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CHECK report for BUScorrect on malbec1

This page was generated on 2020-08-12 11:22:20 -0400 (Wed, 12 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 210/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BUScorrect 1.7.0
Xiangyu Luo
Snapshot Date: 2020-08-11 14:50:16 -0400 (Tue, 11 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
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
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: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BUScorrect.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BUScorrect_1.7.0.tar.gz
StartedAt: 2020-08-12 05:26:37 -0400 (Wed, 12 Aug 2020)
EndedAt: 2020-08-12 05:30:08 -0400 (Wed, 12 Aug 2020)
EllapsedTime: 210.8 seconds
RetCode: 0
Status:  OK 
CheckDir: BUScorrect.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BUScorrect.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BUScorrect_1.7.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BUScorrect.Rcheck’
* using R version 4.0.2 (2020-06-22)
* 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 ‘1.7.0’
* 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 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 (user + system) or elapsed time > 5s
                    user system elapsed
BUScorrect-package 23.08  0.052  25.724
BUSgibbs           21.80  0.008  23.964
* 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-3.12-bioc/meat/BUScorrect.Rcheck/00check.log’
for details.



Installation output

BUScorrect.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BUScorrect
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘BUScorrect’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-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-3.12-bioc/R/lib -L/usr/local/lib -o BUScorrect.so BUS_Cfunctions.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-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)

Tests output

BUScorrect.Rcheck/tests/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-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: 0.013 mins

  calculating posterior means and posterior modes...

  calculating BIC...



RUNIT TEST PROTOCOL -- Wed Aug 12 05:30:00 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 
  8.704   0.232  10.038 

Example timings

BUScorrect.Rcheck/BUScorrect-Ex.timings

nameusersystemelapsed
BIC_BUS0.1280.0080.138
BUScorrect-package23.080 0.05225.724
BUSexample_data000
BUSgibbs21.800 0.00823.964
IG_index0.1320.0000.132
Subtypes0.1240.0000.124
adjusted_values0.1360.0000.139
baseline_expression_values0.1240.0000.122
calculate_EPSR_gamma0.0040.0000.005
calculate_EPSR_mu0.0040.0000.004
calculate_EPSR_sigma_sq0.0080.0000.007
estimate_IG_indicators0.1240.0000.127
location_batch_effects0.1400.0040.214
postprob_DE0.1240.0000.137
postprob_DE_thr_fun0.1280.0000.212
print.BUSfits0.1520.0000.150
scale_batch_effects0.1200.0000.122
subtype_effects0.1280.0000.197
summary.BUSfits0.1400.0000.219
visualize_data0.0520.0000.099