Tuomas Borman
| Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024) |
| git_url: https://git.bioconductor.org/packages/mia |
| git_branch: RELEASE_3_19 |
| git_last_commit: 38dad1b |
| git_last_commit_date: 2024-04-30 11:32:24 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:38 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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 | ||||
| Package 1257/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mia 1.12.0 (landing page) Tuomas Borman
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the mia package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: mia |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mia.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mia_1.12.0.tar.gz |
| StartedAt: 2024-05-06 22:57:25 -0400 (Mon, 06 May 2024) |
| EndedAt: 2024-05-06 23:04:08 -0400 (Mon, 06 May 2024) |
| EllapsedTime: 402.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: mia.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mia.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mia_1.12.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/mia.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mia/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mia’ version ‘1.12.0’
* 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 ‘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 code 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 ... NOTE
checkRd: (-1) agglomerate-methods.Rd:73-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agglomerate-methods.Rd:76-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agglomerate-methods.Rd:78-80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agglomerate-methods.Rd:81-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agglomerate-methods.Rd:84-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDiversity.Rd:94-96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDiversity.Rd:97-100: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) estimateDiversity.Rd:149-151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDiversity.Rd:153-162: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) estimateDiversity.Rd:167-176: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDiversity.Rd:178-183: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDiversity.Rd:185-192: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDiversity.Rd:194: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDominance.Rd:99-101: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDominance.Rd:103-112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDominance.Rd:114-126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDominance.Rd:128-137: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) estimateEvenness.Rd:75-76: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) estimateRichness.Rd:87-104: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) estimateRichness.Rd:119-126: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) getExperimentCrossAssociation.Rd:66-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getExperimentCrossAssociation.Rd:71-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hierarchy-tree.Rd:28-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hierarchy-tree.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) importHUMAnN.Rd:17-19: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) importHUMAnN.Rd:23-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importMetaPhlAn.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importMetaPhlAn.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importMetaPhlAn.Rd:32-34: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) importQIIME2.Rd:47-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importQIIME2.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) isContaminant.Rd:83-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) isContaminant.Rd:86-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeTreeSEFromBiom.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) meltAssay.Rd:67-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) taxonomy-methods.Rd:101-102: Lost braces in \itemize; meant \describe ?
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* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Unknown package ‘https’ in Rd xrefs
* 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 ... NOTE
Note: found 101 marked UTF-8 strings
* 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
runCCA 29.569 0.081 29.652
calculateDMN 27.013 0.015 27.031
hierarchy-tree 6.666 0.386 7.051
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/mia.Rcheck/00check.log’
for details.
mia.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mia ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘mia’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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)
mia.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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':
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
expand.grid, I, 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
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 3.86 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.
initial value 0.383462
iter 5 value 0.161655
iter 10 value 0.113278
final value 0.003270
converged
initial value 0.000000
final value 0.000000
converged
initial value 0.000000
final value 0.000000
converged
[ FAIL 0 | WARN 66 | SKIP 2 | PASS 957 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• require("miaTime", quietly = TRUE) is not TRUE (2): 'test-2mergeSEs.R:382:5',
'test-3agglomerate.R:88:5'
[ FAIL 0 | WARN 66 | SKIP 2 | PASS 957 ]
>
> proc.time()
user system elapsed
172.720 24.563 198.130
mia.Rcheck/mia-Ex.timings
| name | user | system | elapsed | |
| addCluster | 0.221 | 0.005 | 0.226 | |
| addDivergence | 0.506 | 0.029 | 0.536 | |
| agglomerate-methods | 2.905 | 0.050 | 2.955 | |
| calculateDMN | 27.013 | 0.015 | 27.031 | |
| calculateJSD | 1.435 | 0.239 | 1.676 | |
| calculateOverlap | 0.048 | 0.001 | 0.049 | |
| calculateUnifrac | 0.117 | 0.004 | 0.121 | |
| estimateDiversity | 4.079 | 0.361 | 4.442 | |
| estimateDominance | 0.106 | 0.010 | 0.116 | |
| estimateEvenness | 0.025 | 0.002 | 0.027 | |
| estimateRichness | 0.102 | 0.002 | 0.105 | |
| getExperimentCrossAssociation | 1.862 | 0.011 | 1.874 | |
| getPrevalence | 1.523 | 0.031 | 1.555 | |
| hierarchy-tree | 6.666 | 0.386 | 7.051 | |
| importHUMAnN | 0.091 | 0.001 | 0.093 | |
| importMetaPhlAn | 1.369 | 0.014 | 1.383 | |
| importMothur | 0.080 | 0.002 | 0.082 | |
| importQIIME2 | 0.333 | 0.047 | 0.381 | |
| isContaminant | 0.108 | 0.002 | 0.109 | |
| makePhyloseqFromTreeSE | 0.641 | 0.029 | 0.674 | |
| makeTreeSEFromBiom | 0.194 | 0.003 | 0.197 | |
| makeTreeSEFromDADA2 | 2.559 | 0.078 | 2.636 | |
| makeTreeSEFromPhyloseq | 0.468 | 0.027 | 0.497 | |
| meltAssay | 0.338 | 0.031 | 0.369 | |
| merge-methods | 0.494 | 0.012 | 0.506 | |
| mergeSEs | 1.867 | 0.055 | 1.921 | |
| mia-datasets | 0.184 | 0.002 | 0.186 | |
| perSampleDominantTaxa | 0.740 | 0.012 | 0.753 | |
| relabundance | 0.163 | 0.006 | 0.169 | |
| runCCA | 29.569 | 0.081 | 29.652 | |
| runDPCoA | 0.119 | 0.003 | 0.122 | |
| runNMDS | 0.091 | 0.002 | 0.092 | |
| splitByRanks | 2.878 | 0.062 | 2.940 | |
| splitOn | 1.234 | 0.017 | 1.250 | |
| subsampleCounts | 0.559 | 0.012 | 0.571 | |
| subsetSamples | 0.297 | 0.003 | 0.300 | |
| summaries | 0.988 | 0.006 | 0.995 | |
| taxonomy-methods | 0.360 | 0.003 | 0.364 | |
| transformAssay | 0.053 | 0.000 | 0.054 | |