David Rasp
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/BEclear |
| Branch: RELEASE_3_8 |
| Last Commit: e124e81 |
| Last Changed Date: 2018-10-30 11:41:58 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:25:23 -0400 (Sat, 13 Apr 2019).
| Package 118/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BEclear 1.14.0 David Rasp
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: BEclear |
| Version: 1.14.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BEclear.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BEclear_1.14.0.tar.gz |
| StartedAt: 2019-04-13 00:42:24 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 00:49:12 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 407.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BEclear.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BEclear.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BEclear_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/BEclear.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BEclear/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BEclear' version '1.14.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'BEclear' 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
BEclear-package 0.50 0.05 16.83
correctBatchEffect 0.35 0.01 16.71
imputeMissingData 0.13 0.05 16.06
clearBEgenes 0.12 0.05 11.14
calcSummary 0.08 0.06 10.61
countValuesToPredict 0.13 0.00 11.25
calcScore 0.10 0.02 11.16
calcPvalues 0.10 0.01 6.17
makeBoxplot 0.07 0.03 11.48
calcMedians 0.04 0.00 6.01
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
BEclear-package 0.63 0.02 17.77
correctBatchEffect 0.45 0.05 19.16
imputeMissingData 0.16 0.04 17.50
clearBEgenes 0.17 0.00 12.81
makeBoxplot 0.17 0.00 11.00
countValuesToPredict 0.13 0.01 11.49
calcSummary 0.11 0.02 11.56
calcMedians 0.10 0.01 5.33
calcScore 0.06 0.03 10.84
calcPvalues 0.07 0.00 6.47
* 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
BEclear.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/BEclear_1.14.0.tar.gz && rm -rf BEclear.buildbin-libdir && mkdir BEclear.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BEclear.buildbin-libdir BEclear_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL BEclear_1.14.0.zip && rm BEclear_1.14.0.tar.gz BEclear_1.14.0.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 192k 100 192k 0 0 5115k 0 --:--:-- --:--:-- --:--:-- 5670k
install for i386
* installing *source* package 'BEclear' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required namespace: BEclear
*** installing help indices
converting help for package 'BEclear'
finding HTML links ... done
BEclear-example-methylation-data html
BEclear-example-sample-data html
BEclear-package html
calcBlockFrame html
calcMedians html
calcMediansForBatch html
calcPositions html
calcPvalsForBatch html
calcPvalues html
calcScore html
calcSummary html
clearBEgenes html
combineBlocks html
correctBatchEffect html
countValuesToPredict html
dlossp html
ex.corrected.data html
findWrongValues html
gdepoch html
imputeMissingData html
imputeMissingDataForBlock html
loss html
makeBoxplot html
nnz html
replaceWrongValues html
runGradientDescent html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'BEclear' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BEclear' as BEclear_1.14.0.zip
* DONE (BEclear)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'BEclear' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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BEclear.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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(BEclear)
Loading required package: BiocParallel
>
> test_check("BEclear")
INFO [2019-04-13 00:48:29] Calculating the medians for 2 batches
INFO [2019-04-13 00:48:32] Calculating the medians for 3 batches
INFO [2019-04-13 00:48:37] Calculating the p-values for 2 batches
INFO [2019-04-13 00:48:40] Calculating the p-values for 3 batches
INFO [2019-04-13 00:48:43] Calculating the p-values for 3 batches
INFO [2019-04-13 00:48:47] Adjusting p-values
INFO [2019-04-13 00:48:47] 3 wrong values found
INFO [2019-04-13 00:48:47] Replacing values below 0 or above 1:
INFO [2019-04-13 00:48:47] 3 values replaced
== testthat results ===========================================================
OK: 71 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
2.62 0.12 20.51
|
BEclear.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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(BEclear)
Loading required package: BiocParallel
>
> test_check("BEclear")
INFO [2019-04-13 00:48:49] Calculating the medians for 2 batches
INFO [2019-04-13 00:48:52] Calculating the medians for 3 batches
INFO [2019-04-13 00:48:57] Calculating the p-values for 2 batches
INFO [2019-04-13 00:49:00] Calculating the p-values for 3 batches
INFO [2019-04-13 00:49:04] Calculating the p-values for 3 batches
INFO [2019-04-13 00:49:08] Adjusting p-values
INFO [2019-04-13 00:49:08] 3 wrong values found
INFO [2019-04-13 00:49:08] Replacing values below 0 or above 1:
INFO [2019-04-13 00:49:08] 3 values replaced
== testthat results ===========================================================
OK: 71 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
2.35 0.23 20.81
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BEclear.Rcheck/examples_i386/BEclear-Ex.timings
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BEclear.Rcheck/examples_x64/BEclear-Ex.timings
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