| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-31 17:03:04 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
| 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 1264/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| microbiomeMarker 1.10.0 (landing page) Yang Cao
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
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: 1.10.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:microbiomeMarker.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings microbiomeMarker_1.10.0.tar.gz |
| StartedAt: 2024-05-31 05:31:52 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 05:42:55 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 663.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: microbiomeMarker.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:microbiomeMarker.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings microbiomeMarker_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/microbiomeMarker.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘microbiomeMarker/DESCRIPTION’ ... OK
* this is package ‘microbiomeMarker’ version ‘1.10.0’
* 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 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 loading without being on the library search path ... 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 17.882 0.960 18.842
plot_cladogram 7.868 0.084 7.952
run_aldex 6.885 0.604 7.489
plot_heatmap 6.913 0.260 7.173
run_lefse 6.228 0.324 6.551
run_deseq2 5.439 0.136 5.575
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
See
‘/home/biocbuild/bbs-3.19-bioc/meat/microbiomeMarker.Rcheck/00check.log’
for details.
microbiomeMarker.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL microbiomeMarker ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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.fail
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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 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
microbiomeMarker.Rcheck/microbiomeMarker-Ex.timings
| name | user | system | elapsed | |
| abundances-methods | 0.097 | 0.005 | 0.101 | |
| aggregate_taxa | 0.596 | 0.020 | 0.616 | |
| assign-marker_table | 2.812 | 0.084 | 2.896 | |
| confounder | 1.683 | 0.007 | 1.691 | |
| effect_size-plot | 4.012 | 0.076 | 4.088 | |
| extract_posthoc_res | 0.12 | 0.00 | 0.12 | |
| import_dada2 | 0.068 | 0.004 | 0.072 | |
| import_picrust2 | 0.035 | 0.000 | 0.035 | |
| import_qiime2 | 0.214 | 0.012 | 0.227 | |
| marker_table-methods | 2.615 | 0.004 | 2.619 | |
| microbiomeMarker | 0.015 | 0.000 | 0.015 | |
| nmarker-methods | 0.000 | 0.002 | 0.002 | |
| normalize-methods | 0.097 | 0.001 | 0.099 | |
| phyloseq2DESeq2 | 0.522 | 0.004 | 0.527 | |
| phyloseq2edgeR | 0.137 | 0.000 | 0.138 | |
| phyloseq2metagenomeSeq | 0.156 | 0.016 | 0.172 | |
| plot_abundance | 3.900 | 0.023 | 3.925 | |
| plot_cladogram | 7.868 | 0.084 | 7.952 | |
| plot_heatmap | 6.913 | 0.260 | 7.173 | |
| plot_postHocTest | 1.067 | 0.004 | 1.071 | |
| plot_sl_roc | 4.033 | 0.136 | 4.172 | |
| postHocTest | 0.117 | 0.000 | 0.117 | |
| run_aldex | 6.885 | 0.604 | 7.489 | |
| run_ancom | 0 | 0 | 0 | |
| run_ancombc | 17.882 | 0.960 | 18.842 | |
| run_deseq2 | 5.439 | 0.136 | 5.575 | |
| run_edger | 2.751 | 0.080 | 2.831 | |
| run_lefse | 6.228 | 0.324 | 6.551 | |
| run_limma_voom | 2.547 | 0.068 | 2.616 | |
| run_metagenomeseq | 3.230 | 0.084 | 3.314 | |
| run_posthoc_test | 0.539 | 0.000 | 0.540 | |
| run_simple_stat | 2.733 | 0.020 | 2.753 | |
| run_sl | 1.558 | 0.016 | 1.575 | |
| run_test_multiple_groups | 2.919 | 0.032 | 2.951 | |
| run_test_two_groups | 2.824 | 0.072 | 2.897 | |
| subset_marker | 2.579 | 0.040 | 2.620 | |
| summarize_taxa | 0.294 | 0.000 | 0.294 | |
| transform_abundances | 0.128 | 0.028 | 0.156 | |