2
selfConsist step 3
selfConsist step 4
Convergence after 4 rounds.
Initializing error rates to maximum possible estimate.
selfConsist step 1 .
selfConsist step 2
selfConsist step 3
selfConsist step 4
Convergence after 4 rounds.
mia.Rcheck/mia-Ex.timings
| name | user | system | elapsed | |
| agglomerate-methods | 12.36 | 0.77 | 13.19 | |
| calculateDMN | 1.32 | 0.03 | 1.36 | |
| calculateDistance | 0.01 | 0.00 | 0.02 | |
| calculateJSD | 4.55 | 1.89 | 6.44 | |
| calculateOverlap | 0.13 | 0.00 | 0.12 | |
| calculateUnifrac | 0.22 | 0.00 | 0.22 | |
| estimateDivergence | 1.25 | 0.16 | 1.41 | |
| estimateDiversity | 7.75 | 1.78 | 9.53 | |
| estimateDominance | 0.21 | 0.00 | 0.22 | |
| estimateEvenness | 0.07 | 0.02 | 0.07 | |
| estimateRichness | 0.26 | 0.01 | 0.28 | |
| getAbundance | 0.35 | 0.20 | 0.55 | |
| getExperimentCrossCorrelation | 7.53 | 1.46 | 10.53 | |
| getPrevalence | 5.17 | 0.18 | 5.36 | |
| isContaminant | 0.33 | 0.00 | 0.33 | |
| loadFromMetaphlan | 0.93 | 0.00 | 0.94 | |
| loadFromMothur | 0.04 | 0.02 | 0.04 | |
| loadFromQIIME2 | 0.79 | 0.14 | 1.16 | |
| makePhyloseqFromTreeSummarizedExperiment | 1.36 | 0.20 | 1.56 | |
| makeSummarizedExperimentFromBiom | 0.05 | 0.00 | 0.05 | |
| makeTreeSummarizedExperimentFromDADA2 | 8.64 | 0.41 | 9.05 | |
| makeTreeSummarizedExperimentFromPhyloseq | 1.56 | 0.17 | 1.73 | |
| meltAssay | 0.78 | 0.27 | 1.05 | |
| merge-methods | 1.67 | 0.09 | 1.77 | |
| perSampleDominantTaxa | 2.20 | 0.58 | 2.78 | |
| relabundance | 0.49 | 0.16 | 0.64 | |
| runCCA | 1.37 | 0.48 | 1.86 | |
| runDPCoA | 0.32 | 0.00 | 0.31 | |
| runNMDS | 0.15 | 0.02 | 0.18 | |
| splitByRanks | 5.78 | 0.25 | 6.03 | |
| subsampleCounts | 1.38 | 0.28 | 1.65 | |
| subsetSamples | 0.89 | 0.18 | 1.08 | |
| summaries | 2.37 | 0.16 | 2.53 | |
| taxonomy-methods | 20.79 | 2.83 | 23.61 | |
| transformCounts | 0.43 | 0.01 | 0.45 | |