Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2024-03-04 11:39:30 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 1237/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiomeMarker 1.9.0  (landing page)
Yang Cao
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/microbiomeMarker
git_branch: devel
git_last_commit: afe4745
git_last_commit_date: 2023-11-04 12:01:59 -0500 (Sat, 04 Nov 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for microbiomeMarker on merida1


To the developers/maintainers of the microbiomeMarker package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/microbiomeMarker.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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.

raw results


Summary

Package: microbiomeMarker
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:microbiomeMarker.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings microbiomeMarker_1.9.0.tar.gz
StartedAt: 2024-03-02 06:43:40 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 07:06:31 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 1370.5 seconds
RetCode: 0
Status:   OK  
CheckDir: microbiomeMarker.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:microbiomeMarker.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings microbiomeMarker_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/microbiomeMarker.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘microbiomeMarker/DESCRIPTION’ ... OK
* this is package ‘microbiomeMarker’ version ‘1.9.0’
* 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 ‘microbiomeMarker’ 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
run_ancombc              43.962  0.459  53.264
run_aldex                21.640  1.405  26.834
plot_cladogram           20.881  0.348  24.731
run_lefse                14.196  0.190  17.148
plot_heatmap             13.705  0.219  16.162
run_deseq2               13.496  0.141  16.514
plot_abundance           10.706  0.139  13.381
plot_sl_roc               9.823  0.215  11.918
run_metagenomeseq         8.555  0.108  10.275
effect_size-plot          7.838  0.167   9.385
run_test_multiple_groups  7.935  0.065   9.122
run_test_two_groups       7.906  0.075   9.683
run_simple_stat           7.263  0.072   8.576
run_edger                 7.172  0.089   9.074
marker_table-methods      7.052  0.093   8.474
subset_marker             7.074  0.062   8.557
run_limma_voom            6.869  0.069   8.208
assign-marker_table       6.226  0.254   6.591
confounder                4.970  0.093   5.120
* 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: OK


Installation output

microbiomeMarker.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL microbiomeMarker
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘microbiomeMarker’ ...
** 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 (microbiomeMarker)

Tests output

microbiomeMarker.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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(microbiomeMarker)
> 
> test_check("microbiomeMarker")
conditions vector supplied
operating in serial mode
computing center with all features
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
operating in serial mode
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
`set.seed(2020)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(2020); .Random.seed` for the full vector
...
46OTUs were removed because they are no longer 
present in any sample after random subsampling

...
`set.seed(2020)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(2020); .Random.seed` for the full vector
...
46OTUs were removed because they are no longer 
present in any sample after random subsampling

...
`set.seed(2020)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(2020); .Random.seed` for the full vector
...
46OTUs were removed because they are no longer 
present in any sample after random subsampling

...
`set.seed(2020)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(2020); .Random.seed` for the full vector
...
46OTUs were removed because they are no longer 
present in any sample after random subsampling

...
Default value being used.
Default value being used.
Default value being used.
Default value being used.
converting counts to integer mode
Loading required package: ggplot2
Loading required package: lattice
[ FAIL 0 | WARN 42 | SKIP 8 | PASS 221 ]

══ Skipped tests (8) ═══════════════════════════════════════════════════════════
• On CRAN (7): 'test-ancom.R:46:5', 'test-edgeR.R:9:5', 'test-lefse.R:19:5',
  'test-limma-voom.R:15:5', 'test-multiple-groups-test.R:27:5',
  'test-multiple-groups-test.R:54:9', 'test-two-group-test.R:24:5'
• empty test (1): 'test-ancombc.R:1:1'

[ FAIL 0 | WARN 42 | SKIP 8 | PASS 221 ]
> 
> proc.time()
   user  system elapsed 
169.579   5.967 212.800 

Example timings

microbiomeMarker.Rcheck/microbiomeMarker-Ex.timings

nameusersystemelapsed
abundances-methods0.1750.0070.420
aggregate_taxa1.1410.0481.207
assign-marker_table6.2260.2546.591
confounder4.9700.0935.120
effect_size-plot7.8380.1679.385
extract_posthoc_res0.2380.0100.288
import_dada20.1490.0060.185
import_picrust20.0770.0040.095
import_qiime20.4210.0880.681
marker_table-methods7.0520.0938.474
microbiomeMarker0.0330.0030.044
nmarker-methods0.0040.0000.004
normalize-methods0.2020.0110.246
phyloseq2DESeq21.1610.0231.594
phyloseq2edgeR0.3120.0160.391
phyloseq2metagenomeSeq0.3410.0140.421
plot_abundance10.706 0.13913.381
plot_cladogram20.881 0.34824.731
plot_heatmap13.705 0.21916.162
plot_postHocTest3.2500.0353.804
plot_sl_roc 9.823 0.21511.918
postHocTest0.1830.0100.227
run_aldex21.640 1.40526.834
run_ancom0.0010.0010.001
run_ancombc43.962 0.45953.264
run_deseq213.496 0.14116.514
run_edger7.1720.0899.074
run_lefse14.196 0.19017.148
run_limma_voom6.8690.0698.208
run_metagenomeseq 8.555 0.10810.275
run_posthoc_test1.2920.0171.549
run_simple_stat7.2630.0728.576
run_sl4.0290.0434.681
run_test_multiple_groups7.9350.0659.122
run_test_two_groups7.9060.0759.683
subset_marker7.0740.0628.557
summarize_taxa0.8710.0111.025
transform_abundances0.2830.0590.389