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CHECK report for bayNorm on tokay1

This page was generated on 2019-04-13 11:29:47 -0400 (Sat, 13 Apr 2019).

Package 106/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bayNorm 1.0.9
Wenhao Tang
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 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
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: 1.0.9
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bayNorm.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings bayNorm_1.0.9.tar.gz
StartedAt: 2019-04-13 00:39:34 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 00:45:24 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 349.7 seconds
RetCode: 0
Status:  OK  
CheckDir: bayNorm.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bayNorm.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings bayNorm_1.0.9.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/bayNorm.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/bayNorm/libs/i386/bayNorm.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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. 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
bayNorm_sup          9.34   0.01    9.35
noisy_gene_detection 8.41   0.00    8.41
Prior_fun            8.03   0.05    8.08
bayNorm              8.03   0.00    8.04
BB_Fun               7.43   0.01    7.46
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
BB_Fun               10.09   0.02   10.11
Prior_fun            10.00   0.03   10.03
noisy_gene_detection  9.59   0.00    9.60
bayNorm_sup           9.16   0.00    9.15
bayNorm               9.14   0.00    9.14
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/bayNorm.Rcheck/00check.log'
for details.



Installation output

bayNorm.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/bayNorm_1.0.9.tar.gz && rm -rf bayNorm.buildbin-libdir && mkdir bayNorm.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bayNorm.buildbin-libdir bayNorm_1.0.9.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL bayNorm_1.0.9.zip && rm bayNorm_1.0.9.tar.gz bayNorm_1.0.9.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1327k  100 1327k    0     0  14.0M      0 --:--:-- --:--:-- --:--:-- 14.7M

install for i386

* installing *source* package 'bayNorm' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppProgress/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppProgress/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c bayNorm_main.cpp -o bayNorm_main.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o bayNorm.dll tmp.def RcppExports.o bayNorm_main.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/bayNorm.buildbin-libdir/bayNorm/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'bayNorm'
    finding HTML links ... done
    AdjustSIZE_fun                          html  
    BB_Fun                                  html  
    BetaFun                                 html  
    DownSampling                            html  
    EXAMPLE_DATA_list                       html  
    EstPrior                                html  
    NOISY_FUN                               html  
    Prior_fun                               html  
    SyntheticControl                        html  
    bayNorm                                 html  
    bayNorm_sup                             html  
    noisy_gene_detection                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'bayNorm' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppProgress/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppProgress/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c bayNorm_main.cpp -o bayNorm_main.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o bayNorm.dll tmp.def RcppExports.o bayNorm_main.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/bayNorm.buildbin-libdir/bayNorm/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bayNorm' as bayNorm_1.0.9.zip
* DONE (bayNorm)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'bayNorm' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

bayNorm.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  16.81    0.50   17.31 

bayNorm.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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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== testthat results  ===========================================================
OK: 2 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  19.50    0.29   19.78 

Example timings

bayNorm.Rcheck/examples_i386/bayNorm-Ex.timings

nameusersystemelapsed
AdjustSIZE_fun0.040.000.03
BB_Fun7.430.017.46
BetaFun0.000.020.01
DownSampling0.000.020.02
EXAMPLE_DATA_list0.000.010.01
EstPrior0.190.000.19
NOISY_FUN0.440.170.61
Prior_fun8.030.058.08
SyntheticControl0.000.020.01
bayNorm8.030.008.04
bayNorm_sup9.340.019.35
noisy_gene_detection8.410.008.41

bayNorm.Rcheck/examples_x64/bayNorm-Ex.timings

nameusersystemelapsed
AdjustSIZE_fun0.010.000.02
BB_Fun10.09 0.0210.11
BetaFun0.020.000.01
DownSampling0.000.000.13
EXAMPLE_DATA_list000
EstPrior0.110.010.12
NOISY_FUN0.320.030.36
Prior_fun10.00 0.0310.03
SyntheticControl0.020.000.02
bayNorm9.140.009.14
bayNorm_sup9.160.009.15
noisy_gene_detection9.590.009.60