Chloe H. Lee
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/proBatch |
| Branch: RELEASE_3_9 |
| Last Commit: 6640beb |
| Last Changed Date: 2019-05-02 11:54:14 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:43:47 -0400 (Wed, 16 Oct 2019).
| Package 1251/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| proBatch 1.0.0 Chloe H. Lee
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: proBatch |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proBatch.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings proBatch_1.0.0.tar.gz |
| StartedAt: 2019-10-16 06:07:55 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:16:10 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 495.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: proBatch.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proBatch.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings proBatch_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/proBatch.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'proBatch/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'proBatch' version '1.0.0'
* 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 'proBatch' 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
Examples with CPU or elapsed time > 5s
user system elapsed
plot_with_fitting_curve 30.95 6.75 37.70
adjust_batch_trend 27.70 8.83 36.55
correct_batch_effects 26.58 8.42 35.02
plot_PVCA 5.67 0.02 15.90
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
adjust_batch_trend 32.44 11.50 43.94
correct_batch_effects 31.50 11.09 42.61
plot_with_fitting_curve 30.16 10.31 40.50
* 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
proBatch.Rcheck/00install.out
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###
### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/proBatch_1.0.0.tar.gz && rm -rf proBatch.buildbin-libdir && mkdir proBatch.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=proBatch.buildbin-libdir proBatch_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL proBatch_1.0.0.zip && rm proBatch_1.0.0.tar.gz proBatch_1.0.0.zip
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install for i386
* installing *source* package 'proBatch' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'proBatch'
finding HTML links ... done
adjust_batch_trend html
center_peptide_batch_medians html
color_list_to_df html
correct_batch_effects html
correct_with_ComBat html
create_peptide_annotation html
date_to_sample_order html
dates_to_posix html
dot-corr_distribution html
dot-corr_distribution_prot html
example_peptide_annotation html
example_proteome html
example_proteome_matrix html
example_sample_annotation html
fit_nonlinear html
generate_colors_for_numeric html
get_peptide_corr_df html
get_sample_corr_distrib html
log_transform html
long_to_matrix html
matrix_to_long html
merge_rare_levels html
normalize html
normalize_data html
normalize_sample_medians html
plot_PCA html
plot_PVCA html
plot_corr_matrix html
plot_heatmap html
plot_hierarchical_clustering html
plot_iRT html
plot_peptide_corr_distribution html
plot_peptides_of_one_protein html
plot_protein_corrplot html
plot_sample_corr_distribution html
plot_sample_corr_heatmap html
plot_sample_mean_or_boxplot html
plot_single_feature html
plot_spike_in html
plot_with_fitting_curve html
proBatch html
quantile_normalize html
sample_annotation_to_colors html
sample_color_scheme 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 'proBatch' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'proBatch' as proBatch_1.0.0.zip
* DONE (proBatch)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'proBatch' successfully unpacked and MD5 sums checked
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proBatch.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(proBatch)
>
> test_check("proBatch")
Standardizing Data across genes
== testthat results ===========================================================
[ OK: 144 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
>
> proc.time()
user system elapsed
16.79 1.03 17.81
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proBatch.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(proBatch)
>
> test_check("proBatch")
Standardizing Data across genes
== testthat results ===========================================================
[ OK: 144 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
16.42 0.60 17.03
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proBatch.Rcheck/examples_i386/proBatch-Ex.timings
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proBatch.Rcheck/examples_x64/proBatch-Ex.timings
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