David Rasp
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/BEclear |
| Branch: RELEASE_3_10 |
| Last Commit: 0537966 |
| Last Changed Date: 2019-10-29 13:09:18 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:41:59 -0400 (Wed, 15 Apr 2020).
| Package 132/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BEclear 2.2.0 David Rasp
| malbec1 | Linux (Ubuntu 18.04.4 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: 2.2.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BEclear.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BEclear_2.2.0.tar.gz |
| StartedAt: 2020-04-15 00:38:12 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 00:39:42 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 90.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BEclear.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BEclear.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BEclear_2.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/BEclear.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BEclear/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BEclear’ version ‘2.2.0’
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
.github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
calcBatchEffects 30.829 15.059 7.411
BEclear-package 8.261 4.735 2.282
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/BEclear.Rcheck/00check.log’
for details.
BEclear.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BEclear ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘BEclear’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c localLoss.cpp -o localLoss.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BEclear.so RcppExports.o localLoss.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-BEclear/00new/BEclear/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help Loading required namespace: BEclear *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BEclear)
BEclear.Rcheck/tests/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-apple-darwin15.6.0 (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 [2020-04-15 00:39:31] Calculate the batch effects for 2 batches
INFO [2020-04-15 00:39:31] Calculate the batch effects for 3 batches
INFO [2020-04-15 00:39:31] Calculate the batch effects for 3 batches
INFO [2020-04-15 00:39:32] Adjusting p-values
INFO [2020-04-15 00:39:32] Transforming matrix to data.table
INFO [2020-04-15 00:39:32] Calculate the batch effects for 4 batches
INFO [2020-04-15 00:39:32] Adjusting p-values
INFO [2020-04-15 00:39:32] Generating a summary table
INFO [2020-04-15 00:39:32] Calculating the scores for 4 batches
INFO [2020-04-15 00:39:32] Generating a summary table
INFO [2020-04-15 00:39:32] Generating a summary table
INFO [2020-04-15 00:39:33] Transforming matrix to data.table
INFO [2020-04-15 00:39:33] Calculate the batch effects for 3 batches
INFO [2020-04-15 00:39:33] Adjusting p-values
INFO [2020-04-15 00:39:33] Generating a summary table
INFO [2020-04-15 00:39:33] Calculating the scores for 3 batches
INFO [2020-04-15 00:39:33] Removing values with batch effect:
INFO [2020-04-15 00:39:33] 4 values ( 26.6666666666667 % of the data) set to NA
INFO [2020-04-15 00:39:33] Starting the imputation of missing values.
INFO [2020-04-15 00:39:33] This might take a while.
INFO [2020-04-15 00:39:33] BEclear imputation is started:
INFO [2020-04-15 00:39:33] block size: 60 x 60
INFO [2020-04-15 00:39:33] Impute missing data for block 1 of 1
INFO [2020-04-15 00:39:33] Replacing values below 0 or above 1:
INFO [2020-04-15 00:39:33] 0 values replaced
WARN [2020-04-15 00:39:33] 3 values are above 1 or below 0. Check your data
WARN [2020-04-15 00:39:33] Replacing them with missing values
INFO [2020-04-15 00:39:33] Transforming matrix to data.table
INFO [2020-04-15 00:39:33] Calculate the batch effects for 3 batches
INFO [2020-04-15 00:39:33] Adjusting p-values
INFO [2020-04-15 00:39:33] Generating a summary table
INFO [2020-04-15 00:39:33] Calculating the scores for 3 batches
INFO [2020-04-15 00:39:33] Removing values with batch effect:
INFO [2020-04-15 00:39:33] 3 values ( 20 % of the data) set to NA
INFO [2020-04-15 00:39:33] Starting the imputation of missing values.
INFO [2020-04-15 00:39:33] This might take a while.
INFO [2020-04-15 00:39:33] BEclear imputation is started:
INFO [2020-04-15 00:39:33] block size: 60 x 60
INFO [2020-04-15 00:39:33] Impute missing data for block 1 of 1
INFO [2020-04-15 00:39:33] Replacing values below 0 or above 1:
INFO [2020-04-15 00:39:33] 0 values replaced
WARN [2020-04-15 00:39:33] 2 values are above 1 or below 0. Check your data
WARN [2020-04-15 00:39:33] Replacing them with missing values
WARN [2020-04-15 00:39:33] The following samples are annotated in the sample matrix,
WARN [2020-04-15 00:39:33] Dropping those samples now
WARN [2020-04-15 00:39:33] Sample names aren't unique
WARN [2020-04-15 00:39:33] Transforming them to unique IDs. List with annotations will be added to the results
INFO [2020-04-15 00:39:33] Transforming matrix to data.table
INFO [2020-04-15 00:39:33] Calculate the batch effects for 2 batches
INFO [2020-04-15 00:39:33] Adjusting p-values
INFO [2020-04-15 00:39:33] Generating a summary table
INFO [2020-04-15 00:39:33] There were no batch effects detected
INFO [2020-04-15 00:39:33] Starting the imputation of missing values.
INFO [2020-04-15 00:39:33] This might take a while.
INFO [2020-04-15 00:39:33] BEclear imputation is started:
INFO [2020-04-15 00:39:33] block size: 60 x 60
INFO [2020-04-15 00:39:33] Impute missing data for block 1 of 1
INFO [2020-04-15 00:39:33] Replacing values below 0 or above 1:
INFO [2020-04-15 00:39:33] 0 values replaced
INFO [2020-04-15 00:39:33] 3 values outside of the boundaries found
INFO [2020-04-15 00:39:33] Starting the imputation of missing values.
INFO [2020-04-15 00:39:33] This might take a while.
INFO [2020-04-15 00:39:33] BEclear imputation is started:
INFO [2020-04-15 00:39:33] block size: 10 x 10
INFO [2020-04-15 00:39:33] loading futile.logger package
INFO [2020-04-15 00:39:33] Impute missing data for block 1 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 2 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 3 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 4 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 5 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 6 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 7 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 8 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 9 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 10 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 11 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 12 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 13 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 14 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 15 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 16 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 17 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 18 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 19 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 20 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 21 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 22 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 23 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 24 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 25 of 25
INFO [2020-04-15 00:39:34] Starting the imputation of missing values.
INFO [2020-04-15 00:39:34] This might take a while.
INFO [2020-04-15 00:39:34] BEclear imputation is started:
INFO [2020-04-15 00:39:34] block size: 0 x 0
INFO [2020-04-15 00:39:34] loading futile.logger package
INFO [2020-04-15 00:39:34] Impute missing data for block 1 of 1
INFO [2020-04-15 00:39:34] Replacing values below 0 or above 1:
INFO [2020-04-15 00:39:34] 3 values replaced
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 83 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
10.911 8.158 5.888
BEclear.Rcheck/BEclear-Ex.timings
| name | user | system | elapsed | |
| BEclear-package | 8.261 | 4.735 | 2.282 | |
| calcBatchEffects | 30.829 | 15.059 | 7.411 | |
| calcScore | 1.676 | 1.050 | 0.632 | |
| calcSummary | 0.844 | 0.750 | 0.292 | |
| clearBEgenes | 0.940 | 0.711 | 0.295 | |
| correctBatchEffect | 3.527 | 1.173 | 0.594 | |
| countValuesToPredict | 0.922 | 0.978 | 0.308 | |
| findOutsideValues | 0.904 | 0.323 | 0.694 | |
| imputeMissingData | 1.336 | 1.410 | 0.503 | |
| makeBoxplot | 2.745 | 0.666 | 0.348 | |
| preprocessBEclear | 0.029 | 0.037 | 0.009 | |
| replaceOutsideValues | 0.069 | 0.088 | 0.020 | |