Package: BUScorrect

Version: 1.4.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:BUScorrect.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings BUScorrect_1.4.0.tar.gz

StartedAt: 2020-04-15 05:57:20 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:00:54 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 213.7 seconds

RetCode: 0

Status:  OK

CheckDir: BUScorrect.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:BUScorrect.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings BUScorrect_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/BUScorrect.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BUScorrect/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BUScorrect’ version ‘1.4.0’
* 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 for sufficient/correct file permissions ... 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
BUScorrect-package 22.788  0.096  25.677
BUSgibbs           21.932  0.048  24.260
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/BUScorrect.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL BUScorrect
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘BUScorrect’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c BUS_Cfunctions.c -o BUS_Cfunctions.o
gcc -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o BUScorrect.so BUS_Cfunctions.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-BUScorrect/00new/BUScorrect/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 (BUScorrect)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.

> 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 -- Wed Apr 15 06:00:45 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 
  7.932   0.380   8.802 

name	user	system	elapsed
BIC_BUS	0.140	0.008	0.151
BUScorrect-package	22.788	0.096	25.677
BUSexample_data	0.000	0.000	0.001
BUSgibbs	21.932	0.048	24.260
IG_index	0.116	0.000	0.116
Subtypes	0.096	0.012	0.108
adjusted_values	0.128	0.016	0.150
baseline_expression_values	0.116	0.000	0.114
calculate_EPSR_gamma	0.004	0.000	0.004
calculate_EPSR_mu	0.004	0.000	0.016
calculate_EPSR_sigma_sq	0.008	0.000	0.006
estimate_IG_indicators	0.120	0.000	0.121
location_batch_effects	0.116	0.000	0.178
postprob_DE	0.136	0.000	0.135
postprob_DE_thr_fun	0.108	0.000	0.111
print.BUSfits	0.120	0.000	0.208
scale_batch_effects	0.124	0.000	0.151
subtype_effects	0.144	0.000	0.197
summary.BUSfits	0.112	0.000	0.113
visualize_data	0.044	0.000	0.046