Yue Zhao
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/animalcules |
| Branch: RELEASE_3_11 |
| Last Commit: 8ee81de |
| Last Changed Date: 2020-06-18 11:27:45 -0400 (Thu, 18 Jun 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:05 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE animalcules PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 57/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| animalcules 1.4.0 Yue Zhao
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: animalcules |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:animalcules.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings animalcules_1.4.0.tar.gz |
| StartedAt: 2020-10-17 01:31:31 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 01:40:18 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 526.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: animalcules.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:animalcules.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings animalcules_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/animalcules.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'animalcules/DESCRIPTION' ... OK
* this is package 'animalcules' version '1.4.0'
* 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 whether package 'animalcules' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Namespace in Imports field not imported from: 'reactable'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
alpha_div_boxplot: no visible binding for global variable 'richness'
differential_abundance: no visible binding for global variable 'padj'
differential_abundance: no visible binding for global variable 'pValue'
differential_abundance: no visible binding for global variable
'log2FoldChange'
diversities_help: no visible binding for global variable 'x'
find_biomarker: no visible binding for global variable 'rowname'
find_biomarker: no visible binding for global variable 'importance'
find_biomarker: no visible binding for global variable '.'
find_biomarker: no visible binding for global variable 'Overall'
find_biomarker: no visible binding for global variable 'y'
find_biomarker: no visible binding for global variable 'm'
find_biomarker: no visible binding for global variable 'd'
relabu_barplot: no visible binding for global variable '.'
relabu_boxplot: no visible binding for global variable '.'
relabu_heatmap: no visible binding for global variable '.'
upsample_counts: no visible binding for global variable '.'
Undefined global functions or variables:
. Overall d importance log2FoldChange m pValue padj richness rowname
x y
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
find_biomarker 10.29 0.05 10.36
dimred_tsne 6.53 0.17 9.71
differential_abundance 5.07 0.25 5.34
alpha_div_boxplot 0.90 0.30 8.25
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
find_biomarker 10.38 0.03 10.41
dimred_tsne 6.77 0.05 6.86
differential_abundance 6.08 0.05 6.12
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/animalcules.Rcheck/00check.log'
for details.
animalcules.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/animalcules_1.4.0.tar.gz && rm -rf animalcules.buildbin-libdir && mkdir animalcules.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=animalcules.buildbin-libdir animalcules_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL animalcules_1.4.0.zip && rm animalcules_1.4.0.tar.gz animalcules_1.4.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1846k 100 1846k 0 0 23.8M 0 --:--:-- --:--:-- --:--:-- 26.1M
install for i386
* installing *source* package 'animalcules' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'animalcules'
finding HTML links ... done
alpha_div_boxplot html
alpha_div_test html
animalcules-package html
counts_to_logcpm html
counts_to_relabu html
df_char_to_factor html
differential_abundance html
dimred_pca html
dimred_pcoa html
dimred_tsne html
dimred_umap html
diversities html
diversities_help html
diversity_beta_boxplot html
diversity_beta_heatmap html
diversity_beta_test html
do_alpha_div_test html
filter_categorize html
filter_summary_bar_density html
filter_summary_pie_box html
find_biomarker html
find_taxon_mat html
find_taxonomy html
find_taxonomy_300 html
gini_simpson html
grep_tid html
inverse_simpson html
is_categorical html
is_integer0 html
is_integer1 html
mae_pick_organisms html
mae_pick_samples html
pct2str html
percent html
read_pathoscope_data html
relabu_barplot html
relabu_boxplot html
relabu_heatmap html
run_animalcules html
shannon html
simpson_index html
upsample_counts html
write_to_biom html
** 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
install for x64
* installing *source* package 'animalcules' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'animalcules' as animalcules_1.4.0.zip
* DONE (animalcules)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'animalcules' successfully unpacked and MD5 sums checked
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animalcules.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(animalcules)
>
> test_check("animalcules")
== testthat results ===========================================================
[ OK: 39 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
42.10 1.71 44.82
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animalcules.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(animalcules)
>
> test_check("animalcules")
== testthat results ===========================================================
[ OK: 39 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
46.81 0.76 48.28
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animalcules.Rcheck/examples_i386/animalcules-Ex.timings
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animalcules.Rcheck/examples_x64/animalcules-Ex.timings
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