Package: Prize

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Prize_1.8.0.tar.gz

StartedAt: 2018-04-12 07:51:13 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 07:52:43 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 90.6 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 --no-vignettes --timings Prize_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/Prize.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.8.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
Prize-package 8.229  0.044   8.424
* 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

* installing *source* package ‘Prize’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Prize)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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 -- Thu Apr 12 07:52:39 2018 
*********************************************** 
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 
  8.033   0.134   8.330 

name	user	system	elapsed
AIJ	2.188	0.013	2.241
AIP	1.421	0.011	1.453
CI	1.912	0.008	1.946
GCR	1.869	0.005	1.904
ICR	3.466	0.008	3.529
IP	3.174	0.009	3.238
Prize-package	8.229	0.044	8.424
RM	0.327	0.002	0.329
ahmatrix	0.001	0.000	0.001
ahp	0.291	0.002	0.294
ahp_matrix	0.001	0.000	0.002
ahp_plot	2.574	0.018	2.626
ahp_weights	2.270	0.033	2.329
ahplot	0.206	0.005	0.217
crplot	0.282	0.005	0.294
dplot	0.187	0.003	0.195
gaggregate	3.691	0.041	3.797
pipeline	2.428	0.013	2.484
rainbow_plot	2.567	0.015	2.641
rainbowplot	0.238	0.002	0.247
rating	0.662	0.002	0.682
saaty_inconsistency	3.072	0.015	3.125
simulation	2.473	0.013	2.557
weight	0.608	0.001	0.626
weight_plot	2.369	0.013	2.423
wplot	0.521	0.002	0.537