Wenhao Tang
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/bayNorm |
| git_branch: RELEASE_3_13 |
| git_last_commit: cbf997b |
| git_last_commit_date: 2021-05-19 12:38:44 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:35 -0400 (Fri, 15 Oct 2021).
|
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. |
| Package 129/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bayNorm 1.10.0 (landing page) Wenhao Tang
| 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: bayNorm |
| Version: 1.10.0 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:bayNorm.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings bayNorm_1.10.0.tar.gz |
| StartedAt: 2021-10-14 08:57:20 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 08:59:33 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 133.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: bayNorm.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:bayNorm.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings bayNorm_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-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 ‘1.10.0’ * 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 ... 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 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: 1 NOTE See ‘/home/biocbuild/bbs-3.13-bioc/meat/bayNorm.Rcheck/00check.log’ for details.
bayNorm.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL bayNorm
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘bayNorm’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/lib -L/usr/local/lib -o bayNorm.so RcppExports.o bayNorm_main.o -fopenmp -L/home/biocbuild/bbs-3.13-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.13-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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)
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
6.591 0.340 6.919
bayNorm.Rcheck/bayNorm-Ex.timings
| name | user | system | elapsed | |
| AdjustSIZE_fun | 0.008 | 0.000 | 0.008 | |
| BB_Fun | 0.077 | 0.000 | 0.078 | |
| BetaFun | 0.011 | 0.000 | 0.011 | |
| Check_input | 0.006 | 0.000 | 0.006 | |
| DownSampling | 0.002 | 0.000 | 0.002 | |
| EXAMPLE_DATA_list | 0.002 | 0.000 | 0.002 | |
| EstPrior | 0.003 | 0.000 | 0.003 | |
| EstPrior_rcpp | 0.001 | 0.000 | 0.002 | |
| EstPrior_sprcpp | 0.001 | 0.000 | 0.002 | |
| NOISY_FUN | 0.133 | 0.008 | 0.141 | |
| Prior_fun | 0.044 | 0.000 | 0.044 | |
| SyntheticControl | 0.004 | 0.000 | 0.005 | |
| asMatrix | 0.002 | 0.000 | 0.002 | |
| as_matrix | 0.000 | 0.002 | 0.002 | |
| bayNorm | 0.045 | 0.001 | 0.046 | |
| bayNorm_sup | 0.047 | 0.000 | 0.048 | |
| noisy_gene_detection | 0.077 | 0.000 | 0.077 | |
| t_sp | 0.002 | 0.000 | 0.002 | |