Multiple platform build/check report for BioC 3.9 - CHECK report for Prize on tokay2

Package: Prize

Version: 1.14.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Prize.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Prize_1.14.0.tar.gz

StartedAt: 2019-10-16 06:07:38 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:10:16 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 158.5 seconds

RetCode: 0

Status: OK

CheckDir: Prize.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Prize.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Prize_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Prize.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
Prize-package 6.83   0.04    6.97
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
Prize-package 5.03   0.01    5.05
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Prize_1.14.0.tar.gz && rm -rf Prize.buildbin-libdir && mkdir Prize.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Prize.buildbin-libdir Prize_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Prize_1.14.0.zip && rm Prize_1.14.0.tar.gz Prize_1.14.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 35889  100 35889    0     0   203k      0 --:--:-- --:--:-- --:--:--  212k

install for i386

* installing *source* package 'Prize' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Prize'
    finding HTML links ... done
    AIJ                                     html  
    AIP                                     html  
    CI                                      html  
    GCR                                     html  
    ICR                                     html  
    IP                                      html  
    Prize-package                           html  
    RM                                      html  
    aggreg.judgement-data                   html  
    ahmatrix                                html  
    ahmatrixObj-class                       html  
    ahp                                     html  
    ahpObj-class                            html  
    ahp_matrix                              html  
    ahp_plot                                html  
    ahp_weights                             html  
    ahplot                                  html  
    ariAggreg-class                         html  
    crplot                                  html  
    dplot                                   html  
    epitope.PCM-data                        html  
    epitopeLength.PCM-data                  html  
    epitopeNum.PCM-data                     html  
    epitope_num_rating-data                 html  
    epitope_size_rating-data                html  
    freq.PCM-data                           html  
    freq_exp_rating-data                    html  
    gaggregate                              html  
    genes.list-data                         html  
    geoAggreg-class                         html  
    ind1-data                               html  
    ind2-data                               html  
    ind3-data                               html  
    ind4-data                               html  
    normal.PCM-data                         html  
    normal_exp_rating-data                  html  
    numEpitope_alternative_category-data    html  
    number-data                             html  
    pipeline                                html  
    pipelineObj-class                       html  
    rainbow_plot                            html  
    rainbowplot                             html  
    rating                                  html  
    ratingObj-class                         html  
    saaty_inconsistency                     html  
    simulation                              html  
    tumor.PCM-data                          html  
    tumor_exp_rating-data                   html  
    weight                                  html  
    weight_plot                             html  
    wplot                                   html  
** 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

install for x64

* installing *source* package 'Prize' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Prize' as Prize_1.14.0.zip
* DONE (Prize)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Prize' successfully unpacked and MD5 sums checked


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 06:10:02 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 
   7.42    0.06    8.85


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 06:10:10 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 
   7.09    0.15    7.23

name	user	system	elapsed
AIJ	1.97	0.02	1.99
AIP	1.18	0.00	1.18
CI	1.6	0.0	1.6
GCR	2.23	0.02	2.25
ICR	2.81	0.00	2.81
IP	3.83	0.00	3.83
Prize-package	6.83	0.04	6.97
RM	0.39	0.00	0.39
ahmatrix	0	0	0
ahp	0.25	0.00	0.25
ahp_matrix	0	0	0
ahp_plot	2.22	0.00	2.22
ahp_weights	2.80	0.00	2.79
ahplot	0.03	0.00	0.03
crplot	0.23	0.00	0.23
dplot	0.19	0.00	0.19
gaggregate	3.53	0.01	3.55
pipeline	2.41	0.02	2.42
rainbow_plot	2.37	0.03	2.41
rainbowplot	0.22	0.00	0.21
rating	0.5	0.0	0.5
saaty_inconsistency	2.83	0.02	2.85
simulation	3.06	0.00	3.06
weight	0.78	0.00	0.78
weight_plot	2.88	0.00	2.88
wplot	0.51	0.01	0.53

name	user	system	elapsed
AIJ	1.67	0.00	1.67
AIP	1.06	0.00	1.07
CI	1.54	0.02	1.56
GCR	1.64	0.00	1.64
ICR	2.75	0.00	2.75
IP	2.8	0.0	2.8
Prize-package	5.03	0.01	5.05
RM	0.30	0.00	0.29
ahmatrix	0	0	0
ahp	0.27	0.00	0.27
ahp_matrix	0	0	0
ahp_plot	2.19	0.02	2.21
ahp_weights	2.11	0.00	2.11
ahplot	0.03	0.00	0.04
crplot	0.23	0.00	0.23
dplot	0.19	0.01	0.20
gaggregate	3.03	0.00	3.03
pipeline	1.97	0.04	2.00
rainbow_plot	2.05	0.00	2.05
rainbowplot	0.23	0.00	0.24
rating	0.55	0.00	0.54
saaty_inconsistency	2.65	0.00	2.66
simulation	2.11	0.00	2.11
weight	0.52	0.00	0.51
weight_plot	2.09	0.00	2.10
wplot	0.30	0.00	0.29

CHECK report for Prize on tokay2

Summary

Command output

Installation output

Tests output

Example timings