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CHECK report for Prize on malbec2

This page was generated on 2019-10-16 12:07:01 -0400 (Wed, 16 Oct 2019).

Package 1249/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Prize 1.14.0
Daryanaz Dargahi
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/Prize
Branch: RELEASE_3_9
Last Commit: 1a3b9c5
Last Changed Date: 2019-05-02 11:53:56 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Prize
Version: 1.14.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Prize.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Prize_1.14.0.tar.gz
StartedAt: 2019-10-16 04:04:10 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:05:38 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 88.7 seconds
RetCode: 0
Status:  OK 
CheckDir: Prize.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Prize.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Prize_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/Prize.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.14.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
Prize-package 7.194  0.003   7.238
* 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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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Prize
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘Prize’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Prize)

Tests output

Prize.Rcheck/tests/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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("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 -- Wed Oct 16 04:05:35 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 
  8.054   0.068   8.228 

Example timings

Prize.Rcheck/Prize-Ex.timings

nameusersystemelapsed
AIJ1.8680.0111.994
AIP1.0110.0011.012
CI1.7010.0001.701
GCR2.2080.0082.216
ICR3.0650.0003.065
IP3.1230.0003.123
Prize-package7.1940.0037.238
RM0.3120.0000.312
ahmatrix0.0000.0000.001
ahp0.2740.0000.274
ahp_matrix0.0010.0000.001
ahp_plot2.1410.0052.145
ahp_weights2.3860.0002.387
ahplot0.0440.0000.045
crplot0.2860.0000.286
dplot0.1140.0000.114
gaggregate4.1100.0044.116
pipeline2.6440.0002.643
rainbow_plot2.0270.0002.027
rainbowplot0.2260.0000.227
rating0.510.000.51
saaty_inconsistency2.9550.0002.955
simulation2.0090.0002.008
weight0.6720.0000.673
weight_plot2.1380.0002.138
wplot0.3970.0000.398