Yang Cao
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/microbiomeMarker |
| git_branch: RELEASE_3_17 |
| git_last_commit: 63594b2 |
| git_last_commit_date: 2023-04-25 11:33:28 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:37:14 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1222/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| microbiomeMarker 1.6.0 (landing page) Yang Cao
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: microbiomeMarker |
| Version: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2023-10-16 03:52:59 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 04:17:13 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 1453.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: microbiomeMarker.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/microbiomeMarker.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘microbiomeMarker/DESCRIPTION’ ... OK
* this is package ‘microbiomeMarker’ version ‘1.6.0’
* 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 43.681 0.254 57.290
run_aldex 21.879 1.335 30.419
plot_cladogram 19.967 0.304 26.148
run_lefse 14.644 0.281 19.969
plot_heatmap 14.444 0.215 18.917
run_deseq2 13.351 0.072 17.335
plot_abundance 11.095 0.083 14.389
plot_sl_roc 9.717 0.179 12.682
run_metagenomeseq 8.381 0.085 11.142
run_test_two_groups 7.802 0.043 10.455
run_test_multiple_groups 7.767 0.036 10.331
effect_size-plot 7.353 0.056 9.774
assign-marker_table 7.103 0.221 9.315
run_simple_stat 7.065 0.043 9.613
marker_table-methods 7.058 0.038 9.032
run_edger 6.876 0.038 8.880
subset_marker 6.843 0.032 9.322
run_limma_voom 6.795 0.054 8.974
confounder 3.947 0.044 5.269
run_sl 3.896 0.027 5.256
* 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: OK
microbiomeMarker.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL microbiomeMarker ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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)
microbiomeMarker.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 43 | SKIP 8 | PASS 217 ]
══ 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 43 | SKIP 8 | PASS 217 ]
>
> proc.time()
user system elapsed
173.546 5.740 242.815
microbiomeMarker.Rcheck/microbiomeMarker-Ex.timings
| name | user | system | elapsed | |
| abundances-methods | 0.154 | 0.011 | 0.217 | |
| aggregate_taxa | 2.357 | 0.045 | 3.086 | |
| assign-marker_table | 7.103 | 0.221 | 9.315 | |
| confounder | 3.947 | 0.044 | 5.269 | |
| effect_size-plot | 7.353 | 0.056 | 9.774 | |
| extract_posthoc_res | 0.247 | 0.012 | 0.343 | |
| import_dada2 | 0.154 | 0.006 | 0.218 | |
| import_picrust2 | 0.077 | 0.004 | 0.107 | |
| import_qiime2 | 0.506 | 0.091 | 0.787 | |
| marker_table-methods | 7.058 | 0.038 | 9.032 | |
| microbiomeMarker | 0.033 | 0.003 | 0.046 | |
| nmarker-methods | 0.003 | 0.001 | 0.003 | |
| normalize-methods | 0.212 | 0.012 | 0.289 | |
| phyloseq2DESeq2 | 1.187 | 0.012 | 1.521 | |
| phyloseq2edgeR | 0.375 | 0.015 | 0.492 | |
| phyloseq2metagenomeSeq | 0.341 | 0.006 | 0.440 | |
| plot_abundance | 11.095 | 0.083 | 14.389 | |
| plot_cladogram | 19.967 | 0.304 | 26.148 | |
| plot_heatmap | 14.444 | 0.215 | 18.917 | |
| plot_postHocTest | 2.610 | 0.026 | 3.470 | |
| plot_sl_roc | 9.717 | 0.179 | 12.682 | |
| postHocTest | 0.198 | 0.010 | 0.278 | |
| run_aldex | 21.879 | 1.335 | 30.419 | |
| run_ancom | 0.000 | 0.000 | 0.003 | |
| run_ancombc | 43.681 | 0.254 | 57.290 | |
| run_deseq2 | 13.351 | 0.072 | 17.335 | |
| run_edger | 6.876 | 0.038 | 8.880 | |
| run_lefse | 14.644 | 0.281 | 19.969 | |
| run_limma_voom | 6.795 | 0.054 | 8.974 | |
| run_metagenomeseq | 8.381 | 0.085 | 11.142 | |
| run_posthoc_test | 1.384 | 0.023 | 1.884 | |
| run_simple_stat | 7.065 | 0.043 | 9.613 | |
| run_sl | 3.896 | 0.027 | 5.256 | |
| run_test_multiple_groups | 7.767 | 0.036 | 10.331 | |
| run_test_two_groups | 7.802 | 0.043 | 10.455 | |
| subset_marker | 6.843 | 0.032 | 9.322 | |
| summarize_taxa | 0.868 | 0.009 | 1.167 | |
| transform_abundances | 0.281 | 0.058 | 0.472 | |