Leo Lahti
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/microbiome |
| Branch: RELEASE_3_10 |
| Last Commit: 11ae6af |
| Last Changed Date: 2019-10-29 13:10:41 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:28:55 -0400 (Wed, 15 Apr 2020).
| Package 1039/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| microbiome 1.8.0 Leo Lahti
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: microbiome |
| Version: 1.8.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:microbiome.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings microbiome_1.8.0.tar.gz |
| StartedAt: 2020-04-15 04:45:27 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:49:48 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 261.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: microbiome.Rcheck |
| Warnings: 4 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:microbiome.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings microbiome_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/microbiome.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'microbiome/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'microbiome' version '1.8.0'
* 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 'microbiome' 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 ... 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 ... WARNING
Documented arguments not in \usage in documentation object 'core':
'...'
Documented arguments not in \usage in documentation object 'rare':
'...'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
atlas1006.rda 233Kb 128Kb xz
dietswap.rda 45Kb 28Kb xz
hitchip.taxonomy.rda 402Kb 115Kb xz
peerj32.rda 113Kb 87Kb xz
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... WARNING
Found the following significant warnings:
Warning: 'noncore_abundance' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:
Warning: 'noncore_abundance' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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: 4 WARNINGs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/microbiome.Rcheck/00check.log'
for details.
microbiome.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/microbiome_1.8.0.tar.gz && rm -rf microbiome.buildbin-libdir && mkdir microbiome.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=microbiome.buildbin-libdir microbiome_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL microbiome_1.8.0.zip && rm microbiome_1.8.0.tar.gz microbiome_1.8.0.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 695k 100 695k 0 0 15.3M 0 --:--:-- --:--:-- --:--:-- 16.5M
install for i386
* installing *source* package 'microbiome' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'microbiome'
finding HTML links ... done
abundances html
finding level-2 HTML links ... done
aggregate_taxa html
aggregate_top_taxa html
alpha html
associate html
atlas1006 html
baseline html
bfratio html
bimodality html
bimodality_sarle html
boxplot_abundance html
chunk_reorder html
cmat2table html
collapse_replicates html
core html
core_abundance html
core_heatmap html
core_matrix html
core_members html
coverage html
default_colors html
densityplot html
dietswap html
divergence html
diversities html
diversity html
dominance html
dominant html
estimate_stability html
evenness html
find_optima html
gktau html
global html
group_age html
group_bmi html
heat html
hitchip.taxonomy html
hotplot html
inequality html
intermediate_stability html
is.compositional html
log_modulo_skewness html
low_abundance html
map_levels html
merge_taxa2 html
meta html
microbiome-package html
multimodality html
neat html
neatsort html
noncore_abundance html
noncore_members html
peerj32 html
plot_atlas html
plot_composition html
plot_core html
plot_density html
plot_frequencies html
plot_landscape html
plot_regression html
plot_taxa_prevalence html
plot_tipping html
potential_analysis html
potential_univariate html
prevalence html
quiet html
radial_theta html
rare html
rare_abundance html
rare_members html
rarity html
read_biom2phyloseq html
read_csv2phyloseq html
read_mothur2phyloseq html
read_phyloseq html
readcount html
remove_samples html
remove_taxa html
richness html
spreadplot html
summarize_phyloseq html
taxa html
time_normalize html
time_sort html
timesplit html
top_taxa html
transform html
write_phyloseq html
ztransform 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 'microbiome' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'microbiome' as microbiome_1.8.0.zip
* DONE (microbiome)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'microbiome' successfully unpacked and MD5 sums checked
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microbiome.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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)
> test_check("microbiome")
Loading required package: microbiome
Loading required package: phyloseq
Loading required package: ggplot2
microbiome R package (microbiome.github.com)
Copyright (C) 2011-2019 Leo Lahti,
Sudarshan Shetty et al. <microbiome.github.io>
Attaching package: 'microbiome'
The following object is masked from 'package:ggplot2':
alpha
The following object is masked from 'package:base':
transform
== testthat results ===========================================================
[ OK: 74 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
11.26 0.81 12.17
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microbiome.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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)
> test_check("microbiome")
Loading required package: microbiome
Loading required package: phyloseq
Loading required package: ggplot2
microbiome R package (microbiome.github.com)
Copyright (C) 2011-2019 Leo Lahti,
Sudarshan Shetty et al. <microbiome.github.io>
Attaching package: 'microbiome'
The following object is masked from 'package:ggplot2':
alpha
The following object is masked from 'package:base':
transform
== testthat results ===========================================================
[ OK: 74 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
15.25 0.43 15.71
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microbiome.Rcheck/examples_i386/microbiome-Ex.timings
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microbiome.Rcheck/examples_x64/microbiome-Ex.timings
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