Yang Cao
| Snapshot Date: 2023-03-29 14:00:20 -0400 (Wed, 29 Mar 2023) |
| git_url: https://git.bioconductor.org/packages/microbiomeMarker |
| git_branch: devel |
| git_last_commit: 9ef4bd2 |
| git_last_commit_date: 2022-11-01 11:25:50 -0400 (Tue, 01 Nov 2022) |
| Back to Build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-30 12:33:48 -0400 (Thu, 30 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" | 4547 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1206/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| microbiomeMarker 1.5.0 (landing page) Yang Cao
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| Package: microbiomeMarker |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:microbiomeMarker.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings microbiomeMarker_1.5.0.tar.gz |
| StartedAt: 2023-03-29 21:32:19 -0400 (Wed, 29 Mar 2023) |
| EndedAt: 2023-03-29 21:43:43 -0400 (Wed, 29 Mar 2023) |
| EllapsedTime: 684.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: microbiomeMarker.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:microbiomeMarker.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings microbiomeMarker_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/microbiomeMarker.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘microbiomeMarker/DESCRIPTION’ ... OK
* this is package ‘microbiomeMarker’ version ‘1.5.0’
* 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 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 17.283 0.208 17.490
plot_cladogram 10.681 0.276 10.957
run_aldex 7.177 0.156 7.332
plot_heatmap 6.423 0.120 6.544
run_deseq2 6.384 0.072 6.455
run_lefse 5.479 0.028 5.506
* 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 ...
‘microbiomeMarker-vignette.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
microbiomeMarker.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL microbiomeMarker ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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
R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 ═══════════════════════════════════════════════════════════════
• On CRAN (7)
• empty test (1)
[ FAIL 0 | WARN 43 | SKIP 8 | PASS 217 ]
>
> proc.time()
user system elapsed
75.307 2.479 77.778
microbiomeMarker.Rcheck/microbiomeMarker-Ex.timings
| name | user | system | elapsed | |
| abundances-methods | 0.090 | 0.012 | 0.101 | |
| aggregate_taxa | 1.007 | 0.024 | 1.032 | |
| assign-marker_table | 3.520 | 0.200 | 3.721 | |
| confounder | 1.822 | 0.036 | 1.858 | |
| effect_size-plot | 3.617 | 0.132 | 3.749 | |
| extract_posthoc_res | 0.182 | 0.007 | 0.190 | |
| import_dada2 | 0.094 | 0.008 | 0.102 | |
| import_picrust2 | 0.043 | 0.004 | 0.047 | |
| import_qiime2 | 0.309 | 0.024 | 0.334 | |
| marker_table-methods | 3.300 | 0.028 | 3.328 | |
| microbiomeMarker | 0.016 | 0.004 | 0.020 | |
| nmarker-methods | 0.002 | 0.000 | 0.002 | |
| normalize-methods | 0.116 | 0.012 | 0.127 | |
| phyloseq2DESeq2 | 2.493 | 0.168 | 2.660 | |
| phyloseq2edgeR | 0.153 | 0.000 | 0.152 | |
| phyloseq2metagenomeSeq | 0.183 | 0.004 | 0.188 | |
| plot_abundance | 4.249 | 0.044 | 4.293 | |
| plot_cladogram | 10.681 | 0.276 | 10.957 | |
| plot_heatmap | 6.423 | 0.120 | 6.544 | |
| plot_postHocTest | 1.147 | 0.004 | 1.152 | |
| plot_sl_roc | 4.142 | 0.084 | 4.227 | |
| postHocTest | 0.102 | 0.000 | 0.103 | |
| run_aldex | 7.177 | 0.156 | 7.332 | |
| run_ancom | 0 | 0 | 0 | |
| run_ancombc | 17.283 | 0.208 | 17.490 | |
| run_deseq2 | 6.384 | 0.072 | 6.455 | |
| run_edger | 2.837 | 0.012 | 2.848 | |
| run_lefse | 5.479 | 0.028 | 5.506 | |
| run_limma_voom | 2.722 | 0.003 | 2.725 | |
| run_metagenomeseq | 3.388 | 0.020 | 3.408 | |
| run_posthoc_test | 0.560 | 0.012 | 0.572 | |
| run_simple_stat | 2.918 | 0.007 | 2.925 | |
| run_sl | 1.580 | 0.008 | 1.588 | |
| run_test_multiple_groups | 3.1 | 0.0 | 3.1 | |
| run_test_two_groups | 2.971 | 0.036 | 3.007 | |
| subset_marker | 4.226 | 0.112 | 4.338 | |
| summarize_taxa | 0.301 | 0.000 | 0.301 | |
| transform_abundances | 0.131 | 0.028 | 0.159 | |