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CHECK report for Prize on merida1

This page was generated on 2019-04-16 11:58:48 -0400 (Tue, 16 Apr 2019).

Package 1190/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Prize 1.12.1
Daryanaz Dargahi
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/Prize
Branch: RELEASE_3_8
Last Commit: 489f702
Last Changed Date: 2019-01-04 13:45:08 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  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: Prize
Version: 1.12.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Prize.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Prize_1.12.1.tar.gz
StartedAt: 2019-04-16 02:00:50 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:02:29 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 99.8 seconds
RetCode: 0
Status:  OK 
CheckDir: Prize.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Prize.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Prize_1.12.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/Prize.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Prize/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Prize’ version ‘1.12.1’
* 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 ‘Prize’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
Prize-package 6.908  0.071   7.014
* 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: OK


Installation output

Prize.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Prize
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘Prize’ ...
** R
** 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
* DONE (Prize)

Tests output

Prize.Rcheck/tests/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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("Prize")
Loading required package: shape
Reading individual judgements.
Aggregating individual judgements with geometric mean (AIJ).
Computing group consistency ratio (GCR).
Computing consensus index (CI).
Reading individual judgements.
Aggregating individual priorities with arithmetic mean (AIP).
0 Prioritization_of_DE_genes is processed.
1 Tumor_expression is processed.
2 Normal_expression is processed.
3 Frequency is processed.
4 Epitopes is processed.
4.1 Number_of_epitopes is processed.
4.2 Size_of_epitopes is processed.


RUNIT TEST PROTOCOL -- Tue Apr 16 02:02:24 2019 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Prize RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  9.246   0.206   9.469 

Example timings

Prize.Rcheck/Prize-Ex.timings

nameusersystemelapsed
AIJ2.1380.0472.195
AIP1.4940.0051.507
CI2.1200.0092.137
GCR2.0470.0072.062
ICR3.6340.0223.679
IP3.7020.0073.724
Prize-package6.9080.0717.014
RM0.3780.0010.382
ahmatrix0.0010.0000.000
ahp0.3340.0010.337
ahp_matrix0.0010.0000.001
ahp_plot2.8650.0362.910
ahp_weights2.8550.0332.907
ahplot0.0420.0020.044
crplot0.2820.0010.286
dplot0.1520.0000.154
gaggregate4.3980.0084.427
pipeline2.8850.0222.937
rainbow_plot2.9960.0223.035
rainbowplot0.2910.0010.292
rating0.6730.0010.677
saaty_inconsistency3.6340.0453.709
simulation2.8450.0332.900
weight0.7130.0010.717
weight_plot2.6500.0262.687
wplot0.4960.0020.501