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CHECK report for BUScorrect on tokay1

This page was generated on 2020-08-06 12:07:57 -0400 (Thu, 06 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BUScorrect PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 210/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BUScorrect 1.7.0
Xiangyu Luo
Snapshot Date: 2020-08-05 14:50:59 -0400 (Wed, 05 Aug 2020)
URL: https://git.bioconductor.org/packages/BUScorrect
Branch: master
Last Commit: 11ea1d9
Last Changed Date: 2020-04-27 15:18:46 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 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 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BUScorrect
Version: 1.7.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BUScorrect.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BUScorrect_1.7.0.tar.gz
StartedAt: 2020-08-06 05:02:36 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 05:07:54 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 317.7 seconds
RetCode: 0
Status:  OK  
CheckDir: BUScorrect.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BUScorrect.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BUScorrect_1.7.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BUScorrect.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '1.7.0'
* 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 '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-3.12-bioc/R/library/BUScorrect/libs/i386/BUScorrect.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BUScorrect/libs/x64/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 (user + system) or elapsed time > 5s
                    user system elapsed
BUScorrect-package 23.19   0.28   23.47
BUSgibbs           23.10   0.02   23.12
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
BUScorrect-package 23.25   0.06   23.45
BUSgibbs           20.51   0.05   20.59
* 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-3.12-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/3.12/bioc/src/contrib/BUScorrect_1.7.0.tar.gz && rm -rf BUScorrect.buildbin-libdir && mkdir BUScorrect.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BUScorrect.buildbin-libdir BUScorrect_1.7.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BUScorrect_1.7.0.zip && rm BUScorrect_1.7.0.tar.gz BUScorrect_1.7.0.zip
###
##############################################################################
##############################################################################


  % 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  48.5M      0 --:--:-- --:--:-- --:--:-- 52.8M

install for i386

* installing *source* package 'BUScorrect' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c BUS_Cfunctions.c -o BUS_Cfunctions.o
C:/rtools40/mingw32/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-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/BUScorrect.buildbin-libdir/00LOCK-BUScorrect/00new/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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'BUScorrect' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c BUS_Cfunctions.c -o BUS_Cfunctions.o
C:/rtools40/mingw64/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-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/BUScorrect.buildbin-libdir/BUScorrect/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BUScorrect' as BUScorrect_1.7.0.zip
* DONE (BUScorrect)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BUScorrect' successfully unpacked and MD5 sums checked

Tests output

BUScorrect.Rcheck/tests_i386/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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 -- Thu Aug 06 05:07:41 2020 
*********************************************** 
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 
   5.50    0.39    5.89 

BUScorrect.Rcheck/tests_x64/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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: 0.001 mins

  calculating posterior means and posterior modes...

  calculating BIC...



RUNIT TEST PROTOCOL -- Thu Aug 06 05:07:48 2020 
*********************************************** 
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 
   5.46    0.23    5.78 

Example timings

BUScorrect.Rcheck/examples_i386/BUScorrect-Ex.timings

nameusersystemelapsed
BIC_BUS0.030.090.12
BUScorrect-package23.19 0.2823.47
BUSexample_data000
BUSgibbs23.10 0.0223.12
IG_index0.130.000.13
Subtypes0.140.000.14
adjusted_values0.130.000.12
baseline_expression_values0.130.000.12
calculate_EPSR_gamma000
calculate_EPSR_mu000
calculate_EPSR_sigma_sq0.010.000.02
estimate_IG_indicators0.140.000.14
location_batch_effects0.130.000.12
postprob_DE0.140.000.14
postprob_DE_thr_fun0.090.010.11
print.BUSfits0.10.00.1
scale_batch_effects0.070.000.08
subtype_effects0.110.000.10
summary.BUSfits0.110.000.11
visualize_data0.060.000.07

BUScorrect.Rcheck/examples_x64/BUScorrect-Ex.timings

nameusersystemelapsed
BIC_BUS0.170.000.17
BUScorrect-package23.25 0.0623.45
BUSexample_data000
BUSgibbs20.51 0.0520.59
IG_index0.130.000.13
Subtypes0.140.010.15
adjusted_values0.120.000.13
baseline_expression_values0.110.000.11
calculate_EPSR_gamma0.020.000.01
calculate_EPSR_mu000
calculate_EPSR_sigma_sq000
estimate_IG_indicators0.160.000.15
location_batch_effects0.140.050.19
postprob_DE0.140.000.14
postprob_DE_thr_fun0.120.000.13
print.BUSfits0.130.000.13
scale_batch_effects0.160.000.16
subtype_effects0.120.000.12
summary.BUSfits0.140.000.15
visualize_data0.050.000.04