David Rasp
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/BEclear |
| git_branch: RELEASE_3_14 |
| git_last_commit: 240fe18 |
| git_last_commit_date: 2021-10-26 12:20:44 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:13 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the BEclear package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/BEclear.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 138/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BEclear 2.10.0 (landing page) David Rasp
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: 2.10.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BEclear.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BEclear_2.10.0.tar.gz |
| StartedAt: 2022-04-12 16:07:07 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 16:09:32 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 144.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BEclear.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BEclear.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BEclear_2.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/BEclear.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '2.10.0'
* 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
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* 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 ... 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
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BEclear/libs/i386/BEclear.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BEclear/libs/x64/BEclear.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calcBatchEffects 6.24 0.1 6.33
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calcBatchEffects 7.58 0.05 7.61
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/BEclear.Rcheck/00check.log'
for details.
BEclear.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BEclear_2.10.0.tar.gz && rm -rf BEclear.buildbin-libdir && mkdir BEclear.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BEclear.buildbin-libdir BEclear_2.10.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BEclear_2.10.0.zip && rm BEclear_2.10.0.tar.gz BEclear_2.10.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
31 210k 31 68639 0 0 34013 0 0:00:06 0:00:02 0:00:04 34030
100 210k 100 210k 0 0 104k 0 0:00:02 0:00:02 --:--:-- 104k
install for i386
* installing *source* package 'BEclear' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c localLoss.cpp -o localLoss.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o BEclear.dll tmp.def RcppExports.o localLoss.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/BEclear.buildbin-libdir/00LOCK-BEclear/00new/BEclear/libs/i386
** 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
calcBatchEffects html
calcBatchEffectsForBatch html
calcBlockFrame html
calcPositions html
calcScore html
calcSummary html
clearBEgenes html
combineBlocks html
correctBatchEffect html
countValuesToPredict html
ex.corrected.data html
findOutsideValues html
gdepoch html
imputeMissingData html
imputeMissingDataForBlock html
localLoss html
loss html
makeBoxplot html
preprocessBEclear html
replaceOutsideValues html
runGradientDescent 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 'BEclear' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c localLoss.cpp -o localLoss.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o BEclear.dll tmp.def RcppExports.o localLoss.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/BEclear.buildbin-libdir/BEclear/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BEclear' as BEclear_2.10.0.zip
* DONE (BEclear)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'BEclear' successfully unpacked and MD5 sums checked
|
BEclear.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 [2022-04-12 16:09:17] Calculate the batch effects for 2 batches
INFO [2022-04-12 16:09:17] Calculate the batch effects for 3 batches
INFO [2022-04-12 16:09:18] Calculate the batch effects for 3 batches
INFO [2022-04-12 16:09:18] Adjusting p-values
INFO [2022-04-12 16:09:18] Transforming matrix to data.table
INFO [2022-04-12 16:09:18] Calculate the batch effects for 4 batches
INFO [2022-04-12 16:09:18] Adjusting p-values
INFO [2022-04-12 16:09:18] Generating a summary table
INFO [2022-04-12 16:09:18] Calculating the scores for 4 batches
INFO [2022-04-12 16:09:18] Generating a summary table
INFO [2022-04-12 16:09:18] Generating a summary table
INFO [2022-04-12 16:09:18] 3 values outside of the boundaries found
INFO [2022-04-12 16:09:18] Starting the imputation of missing values.
INFO [2022-04-12 16:09:18] This might take a while.
INFO [2022-04-12 16:09:18] BEclear imputation is started:
INFO [2022-04-12 16:09:18] block size: 10 x 10
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 80 ]
>
> proc.time()
user system elapsed
3.87 0.34 4.42
|
BEclear.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 [2022-04-12 16:09:22] Calculate the batch effects for 2 batches
INFO [2022-04-12 16:09:22] Calculate the batch effects for 3 batches
INFO [2022-04-12 16:09:22] Calculate the batch effects for 3 batches
INFO [2022-04-12 16:09:22] Adjusting p-values
INFO [2022-04-12 16:09:23] Transforming matrix to data.table
INFO [2022-04-12 16:09:23] Calculate the batch effects for 4 batches
INFO [2022-04-12 16:09:23] Adjusting p-values
INFO [2022-04-12 16:09:23] Generating a summary table
INFO [2022-04-12 16:09:23] Calculating the scores for 4 batches
INFO [2022-04-12 16:09:23] Generating a summary table
INFO [2022-04-12 16:09:23] Generating a summary table
INFO [2022-04-12 16:09:23] 3 values outside of the boundaries found
INFO [2022-04-12 16:09:23] Starting the imputation of missing values.
INFO [2022-04-12 16:09:23] This might take a while.
INFO [2022-04-12 16:09:23] BEclear imputation is started:
INFO [2022-04-12 16:09:23] block size: 10 x 10
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 80 ]
>
> proc.time()
user system elapsed
4.03 0.29 4.31
|
|
BEclear.Rcheck/examples_i386/BEclear-Ex.timings
|
BEclear.Rcheck/examples_x64/BEclear-Ex.timings
|