| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:20 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 bayNorm package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 125/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bayNorm 1.17.0 (landing page) Wenhao Tang
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: bayNorm |
| Version: 1.17.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bayNorm.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings bayNorm_1.17.0.tar.gz |
| StartedAt: 2022-12-28 21:47:24 -0500 (Wed, 28 Dec 2022) |
| EndedAt: 2022-12-28 21:49:56 -0500 (Wed, 28 Dec 2022) |
| EllapsedTime: 151.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: bayNorm.Rcheck |
| Warnings: 0 |
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### Running command:
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### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bayNorm.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings bayNorm_1.17.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/bayNorm.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'bayNorm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'bayNorm' version '1.17.0'
* 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 whether package 'bayNorm' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/bayNorm/libs/x64/bayNorm.dll':
Found '_assert', possibly from 'assert' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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 nor [v]sprintf. 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 ... 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
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/bayNorm.Rcheck/00check.log'
for details.
bayNorm.Rcheck/00install.out
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###
### Running command:
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### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL bayNorm
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'bayNorm' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++11
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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++ -shared -s -static-libgcc -o bayNorm.dll tmp.def RcppExports.o bayNorm_main.o -fopenmp -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-bayNorm/00new/bayNorm/libs/x64
** 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
** 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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
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(bayNorm)
>
> test_check("bayNorm")
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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
>
> proc.time()
user system elapsed
5.79 0.37 6.73
bayNorm.Rcheck/bayNorm-Ex.timings
| name | user | system | elapsed | |
| AdjustSIZE_fun | 0 | 0 | 0 | |
| BB_Fun | 0.43 | 0.02 | 0.46 | |
| BetaFun | 0.00 | 0.01 | 0.01 | |
| Check_input | 0.01 | 0.00 | 0.02 | |
| DownSampling | 0 | 0 | 0 | |
| EXAMPLE_DATA_list | 0.00 | 0.02 | 0.01 | |
| EstPrior | 0 | 0 | 0 | |
| EstPrior_rcpp | 0 | 0 | 0 | |
| EstPrior_sprcpp | 0.00 | 0.01 | 0.02 | |
| NOISY_FUN | 0.11 | 0.00 | 0.11 | |
| Prior_fun | 0.02 | 0.03 | 0.05 | |
| SyntheticControl | 0.01 | 0.00 | 0.01 | |
| asMatrix | 0 | 0 | 0 | |
| as_matrix | 0 | 0 | 0 | |
| bayNorm | 0.05 | 0.00 | 0.05 | |
| bayNorm_sup | 0.02 | 0.03 | 0.05 | |
| noisy_gene_detection | 0.07 | 0.02 | 0.09 | |
| t_sp | 0 | 0 | 0 | |