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CHECK report for struct on tokay2

This page was generated on 2020-10-17 11:57:53 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE struct PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1751/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
struct 1.0.0
Gavin Rhys Lloyd
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/struct
Branch: RELEASE_3_11
Last Commit: 1a9f831
Last Changed Date: 2020-04-27 15:33:43 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: struct
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:struct.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings struct_1.0.0.tar.gz
StartedAt: 2020-10-17 08:41:21 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 08:45:13 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 232.1 seconds
RetCode: 0
Status:  OK  
CheckDir: struct.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:struct.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings struct_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/struct.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'struct/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'struct' version '1.0.0'
* 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 'struct' 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
** running examples for arch 'x64' ... OK
* 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


Installation output

struct.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/struct_1.0.0.tar.gz && rm -rf struct.buildbin-libdir && mkdir struct.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=struct.buildbin-libdir struct_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL struct_1.0.0.zip && rm struct_1.0.0.tar.gz struct_1.0.0.zip
###
##############################################################################
##############################################################################


  % 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  249k  100  249k    0     0   433k      0 --:--:-- --:--:-- --:--:--  438k

install for i386

* installing *source* package 'struct' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'struct'
    finding HTML links ... done
    as.DatasetExperiment-SummarizedExperiment-method
                                            html  
    as.DatasetExperiment                    html  
    as.SummarizedExperiment-DatasetExperiment-method
                                            html  
    as.SummarizedExperiment                 html  
    as_data_frame                           html  
    cash-set-struct_class-method            html  
    cash-struct_class-method                html  
    chart                                   html  
    chart_example                           html  
    chart_names                             html  
    chart_plot                              html  
    entity                                  html  
    entity_stato                            html  
    enum                                    html  
    enum_stato                              html  
    example_iterator                        html  
    example_model                           html  
    export_data                             html  
    iris_DatasetExperiment                  html  
    is_output                               html  
    is_param                                html  
    iterator                                html  
    metric                                  html  
    model                                   html  
    model_apply                             html  
    model_reverse                           html  
    model_seq                               html  
    models                                  html  
    new_struct                              html  
    optimiser                               html  
    output_ids                              html  
    output_list                             html  
    output_name                             html  
    output_obj                              html  
    output_value                            html  
    param_ids                               html  
    param_list                              html  
    param_name                              html  
    param_obj                               html  
    param_value                             html  
    predict                                 html  
    predicted                               html  
    predicted_name                          html  
    preprocessing                           html  
    resampler                               html  
    result                                  html  
    result_name                             html  
    set_obj_method                          html  
    set_obj_show                            html  
    set_struct_obj                          html  
    stato                                   html  
    struct                                  html  
    struct_DatasetExperiment                html  
    struct_class-class                      html  
    struct_class                            html  
    struct_template                         html  
    test_metric                             html  
    train                                   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 'struct' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'struct' as struct_1.0.0.zip
* DONE (struct)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'struct' successfully unpacked and MD5 sums checked

Tests output

struct.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(struct)
> library(SummarizedExperiment)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

> 
> test_check("struct")
== testthat results  ===========================================================
[ OK: 88 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
   8.96    0.65    9.61 

struct.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(struct)
> library(SummarizedExperiment)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

> 
> test_check("struct")
== testthat results  ===========================================================
[ OK: 88 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
   8.73    0.46    9.18 

Example timings

struct.Rcheck/examples_i386/struct-Ex.timings

nameusersystemelapsed
cash-set-struct_class-method0.030.000.03
cash-struct_class-method000
chart000
chart_example0.010.000.02
chart_names0.020.000.02
chart_plot0.080.000.07
entity000
entity_stato000
enum0.010.000.02
enum_stato000
example_iterator0.050.000.05
example_model0.140.080.21
export_data000
iris_DatasetExperiment0.010.010.04
is_output0.020.000.01
is_param000
iterator0.120.020.14
metric000
model0.230.010.25
model_apply0.130.000.12
model_reverse0.020.020.03
model_seq0.590.110.70
models000
new_struct000
optimiser000
output_ids0.020.000.02
output_list0.020.000.01
output_name0.010.000.02
output_obj000
output_value0.080.000.08
param_ids000
param_list000
param_name000
param_obj0.020.000.01
param_value000
predict0.030.000.03
predicted0.110.000.11
predicted_name000
preprocessing0.010.000.02
resampler000
result0.020.000.02
result_name000
set_obj_method0.030.000.03
set_obj_show0.030.000.03
stato0.700.080.86
struct_class-class000
struct_template000
test_metric000
train0.050.000.05

struct.Rcheck/examples_x64/struct-Ex.timings

nameusersystemelapsed
cash-set-struct_class-method0.020.000.02
cash-struct_class-method000
chart000
chart_example000
chart_names0.010.000.02
chart_plot0.050.000.05
entity000
entity_stato000
enum000
enum_stato0.000.010.01
example_iterator0.030.000.03
example_model0.080.040.11
export_data000
iris_DatasetExperiment0.000.010.02
is_output000
is_param000
iterator0.080.000.08
metric000
model0.120.000.12
model_apply0.060.000.06
model_reverse0.020.000.02
model_seq0.470.000.47
models000
new_struct000
optimiser000
output_ids000
output_list0.030.000.04
output_name000
output_obj000
output_value0.080.000.07
param_ids000
param_list0.020.000.02
param_name000
param_obj000
param_value000
predict0.030.000.04
predicted0.110.000.11
predicted_name000
preprocessing0.010.000.01
resampler000
result0.020.000.02
result_name000
set_obj_method0.020.000.01
set_obj_show0.010.000.02
stato0.940.010.95
struct_class-class000
struct_template000
test_metric000
train0.030.000.03