Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:21:49 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for microbiomeMarker on palomino3


To the developers/maintainers of the microbiomeMarker package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1174/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiomeMarker 1.2.2  (landing page)
Yang Cao
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/microbiomeMarker
git_branch: RELEASE_3_15
git_last_commit: a51c6f2
git_last_commit_date: 2022-06-15 01:49:04 -0400 (Wed, 15 Jun 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: microbiomeMarker
Version: 1.2.2
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:microbiomeMarker.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings microbiomeMarker_1.2.2.tar.gz
StartedAt: 2022-10-19 01:52:10 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 02:01:32 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 562.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: microbiomeMarker.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:microbiomeMarker.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings microbiomeMarker_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/microbiomeMarker.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'microbiomeMarker/DESCRIPTION' ... OK
* this is package 'microbiomeMarker' version '1.2.2'
* 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 '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 ... ERROR
Running examples in 'microbiomeMarker-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: run_ancombc
> ### Title: Differential analysis of compositions of microbiomes with bias
> ###   correction (ANCOM-BC).
> ### Aliases: run_ancombc
> 
> ### ** Examples
> 
> data(enterotypes_arumugam)
> ps <- phyloseq::subset_samples(
+     enterotypes_arumugam,
+     Enterotype %in% c("Enterotype 3", "Enterotype 2")
+ )
> run_ancombc(ps, group = "Enterotype")
'ancombc' is deprecated 
Use 'ancombc2' instead
`tax_level` is not speficified 
The lowest taxonomic level will be used: 
Otherwise, please speficy `tax_level` by one of the following: 

Error: 'rank' must be an non empty single character value.
Execution halted
* 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: 1 ERROR
See
  'F:/biocbuild/bbs-3.15-bioc/meat/microbiomeMarker.Rcheck/00check.log'
for details.

Installation output

microbiomeMarker.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL microbiomeMarker
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/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 version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 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(microbiomeMarker)
> 
> test_check("microbiomeMarker")
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 32 | SKIP 8 | PASS 217 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (7)
• empty test (1)

[ FAIL 0 | WARN 32 | SKIP 8 | PASS 217 ]
> 
> proc.time()
   user  system elapsed 
  86.42    4.68   91.17

Example timings

microbiomeMarker.Rcheck/microbiomeMarker-Ex.timings

nameusersystemelapsed
abundances-methods0.060.040.11
aggregate_taxa1.750.011.77
assign-marker_table3.390.253.64
confounder2.060.022.07
effect_size-plot2.910.113.02
extract_posthoc_res0.150.010.17
import_dada20.080.000.11
import_picrust20.060.000.08
import_qiime20.360.080.66
marker_table-methods2.670.032.70
microbiomeMarker0.020.000.02
nmarker-methods000
normalize-methods0.090.010.11
phyloseq2DESeq20.550.030.58
phyloseq2edgeR0.160.020.17
phyloseq2metagenomeSeq0.150.020.17
plot_abundance3.690.093.78
plot_cladogram12.77 0.4113.17
plot_heatmap8.250.438.82
plot_postHocTest1.460.031.50
plot_sl_roc5.580.165.73
postHocTest0.190.000.19
run_aldex10.59 1.2211.98
run_ancom000