David Rasp
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/BEclear |
| git_branch: RELEASE_3_13 |
| git_last_commit: 820b246 |
| git_last_commit_date: 2021-05-19 12:13:44 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:29 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the BEclear package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BEclear.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 141/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BEclear 2.8.0 (landing page) David Rasp
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: BEclear |
| Version: 2.8.0 |
| 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_2.8.0.tar.gz |
| StartedAt: 2021-10-14 16:38:53 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 16:41:42 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 169.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BEclear.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_2.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/BEclear.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.8.0’
* 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 ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
.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 (user + system) or elapsed time > 5s
user system elapsed
calcBatchEffects 56.585 0.170 56.818
BEclear-package 14.454 0.067 14.541
* 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-3.13-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/4.1/Resources/library’ * installing *source* package ‘BEclear’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c localLoss.cpp -o localLoss.o clang++ -mmacosx-version-min=10.13 -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/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 [2021-10-14 16:41:23] Calculate the batch effects for 2 batches
INFO [2021-10-14 16:41:24] Calculate the batch effects for 3 batches
INFO [2021-10-14 16:41:24] Calculate the batch effects for 3 batches
INFO [2021-10-14 16:41:24] Adjusting p-values
INFO [2021-10-14 16:41:24] Transforming matrix to data.table
INFO [2021-10-14 16:41:24] Calculate the batch effects for 4 batches
INFO [2021-10-14 16:41:26] Adjusting p-values
INFO [2021-10-14 16:41:26] Generating a summary table
INFO [2021-10-14 16:41:26] Calculating the scores for 4 batches
INFO [2021-10-14 16:41:26] Generating a summary table
INFO [2021-10-14 16:41:26] Generating a summary table
INFO [2021-10-14 16:41:26] Transforming matrix to data.table
INFO [2021-10-14 16:41:26] Calculate the batch effects for 3 batches
INFO [2021-10-14 16:41:26] Adjusting p-values
INFO [2021-10-14 16:41:26] Generating a summary table
INFO [2021-10-14 16:41:26] Calculating the scores for 3 batches
INFO [2021-10-14 16:41:26] Removing values with batch effect:
INFO [2021-10-14 16:41:26] 4 values ( 26.6666666666667 % of the data) set to NA
INFO [2021-10-14 16:41:26] Starting the imputation of missing values.
INFO [2021-10-14 16:41:26] This might take a while.
INFO [2021-10-14 16:41:26] BEclear imputation is started:
INFO [2021-10-14 16:41:26] block size: 60 x 60
INFO [2021-10-14 16:41:26] Impute missing data for block 1 of 1
INFO [2021-10-14 16:41:26] Replacing values below 0 or above 1:
INFO [2021-10-14 16:41:26] 0 values replaced
WARN [2021-10-14 16:41:26] 3 values are above 1 or below 0. Check your data
WARN [2021-10-14 16:41:26] Replacing them with missing values
INFO [2021-10-14 16:41:26] Transforming matrix to data.table
INFO [2021-10-14 16:41:26] Calculate the batch effects for 3 batches
INFO [2021-10-14 16:41:26] Adjusting p-values
INFO [2021-10-14 16:41:26] Generating a summary table
INFO [2021-10-14 16:41:26] Calculating the scores for 3 batches
INFO [2021-10-14 16:41:26] Removing values with batch effect:
INFO [2021-10-14 16:41:26] 3 values ( 20 % of the data) set to NA
INFO [2021-10-14 16:41:26] Starting the imputation of missing values.
INFO [2021-10-14 16:41:26] This might take a while.
INFO [2021-10-14 16:41:26] BEclear imputation is started:
INFO [2021-10-14 16:41:27] block size: 60 x 60
INFO [2021-10-14 16:41:27] Impute missing data for block 1 of 1
INFO [2021-10-14 16:41:27] Replacing values below 0 or above 1:
INFO [2021-10-14 16:41:27] 0 values replaced
WARN [2021-10-14 16:41:27] 2 values are above 1 or below 0. Check your data
WARN [2021-10-14 16:41:27] Replacing them with missing values
WARN [2021-10-14 16:41:27] The following samples are annotated in the sample matrix,
WARN [2021-10-14 16:41:27] Dropping those samples now
WARN [2021-10-14 16:41:27] Sample names aren't unique
WARN [2021-10-14 16:41:27] Transforming them to unique IDs. List with annotations will be added to the results
INFO [2021-10-14 16:41:27] Transforming matrix to data.table
INFO [2021-10-14 16:41:27] Calculate the batch effects for 2 batches
INFO [2021-10-14 16:41:27] Adjusting p-values
INFO [2021-10-14 16:41:27] Generating a summary table
INFO [2021-10-14 16:41:27] There were no batch effects detected
INFO [2021-10-14 16:41:27] Starting the imputation of missing values.
INFO [2021-10-14 16:41:27] This might take a while.
INFO [2021-10-14 16:41:27] BEclear imputation is started:
INFO [2021-10-14 16:41:27] block size: 60 x 60
INFO [2021-10-14 16:41:27] Impute missing data for block 1 of 1
INFO [2021-10-14 16:41:27] Replacing values below 0 or above 1:
INFO [2021-10-14 16:41:27] 0 values replaced
INFO [2021-10-14 16:41:27] 3 values outside of the boundaries found
INFO [2021-10-14 16:41:27] Starting the imputation of missing values.
INFO [2021-10-14 16:41:27] This might take a while.
INFO [2021-10-14 16:41:27] BEclear imputation is started:
INFO [2021-10-14 16:41:27] block size: 10 x 10
INFO [2021-10-14 16:41:27] loading futile.logger package
INFO [2021-10-14 16:41:27] Impute missing data for block 1 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 2 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 3 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 4 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 5 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 6 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 7 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 8 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 9 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 10 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 11 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 12 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 13 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 14 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 15 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 16 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 17 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 18 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 19 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 20 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 21 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 22 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 23 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 24 of 25
INFO [2021-10-14 16:41:27] Impute missing data for block 25 of 25
INFO [2021-10-14 16:41:27] Starting the imputation of missing values.
INFO [2021-10-14 16:41:27] This might take a while.
INFO [2021-10-14 16:41:27] BEclear imputation is started:
INFO [2021-10-14 16:41:27] block size: 0 x 0
INFO [2021-10-14 16:41:27] loading futile.logger package
INFO [2021-10-14 16:41:27] Impute missing data for block 1 of 1
INFO [2021-10-14 16:41:27] Replacing values below 0 or above 1:
INFO [2021-10-14 16:41:27] 3 values replaced
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 83 ]
>
> proc.time()
user system elapsed
6.798 0.288 7.069
BEclear.Rcheck/BEclear-Ex.timings
| name | user | system | elapsed | |
| BEclear-package | 14.454 | 0.067 | 14.541 | |
| calcBatchEffects | 56.585 | 0.170 | 56.818 | |
| calcScore | 1.527 | 0.005 | 1.534 | |
| calcSummary | 1.681 | 0.005 | 1.687 | |
| clearBEgenes | 1.490 | 0.005 | 1.495 | |
| correctBatchEffect | 1.624 | 0.015 | 1.642 | |
| countValuesToPredict | 1.313 | 0.004 | 1.319 | |
| findOutsideValues | 0.530 | 0.013 | 0.544 | |
| imputeMissingData | 1.547 | 0.015 | 1.562 | |
| makeBoxplot | 1.097 | 0.006 | 1.102 | |
| preprocessBEclear | 0.008 | 0.002 | 0.009 | |
| replaceOutsideValues | 0.019 | 0.001 | 0.020 | |