Yang Cao
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/microbiomeMarker |
| git_branch: master |
| git_last_commit: d82163d |
| git_last_commit_date: 2022-03-07 09:54:42 -0400 (Mon, 07 Mar 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:01 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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: - 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1149/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| microbiomeMarker 1.1.2 (landing page) Yang Cao
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: microbiomeMarker |
| Version: 1.1.2 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:microbiomeMarker.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings microbiomeMarker_1.1.2.tar.gz |
| StartedAt: 2022-03-17 19:34:51 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:40:45 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 354.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: microbiomeMarker.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:microbiomeMarker.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings microbiomeMarker_1.1.2.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/microbiomeMarker.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'microbiomeMarker/DESCRIPTION' ... OK
* this is package 'microbiomeMarker' version '1.1.2'
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_cladogram 9.08 0.32 9.39
run_ancombc 7.39 0.01 7.41
run_aldex 5.42 1.21 6.62
plot_heatmap 6.02 0.28 6.29
run_deseq2 5.47 0.02 5.48
plot_sl_roc 4.89 0.12 5.02
* 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
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL microbiomeMarker
###
##############################################################################
##############################################################################
* installing to library 'D:/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
converting help for package 'microbiomeMarker'
finding HTML links ... done
abundances-methods html
finding level-2 HTML links ... done
aggregate_taxa html
assign-marker_table html
assign-otu_table html
data-caporaso html
data-cid_ying html
data-ecam html
data-enterotypes_arumugam html
data-kostic_crc html
data-oxygen html
data-pediatric_ibd html
data-spontaneous_colitis html
effect_size-plot html
extract-methods html
extract_posthoc_res html
get_treedata_phyloseq html
import_dada2 html
import_picrust2 html
import_qiime2 html
marker_table-class html
marker_table-methods html
microbiomeMarker-class html
microbiomeMarker-package html
microbiomeMarker html
nmarker-methods html
normalize-methods html
phyloseq2DESeq2 html
phyloseq2edgeR html
phyloseq2metagenomeSeq html
plot_abundance html
plot_cladogram html
plot_heatmap html
plot_postHocTest html
plot_sl_roc html
postHocTest-class html
postHocTest html
reexports html
run_aldex html
run_ancom html
run_ancombc html
run_deseq2 html
run_edger html
run_lefse html
run_limma_voom html
run_marker html
run_metagenomeseq html
run_posthoc_test html
run_simple_stat html
run_sl html
run_test_multiple_groups html
run_test_two_groups html
subset_marker html
summarize_taxa html
transform_abundances html
*** 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)
Making 'packages.html' ... done
microbiomeMarker.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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
* ...
New names:
* `` -> ...1
* `` -> ...2
* `` -> ...3
* `` -> ...4
* `` -> ...5
* ...
operating in serial mode
New names:
* `` -> ...1
* `` -> ...2
* `` -> ...3
* `` -> ...4
* `` -> ...5
* ...
New names:
* `` -> ...1
* `` -> ...2
* `` -> ...3
* `` -> ...4
* `` -> ...5
* ...
New names:
* `` -> ...1
* `` -> ...2
* `` -> ...3
* `` -> ...4
* `` -> ...5
* ...
New names:
* `` -> ...1
* `` -> ...2
* `` -> ...3
* `` -> ...4
* `` -> ...5
* ...
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
`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 26 | SKIP 8 | PASS 194 ]
== Skipped tests ===============================================================
* On CRAN (7)
* empty test (1)
[ FAIL 0 | WARN 26 | SKIP 8 | PASS 194 ]
>
> proc.time()
user system elapsed
53.00 2.78 55.84
microbiomeMarker.Rcheck/microbiomeMarker-Ex.timings
| name | user | system | elapsed | |
| abundances-methods | 0.05 | 0.02 | 0.06 | |
| aggregate_taxa | 0.86 | 0.03 | 0.89 | |
| assign-marker_table | 2.14 | 0.16 | 2.30 | |
| effect_size-plot | 2.17 | 0.03 | 2.20 | |
| extract_posthoc_res | 0.09 | 0.00 | 0.09 | |
| import_dada2 | 0.04 | 0.00 | 0.05 | |
| import_picrust2 | 0.04 | 0.00 | 0.03 | |
| import_qiime2 | 0.25 | 0.03 | 0.39 | |
| marker_table-methods | 2.03 | 0.00 | 2.04 | |
| microbiomeMarker | 0 | 0 | 0 | |
| nmarker-methods | 0 | 0 | 0 | |
| normalize-methods | 0.10 | 0.00 | 0.09 | |
| phyloseq2DESeq2 | 0.40 | 0.01 | 0.43 | |
| phyloseq2edgeR | 0.08 | 0.05 | 0.12 | |
| phyloseq2metagenomeSeq | 0.11 | 0.01 | 0.13 | |
| plot_abundance | 3.33 | 0.00 | 3.34 | |
| plot_cladogram | 9.08 | 0.32 | 9.39 | |
| plot_heatmap | 6.02 | 0.28 | 6.29 | |
| plot_postHocTest | 1.44 | 0.00 | 1.44 | |
| plot_sl_roc | 4.89 | 0.12 | 5.02 | |
| postHocTest | 0.13 | 0.00 | 0.13 | |
| run_aldex | 5.42 | 1.21 | 6.62 | |
| run_ancom | 0 | 0 | 0 | |
| run_ancombc | 7.39 | 0.01 | 7.41 | |
| run_deseq2 | 5.47 | 0.02 | 5.48 | |
| run_edger | 2.15 | 0.01 | 2.17 | |
| run_lefse | 4.25 | 0.17 | 4.43 | |
| run_limma_voom | 3.38 | 0.00 | 3.37 | |
| run_metagenomeseq | 2.59 | 0.02 | 2.61 | |
| run_posthoc_test | 0.52 | 0.00 | 0.52 | |
| run_simple_stat | 2.25 | 0.00 | 2.25 | |
| run_sl | 2.25 | 0.00 | 2.26 | |
| run_test_multiple_groups | 3.15 | 0.02 | 3.17 | |
| run_test_two_groups | 2.24 | 0.01 | 2.25 | |
| subset_marker | 1.94 | 0.02 | 1.96 | |
| summarize_taxa | 0.27 | 0.00 | 0.27 | |
| transform_abundances | 0.12 | 0.00 | 0.12 | |