Multiple platform build/check report for BioC 3.14 - CHECK results for geva on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: geva

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geva.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings geva_1.2.0.tar.gz

StartedAt: 2022-04-12 20:27:13 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 20:34:44 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 450.6 seconds

RetCode: 0

Status: OK

CheckDir: geva.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geva.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings geva_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/geva.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'geva/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'geva' version '1.2.0'
* package encoding: UTF-8
* 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 'geva' 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
geva.quick    41.94   0.05   42.18
geva.finalize 20.08   0.04   20.10
top.genes     18.47   0.00   18.55
geva.hcluster  7.61   0.01    7.63
geva.cluster   7.29   0.29    7.60
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
geva.quick    43.92   0.05   43.98
geva.finalize 20.00   0.03   20.04
top.genes     19.78   0.00   19.78
geva.cluster   7.51   0.24   44.61
geva.hcluster  6.45   0.02    6.49
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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 http://155.52.207.166/BBS/3.14/bioc/src/contrib/geva_1.2.0.tar.gz && rm -rf geva.buildbin-libdir && mkdir geva.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=geva.buildbin-libdir geva_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL geva_1.2.0.zip && rm geva_1.2.0.tar.gz geva_1.2.0.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  415k  100  415k    0     0   919k      0 --:--:-- --:--:-- --:--:--  922k

install for i386

* installing *source* package 'geva' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'geva'
    finding HTML links ... done
    GEVACluster-class                       html  
    GEVAGroupSet-class                      html  
    GEVAGroupedSummary-class                html  
    GEVAInput-class                         html  
    GEVAQuantiles-class                     html  
    GEVAQuantilesAdjusted-class             html  
    GEVAResults-class                       html  
    GEVASummary-class                       html  
    SVAttribute-class                       html  
    SVTable-class                           html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/geva.buildbin-libdir/00LOCK-geva/00new/geva/help/svtable.html
    TypedList-class                         html  
    generics                                html  
    geva-package                            html  
    geva.cluster                            html  
    geva.dcluster                           html  
    geva.finalize                           html  
    geva.hcluster                           html  
    geva.ideal.example                      html  
    geva.input.correct                      html  
    geva.merge.input                        html  
    geva.quantiles                          html  
    geva.quick                              html  
    geva.summarize                          html  
    top.genes                               html  
** building package indices
** installing vignettes
   'geva.Rmd' using 'UTF-8' 
** 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 'geva' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'geva' as geva_1.2.0.zip
* DONE (geva)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'geva' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.

> library(testthat)
> library(geva)
> 
> test_check("geva")
Merging scores...
Searching for dependent factors...
Searching for specific factors...
Found 54 significant genes:
similar: 33
factor-specific: 7
factor-dependent: 14
Input summarized
Calculating hierarchical clustering...
Found 6 clusters
Merging scores...
Searching for dependent factors...
Searching for specific factors...
Found 60 significant genes:
factor-specific: 18
factor-dependent: 39
similar: 3
Testing plot with GEVAResults
Testing with cluster.method = 'hierarchical'
Calculating hierarchical clustering...
Found 6 clusters
Testing with cluster.method = 'density'
Calculating density clustering...
Found 3 clusters
Testing quantiles grouping
Testing with quantile.method = 'range.slice'
Testing with quantile.method = 'proportional'
Testing with quantile.method = 'density'
Testing with quantile.method = 'k.max.sd'
Testing with quantile.method = 'custom'
Testing plot with GEVACluster and GEVAQuantiles
Reading 'gevainput14fc1eb21960.txt' ...
Reading 'gevainput14fc799696d.txt' ...
Reading 'gevainput14fc3e9846ad.txt' ...
Reading 'gevainput14fc19fc718e.txt' ...
Reading 'gevainput14fc42b16875.txt' ...
Reading 'gevainput14fc6b7d4c32.txt' ...
Reading 'gevainput14fc52bdce7.txt' ...
Reading 'gevainput14fc6b734b2d.txt' ...
Reading 'gevainput14fc2f6b778d.txt' ...
Read 9 columns with 10000 probes
Testing with summary.method = 'mean'
Testing with summary.method = 'median'
Testing with variation.method = 'sd'
Testing with variation.method = 'var'
Testing with variation.method = 'mad'
Testing plot with GEVASummary
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
  51.84    0.42   52.28


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.

> library(testthat)
> library(geva)
> 
> test_check("geva")
Merging scores...
Searching for dependent factors...
Searching for specific factors...
Found 54 significant genes:
similar: 33
factor-specific: 7
factor-dependent: 14
Input summarized
Calculating hierarchical clustering...
Found 6 clusters
Merging scores...
Searching for dependent factors...
Searching for specific factors...
Found 60 significant genes:
factor-specific: 18
factor-dependent: 39
similar: 3
Testing plot with GEVAResults
Testing with cluster.method = 'hierarchical'
Calculating hierarchical clustering...
Found 6 clusters
Testing with cluster.method = 'density'
Calculating density clustering...
Found 3 clusters
Testing quantiles grouping
Testing with quantile.method = 'range.slice'
Testing with quantile.method = 'proportional'
Testing with quantile.method = 'density'
Testing with quantile.method = 'k.max.sd'
Testing with quantile.method = 'custom'
Testing plot with GEVACluster and GEVAQuantiles
Reading 'gevainputafc5a182c37.txt' ...
Reading 'gevainputafc2d433a85.txt' ...
Reading 'gevainputafc7e6c626e.txt' ...
Reading 'gevainputafc3b66ce1.txt' ...
Reading 'gevainputafc73665e9a.txt' ...
Reading 'gevainputafc18bd59bb.txt' ...
Reading 'gevainputafc55b2523.txt' ...
Reading 'gevainputafc616f65.txt' ...
Reading 'gevainputafc354e528f.txt' ...
Read 9 columns with 10000 probes
Testing with summary.method = 'mean'
Testing with summary.method = 'median'
Testing with variation.method = 'sd'
Testing with variation.method = 'var'
Testing with variation.method = 'mad'
Testing plot with GEVASummary
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
  52.68    0.29   52.96

name	user	system	elapsed
SVTable-class	0.01	0.00	0.02
TypedList-class	0	0	0
generics	0.36	0.00	0.36
geva.cluster	7.29	0.29	7.60
geva.dcluster	2.94	0.28	3.22
geva.finalize	20.08	0.04	20.10
geva.hcluster	7.61	0.01	7.63
geva.ideal.example	0.76	0.02	0.78
geva.input.correct	0.13	0.00	0.13
geva.merge.input	0.04	0.00	0.05
geva.quantiles	3.25	0.01	3.26
geva.quick	41.94	0.05	42.18
geva.summarize	0.7	0.0	0.7
top.genes	18.47	0.00	18.55

name	user	system	elapsed
SVTable-class	0	0	0
TypedList-class	0	0	0
generics	0.46	0.00	0.45
geva.cluster	7.51	0.24	44.61
geva.dcluster	2.94	0.17	3.11
geva.finalize	20.00	0.03	20.04
geva.hcluster	6.45	0.02	6.49
geva.ideal.example	0.69	0.00	0.69
geva.input.correct	0.11	0.00	0.11
geva.merge.input	0.03	0.00	0.03
geva.quantiles	2.78	0.03	2.81
geva.quick	43.92	0.05	43.98
geva.summarize	0.72	0.00	0.72
top.genes	19.78	0.00	19.78

CHECK results for geva on tokay2

Summary

Command output

Installation output

Tests output

Example timings