Package: Prize

Version: 1.10.0

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_1.10.0.tar.gz

StartedAt: 2018-10-16 23:20:35 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:22:15 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 99.4 seconds

RetCode: 0

Status:  OK

CheckDir: Prize.Rcheck

Warnings: 0

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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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/Prize.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.10.0’
* 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 ‘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 7.541  0.066   7.653
* 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

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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)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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 Oct 16 23:22:09 2018 
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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 
  8.278   0.206   8.490 

name	user	system	elapsed
AIJ	2.088	0.055	2.152
AIP	1.417	0.006	1.427
CI	2.110	0.007	2.123
GCR	2.317	0.005	2.332
ICR	3.832	0.021	3.880
IP	3.694	0.010	3.721
Prize-package	7.541	0.066	7.653
RM	0.359	0.002	0.362
ahmatrix	0.002	0.000	0.002
ahp	0.347	0.000	0.349
ahp_matrix	0.003	0.000	0.004
ahp_plot	2.761	0.032	2.802
ahp_weights	2.838	0.030	2.879
ahplot	0.051	0.001	0.053
crplot	0.399	0.001	0.402
dplot	0.244	0.001	0.245
gaggregate	4.595	0.010	4.632
pipeline	2.826	0.026	2.876
rainbow_plot	2.559	0.027	2.598
rainbowplot	0.385	0.001	0.387
rating	0.741	0.002	0.747
saaty_inconsistency	3.372	0.033	3.421
simulation	2.515	0.020	2.545
weight	0.727	0.002	0.736
weight_plot	2.723	0.022	2.763
wplot	0.593	0.003	0.598