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This page was generated on 2024-10-11 11:46 -0400 (Fri, 11 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4468
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4723
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4473
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4504
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4452
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4452
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 1246/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiomeMarker 1.11.1  (landing page)
Yang Cao
Snapshot Date: 2024-10-10 13:40 -0400 (Thu, 10 Oct 2024)
git_url: https://git.bioconductor.org/packages/microbiomeMarker
git_branch: devel
git_last_commit: aee056c
git_last_commit_date: 2024-08-21 14:56:00 -0400 (Wed, 21 Aug 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    ERROR  skipped


CHECK results for microbiomeMarker on lconway

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: 1.11.1
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_1.11.1.tar.gz
StartedAt: 2024-10-10 23:40:52 -0400 (Thu, 10 Oct 2024)
EndedAt: 2024-10-10 23:51:48 -0400 (Thu, 10 Oct 2024)
EllapsedTime: 655.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: microbiomeMarker.Rcheck
Warnings: NA

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_1.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/microbiomeMarker.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘microbiomeMarker/DESCRIPTION’ ... OK
* this is package ‘microbiomeMarker’ version ‘1.11.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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 whether startup messages can be suppressed ... 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    13.792  0.118  13.948
run_aldex       7.552  0.830   8.400
plot_cladogram  6.164  0.105   6.276
run_lefse       5.054  0.062   5.121
* 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:
  • 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'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-confounder.R:42:5'): confounder analysis ─────────────────────
  res$pvalue (`actual`) not equal to 0.239 (`expected`).
  
    `actual`: 0.4
  `expected`: 0.2
  
  [ FAIL 1 | WARN 42 | SKIP 8 | PASS 220 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/microbiomeMarker.Rcheck/00check.log’
for details.


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
Warning in fun(libname, pkgname) :
  Package 'microbiomeMarker' is deprecated and will be removed from
  Bioconductor version 3.21
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'microbiomeMarker' is deprecated and will be removed from
  Bioconductor version 3.21
** testing if installed package keeps a record of temporary installation path
* DONE (microbiomeMarker)

Tests output

microbiomeMarker.Rcheck/tests/testthat.Rout.fail


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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)
Warning message:
In fun(libname, pkgname) :
  Package 'microbiomeMarker' is deprecated and will be removed from
  Bioconductor version 3.21
> 
> 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 1 | WARN 42 | SKIP 8 | PASS 220 ]

══ 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'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-confounder.R:42:5'): confounder analysis ─────────────────────
res$pvalue (`actual`) not equal to 0.239 (`expected`).

  `actual`: 0.4
`expected`: 0.2

[ FAIL 1 | WARN 42 | SKIP 8 | PASS 220 ]
Error: Test failures
Execution halted

Example timings

microbiomeMarker.Rcheck/microbiomeMarker-Ex.timings

nameusersystemelapsed
abundances-methods0.0800.0030.083
aggregate_taxa1.2870.0171.304
assign-marker_table2.2120.0492.263
confounder1.4800.0151.497
effect_size-plot2.2290.0202.251
extract_posthoc_res0.1000.0050.105
import_dada20.0550.0030.058
import_picrust20.0280.0020.030
import_qiime20.1920.0440.239
marker_table-methods2.0160.0072.027
microbiomeMarker0.0120.0000.013
nmarker-methods0.0010.0000.002
normalize-methods0.0850.0040.090
phyloseq2DESeq21.2930.0141.307
phyloseq2edgeR0.1130.0070.120
phyloseq2metagenomeSeq0.1260.0030.130
plot_abundance3.1110.0143.129
plot_cladogram6.1640.1056.276
plot_heatmap4.2590.0794.343
plot_postHocTest0.8370.0120.849
plot_sl_roc3.1670.0953.265
postHocTest0.0870.0050.091
run_aldex7.5520.8308.400
run_ancom0.0000.0010.000
run_ancombc13.792 0.11813.948
run_deseq24.4980.0274.528
run_edger2.1600.0202.183
run_lefse5.0540.0625.121
run_limma_voom2.0250.0092.038
run_metagenomeseq2.4620.0202.484
run_posthoc_test0.4190.0040.425
run_simple_stat2.1710.0152.189
run_sl1.2460.0081.255
run_test_multiple_groups2.3240.0112.335
run_test_two_groups2.2730.0112.286
subset_marker2.0750.0092.087
summarize_taxa0.2440.0030.248
transform_abundances0.1140.0170.131