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CHECK report for BUScorrect on tokay1

This page was generated on 2019-04-13 11:29:35 -0400 (Sat, 13 Apr 2019).

Package 188/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BUScorrect 1.0.0
Xiangyu Luo
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/BUScorrect
Branch: RELEASE_3_8
Last Commit: 17ac036
Last Changed Date: 2018-10-30 11:42:10 -0400 (Tue, 30 Oct 2018)
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: BUScorrect
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BUScorrect.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BUScorrect_1.0.0.tar.gz
StartedAt: 2019-04-13 00:55:42 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:00:45 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 302.8 seconds
RetCode: 0
Status:  OK  
CheckDir: BUScorrect.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:BUScorrect.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BUScorrect_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/BUScorrect.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 'BUScorrect/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BUScorrect' version '1.0.0'
* 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 'BUScorrect' 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/BUScorrect/libs/i386/BUScorrect.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (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. 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
BUScorrect-package 20.83   0.20   21.03
BUSgibbs           20.39   0.03   20.43
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
BUSgibbs           18.15   0.03   18.19
BUScorrect-package 16.89   0.05   16.93
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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/BUScorrect.Rcheck/00check.log'
for details.



Installation output

BUScorrect.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/BUScorrect_1.0.0.tar.gz && rm -rf BUScorrect.buildbin-libdir && mkdir BUScorrect.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BUScorrect.buildbin-libdir BUScorrect_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL BUScorrect_1.0.0.zip && rm BUScorrect_1.0.0.tar.gz BUScorrect_1.0.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3249k  100 3249k    0     0  47.6M      0 --:--:-- --:--:-- --:--:-- 50.3M

install for i386

* installing *source* package 'BUScorrect' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c BUS_Cfunctions.c -o BUS_Cfunctions.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o BUScorrect.dll tmp.def BUS_Cfunctions.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/BUScorrect.buildbin-libdir/BUScorrect/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BUScorrect'
    finding HTML links ... done
    BIC_BUS                                 html  
    BUScorrect-package                      html  
    BUSexample_data                         html  
    BUSgibbs                                html  
    IG_index                                html  
    Subtypes                                html  
    adjusted_values                         html  
    baseline_expression_values              html  
    calculate_EPSR_gamma                    html  
    calculate_EPSR_mu                       html  
    calculate_EPSR_sigma_sq                 html  
    estimate_IG_indicators                  html  
    location_batch_effects                  html  
    postprob_DE                             html  
    postprob_DE_thr_fun                     html  
    print.BUSfits                           html  
    scale_batch_effects                     html  
    subtype_effects                         html  
    summary.BUSfits                         html  
    visualize_data                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'BUScorrect' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c BUS_Cfunctions.c -o BUS_Cfunctions.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o BUScorrect.dll tmp.def BUS_Cfunctions.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/BUScorrect.buildbin-libdir/BUScorrect/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BUScorrect' as BUScorrect_1.0.0.zip
* DONE (BUScorrect)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'BUScorrect' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

BUScorrect.Rcheck/tests_i386/runTests.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.

> BiocGenerics:::testPackage("BUScorrect")
  running the Gibbs sampler ...

  The Gibbs sampler takes: 0.002 mins

  calculating posterior means and posterior modes...

  calculating BIC...



RUNIT TEST PROTOCOL -- Sat Apr 13 01:00:33 2019 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BUScorrect RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   6.68    0.28    6.96 

BUScorrect.Rcheck/tests_x64/runTests.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.

> BiocGenerics:::testPackage("BUScorrect")
  running the Gibbs sampler ...

  The Gibbs sampler takes: 0.007 mins

  calculating posterior means and posterior modes...

  calculating BIC...



RUNIT TEST PROTOCOL -- Sat Apr 13 01:00:38 2019 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BUScorrect RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   4.95    0.14    5.07 

Example timings

BUScorrect.Rcheck/examples_i386/BUScorrect-Ex.timings

nameusersystemelapsed
BIC_BUS0.060.020.08
BUScorrect-package20.83 0.2021.03
BUSexample_data000
BUSgibbs20.39 0.0320.43
IG_index0.110.000.10
Subtypes0.080.000.08
adjusted_values0.060.000.07
baseline_expression_values0.080.000.07
calculate_EPSR_gamma0.020.000.02
calculate_EPSR_mu000
calculate_EPSR_sigma_sq000
estimate_IG_indicators0.070.000.07
location_batch_effects0.090.000.09
postprob_DE0.080.000.08
postprob_DE_thr_fun0.060.000.06
print.BUSfits0.080.000.08
scale_batch_effects0.080.000.08
subtype_effects0.060.000.06
summary.BUSfits0.060.000.06
visualize_data0.030.000.03

BUScorrect.Rcheck/examples_x64/BUScorrect-Ex.timings

nameusersystemelapsed
BIC_BUS0.580.010.60
BUScorrect-package16.89 0.0516.93
BUSexample_data000
BUSgibbs18.15 0.0318.19
IG_index0.070.000.06
Subtypes0.060.000.07
adjusted_values0.080.000.07
baseline_expression_values0.060.000.07
calculate_EPSR_gamma0.020.000.01
calculate_EPSR_mu000
calculate_EPSR_sigma_sq000
estimate_IG_indicators0.060.000.06
location_batch_effects0.080.000.08
postprob_DE0.060.000.06
postprob_DE_thr_fun0.070.000.06
print.BUSfits0.080.000.08
scale_batch_effects0.060.000.06
subtype_effects0.080.000.08
summary.BUSfits0.060.000.07
visualize_data0.030.000.03