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This page was generated on 2021-10-23 14:05:53 -0400 (Sat, 23 Oct 2021).

CHECK results for bayNorm on nebbiolo2

To the developers/maintainers of the bayNorm package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bayNorm.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.

raw results

Package 126/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bayNorm 1.11.0  (landing page)
Wenhao Tang
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/bayNorm
git_branch: master
git_last_commit: 9ee70ea
git_last_commit_date: 2021-05-19 12:38:44 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: bayNorm
Version: 1.11.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:bayNorm.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings bayNorm_1.11.0.tar.gz
StartedAt: 2021-10-22 19:10:49 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 19:12:59 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 129.7 seconds
RetCode: 0
Status:   OK  
CheckDir: bayNorm.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:bayNorm.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings bayNorm_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/bayNorm.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.11.0’
* 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 ... 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 ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
* 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 use of PKG_*FLAGS in Makefiles ... 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/bayNorm.Rcheck/00check.log’
for details.



Installation output

bayNorm.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL bayNorm
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘bayNorm’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-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]
 1374 |   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]
 1427 |   int Nrows;
      |       ^~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o bayNorm.so RcppExports.o bayNorm_main.o -fopenmp -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
  6.279   0.284   6.542 

Example timings

bayNorm.Rcheck/bayNorm-Ex.timings

nameusersystemelapsed
AdjustSIZE_fun0.0040.0040.008
BB_Fun0.0980.0010.099
BetaFun0.0110.0000.011
Check_input0.0060.0000.006
DownSampling0.0020.0000.002
EXAMPLE_DATA_list0.0010.0000.002
EstPrior0.0030.0000.003
EstPrior_rcpp0.0010.0000.001
EstPrior_sprcpp0.0010.0000.001
NOISY_FUN0.1220.0040.127
Prior_fun0.0410.0040.045
SyntheticControl0.0020.0020.004
asMatrix0.0000.0010.002
as_matrix0.0020.0000.002
bayNorm0.0580.0080.066
bayNorm_sup0.0460.0010.049
noisy_gene_detection0.0670.0060.073
t_sp0.0010.0000.002