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

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This page was generated on 2022-04-13 12:07:26 -0400 (Wed, 13 Apr 2022).

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*

CHECK results for struct on tokay2

To the developers/maintainers of the struct package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/struct.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

struct 1.6.0 (landing page)
Gavin Rhys Lloyd

Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)

git_url: https://git.bioconductor.org/packages/struct

git_branch: RELEASE_3_14

git_last_commit: 65817c3

git_last_commit_date: 2021-10-26 12:57:08 -0400 (Tue, 26 Oct 2021)

nebbiolo2

Linux (Ubuntu 20.04.4 LTS) / x86_64

tokay2

Windows Server 2012 R2 Standard / x64

machv2

macOS 10.14.6 Mojave / x86_64

Summary

Package: struct

Version: 1.6.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:struct.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings struct_1.6.0.tar.gz

StartedAt: 2022-04-13 03:39:56 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 03:43:39 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 222.9 seconds

RetCode: 0

Status: OK

CheckDir: struct.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:struct.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings struct_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/struct.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 'struct/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'struct' version '1.6.0'
* 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 http://155.52.207.166/BBS/3.14/bioc/src/contrib/struct_1.6.0.tar.gz && rm -rf struct.buildbin-libdir && mkdir struct.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=struct.buildbin-libdir struct_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL struct_1.6.0.zip && rm struct_1.6.0.tar.gz struct_1.6.0.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  259k  100  259k    0     0   761k      0 --:--:-- --:--:-- --:--:--  762k

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.code                                 html  
    as_data_frame                           html  
    autocompletion                          html  
    c-ontology_list-method                  html  
    cash-ontology_list-method               html  
    cash-ontology_term-method               html  
    cash-set-struct_class-method            html  
    cash-struct_class-method                html  
    chart                                   html  
    chart_example                           html  
    chart_names                             html  
    chart_plot                              html  
    citations                               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  
    libraries                               html  
    metric                                  html  
    model                                   html  
    model_apply                             html  
    model_reverse                           html  
    model_seq                               html  
    models                                  html  
    new_struct                              html  
    ontology                                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  
    seq_in                                  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_1.6.0.zip
* DONE (struct)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'struct' successfully unpacked and MD5 sums checked

Tests output

struct.Rcheck/tests_i386/testthat.Rout


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(struct)
> library(SummarizedExperiment)
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

> 
> test_check("struct")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 150 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 150 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
  10.59    0.90   16.59

struct.Rcheck/tests_x64/testthat.Rout


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(struct)
> library(SummarizedExperiment)
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

> 
> test_check("struct")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 150 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 150 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
  15.54    0.60   21.39

Example timings

struct.Rcheck/examples_i386/struct-Ex.timings

name	user	system	elapsed
as.code	0.05	0.00	0.04
cash-ontology_list-method	0	0	0
cash-ontology_term-method	0	0	0
cash-set-struct_class-method	0.01	0.00	0.02
cash-struct_class-method	0	0	0
chart	0	0	0
chart_example	0.02	0.00	0.01
chart_names	0.01	0.00	0.02
chart_plot	0.08	0.00	0.08
citations	0.14	0.01	0.15
entity	0	0	0
entity_stato	0	0	0
enum	0	0	0
enum_stato	0.01	0.00	0.02
example_iterator	0.03	0.02	0.04
example_model	0.19	0.03	0.22
export_data	0	0	0
iris_DatasetExperiment	0.03	0.02	0.05
is_output	0	0	0
is_param	0.02	0.00	0.01
iterator	0.09	0.09	0.19
libraries	0.00	0.01	0.02
metric	0	0	0
model	0.35	0.02	0.36
model_apply	0.09	0.00	0.09
model_reverse	0.03	0.00	0.03
model_seq	0.58	0.00	0.58
models	0.02	0.00	0.02
new_struct	0	0	0
ontology	0.01	0.00	0.01
optimiser	0	0	0
output_ids	0	0	0
output_list	0.06	0.00	0.06
output_name	0	0	0
output_obj	0.02	0.00	0.02
output_value	0.09	0.00	0.09
param_ids	0	0	0
param_list	0.02	0.00	0.02
param_name	0.01	0.00	0.01
param_obj	0	0	0
param_value	0.02	0.00	0.02
predict	0.06	0.00	0.06
predicted	0.16	0.00	0.16
predicted_name	0.01	0.00	0.01
preprocessing	0.02	0.00	0.02
resampler	0	0	0
result	0.05	0.00	0.05
result_name	0	0	0
seq_in	0	0	0
set_obj_method	0.01	0.00	0.01
set_obj_show	0.02	0.00	0.02
stato	0.51	0.06	0.65
struct_class-class	0	0	0
struct_template	0	0	0
test_metric	0	0	0
train	0.06	0.00	0.06

struct.Rcheck/examples_x64/struct-Ex.timings

name	user	system	elapsed
as.code	0.17	0.00	0.17
cash-ontology_list-method	0	0	0
cash-ontology_term-method	0	0	0
cash-set-struct_class-method	0	0	0
cash-struct_class-method	0	0	0
chart	0	0	0
chart_example	0.01	0.00	0.02
chart_names	0.02	0.00	0.02
chart_plot	0.06	0.02	0.07
citations	0.19	0.03	0.36
entity	0	0	0
entity_stato	0	0	0
enum	0.01	0.00	0.01
enum_stato	0	0	0
example_iterator	0.06	0.00	0.06
example_model	0.22	0.06	0.28
export_data	0	0	0
iris_DatasetExperiment	0.07	0.00	0.07
is_output	0	0	0
is_param	0.01	0.00	0.01
iterator	0.69	0.02	0.71
libraries	0	0	0
metric	0.01	0.00	0.01
model	0.27	0.00	0.27
model_apply	0.11	0.00	0.11
model_reverse	0.03	0.00	0.03
model_seq	0.67	0.01	0.68
models	0.02	0.00	0.02
new_struct	0	0	0
ontology	0	0	0
optimiser	0	0	0
output_ids	0.01	0.00	0.02
output_list	0.07	0.00	0.06
output_name	0.01	0.00	0.01
output_obj	0	0	0
output_value	0.11	0.02	0.13
param_ids	0	0	0
param_list	0.02	0.00	0.01
param_name	0	0	0
param_obj	0.01	0.00	0.02
param_value	0	0	0
predict	0.07	0.00	0.06
predicted	0.18	0.00	0.19
predicted_name	0	0	0
preprocessing	0.03	0.00	0.03
resampler	0	0	0
result	0.05	0.00	0.05
result_name	0	0	0
seq_in	0	0	0
set_obj_method	0.02	0.00	0.01
set_obj_show	0.01	0.00	0.02
stato	0.36	0.00	0.36
struct_class-class	0	0	0
struct_template	0	0	0
test_metric	0	0	0
train	0.06	0.00	0.07