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CHECK report for bayNorm on malbec1

This page was generated on 2020-04-15 12:14:49 -0400 (Wed, 15 Apr 2020).

Package 120/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bayNorm 1.4.14
Wenhao Tang
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/bayNorm
Branch: RELEASE_3_10
Last Commit: cd5d5e4
Last Changed Date: 2020-01-09 05:09:00 -0400 (Thu, 09 Jan 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  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: 1.4.14
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:bayNorm.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings bayNorm_1.4.14.tar.gz
StartedAt: 2020-04-15 06:04:53 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:07:40 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 167.2 seconds
RetCode: 0
Status:  OK 
CheckDir: bayNorm.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:bayNorm.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings bayNorm_1.4.14.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/bayNorm.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.14’
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/bayNorm.Rcheck/00check.log’
for details.



Installation output

bayNorm.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL bayNorm
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘bayNorm’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppProgress/include" -I/usr/local/include -fopenmp  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppProgress/include" -I/usr/local/include -fopenmp  -fpic  -g -O2  -Wall -c bayNorm_main.cpp -o bayNorm_main.o
bayNorm_main.cpp: In function ‘Rcpp::List EstPrior_sprcpp(arma::sp_mat)’:
bayNorm_main.cpp:1374:7: warning: variable ‘Nrows’ set but not used [-Wunused-but-set-variable]
   int Nrows;
       ^~~~~
bayNorm_main.cpp: In function ‘Rcpp::List EstPrior_rcpp(Rcpp::NumericMatrix)’:
bayNorm_main.cpp:1427:7: warning: variable ‘Nrows’ set but not used [-Wunused-but-set-variable]
   int Nrows;
       ^~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o bayNorm.so RcppExports.o bayNorm_main.o -fopenmp -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-bayNorm/00new/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 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 (bayNorm)

Tests output

bayNorm.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-pc-linux-gnu (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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  8.328   0.400   8.747 

Example timings

bayNorm.Rcheck/bayNorm-Ex.timings

nameusersystemelapsed
AdjustSIZE_fun0.0040.0000.008
BB_Fun0.5240.0000.541
BetaFun0.0160.0000.015
Check_input0.0080.0000.009
DownSampling0.0040.0000.002
EXAMPLE_DATA_list0.0000.0000.002
EstPrior0.0000.0000.003
EstPrior_rcpp0.0040.0000.002
EstPrior_sprcpp0.0000.0000.001
NOISY_FUN0.1160.0040.123
Prior_fun0.0520.0040.053
SyntheticControl0.0040.0000.004
asMatrix0.0040.0000.002
as_matrix0.0000.0000.002
bayNorm0.0560.0000.058
bayNorm_sup0.0560.0040.061
noisy_gene_detection0.0760.0120.087
t_sp0.0040.0000.002