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CHECK report for bayNorm on merida1

This page was generated on 2019-04-16 12:13:30 -0400 (Tue, 16 Apr 2019).

Package 106/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bayNorm 1.0.9
Wenhao Tang
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/bayNorm
Branch: RELEASE_3_8
Last Commit: 888f4d0
Last Changed Date: 2019-03-26 11:58:57 -0400 (Tue, 26 Mar 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: bayNorm
Version: 1.0.9
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bayNorm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bayNorm_1.0.9.tar.gz
StartedAt: 2019-04-15 22:30:21 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:33:56 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 214.6 seconds
RetCode: 0
Status:  OK 
CheckDir: bayNorm.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bayNorm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bayNorm_1.0.9.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/bayNorm.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bayNorm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bayNorm’ version ‘1.0.9’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘bayNorm’ 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
* 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
bayNorm              8.770  0.016   8.877
bayNorm_sup          8.722  0.016   8.813
Prior_fun            8.664  0.063   8.815
noisy_gene_detection 8.576  0.018   8.663
BB_Fun               8.162  0.016   8.265
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/bayNorm.Rcheck/00check.log’
for details.



Installation output

bayNorm.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL bayNorm
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘bayNorm’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppProgress/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppProgress/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c bayNorm_main.cpp -o bayNorm_main.o
clang++ -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 bayNorm.so RcppExports.o bayNorm_main.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/bayNorm/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (bayNorm)

Tests output

bayNorm.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(bayNorm)
> 
> test_check("bayNorm")

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══ testthat results  ═══════════════════════════════════════════════════════════
OK: 2 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 20.349   0.444  20.995 

Example timings

bayNorm.Rcheck/bayNorm-Ex.timings

nameusersystemelapsed
AdjustSIZE_fun0.0100.0010.012
BB_Fun8.1620.0168.265
BetaFun0.0120.0010.014
DownSampling0.0030.0010.004
EXAMPLE_DATA_list0.0020.0010.004
EstPrior0.1410.0040.149
NOISY_FUN0.5520.0860.643
Prior_fun8.6640.0638.815
SyntheticControl0.0040.0010.005
bayNorm8.7700.0168.877
bayNorm_sup8.7220.0168.813
noisy_gene_detection8.5760.0188.663