Leo Lahti
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/microbiome |
| Branch: RELEASE_3_7 |
| Last Commit: ce71c09 |
| Last Changed Date: 2018-05-23 09:21:39 -0400 (Wed, 23 May 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:44:25 -0400 (Wed, 17 Oct 2018).
| Package 902/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| microbiome 1.2.1 Leo Lahti
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: microbiome |
| Version: 1.2.1 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:microbiome.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings microbiome_1.2.1.tar.gz |
| StartedAt: 2018-10-17 03:20:47 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 03:24:54 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 246.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: microbiome.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:microbiome.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings microbiome_1.2.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/microbiome.Rcheck' * using R version 3.5.1 Patched (2018-07-24 r75005) * 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 '1.2.1' * 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 ... 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * 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: OK
microbiome.Rcheck/00install.out
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/microbiome_1.2.1.tar.gz && rm -rf microbiome.buildbin-libdir && mkdir microbiome.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=microbiome.buildbin-libdir microbiome_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL microbiome_1.2.1.zip && rm microbiome_1.2.1.tar.gz microbiome_1.2.1.zip
###
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install for i386
* installing *source* package 'microbiome' ...
** 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
associate html
atlas1006 html
baseline html
bimodality html
bimodality_sarle html
boxplot_abundance html
chunk_reorder html
cmat2table html
core html
core_abundance html
core_heatmap html
core_matrix html
core_members html
coverage html
densityplot html
dietswap html
divergence html
diversities html
dominance 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
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_members html
rarity html
read_biom2phyloseq html
read_csv2phyloseq html
read_mothur2phyloseq html
read_phyloseq html
remove_samples html
remove_taxa html
richness html
summarize_phyloseq html
taxa html
time_normalize html
time_sort html
top_taxa html
transform html
variable_members html
write_phyloseq html
ztransform html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'microbiome' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'microbiome' as microbiome_1.2.1.zip
* DONE (microbiome)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'microbiome' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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microbiome.Rcheck/tests_i386/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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) 2011-2018 Leo Lahti et al. <microbiome.github.io>
Attaching package: 'microbiome'
The following object is masked from 'package:base':
transform
== testthat results ===========================================================
OK: 69 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
7.51 0.71 8.20
|
microbiome.Rcheck/tests_x64/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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) 2011-2018 Leo Lahti et al. <microbiome.github.io>
Attaching package: 'microbiome'
The following object is masked from 'package:base':
transform
== testthat results ===========================================================
OK: 69 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
8.34 0.34 8.67
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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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