Multiple platform build/check report for BioC 3.14 - CHECK results for dce 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: dce

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dce.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings dce_1.2.0.tar.gz

StartedAt: 2022-04-12 18:15:15 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 18:23:06 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 470.4 seconds

RetCode: 0

Status: OK

CheckDir: dce.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dce.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings dce_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/dce.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 'dce/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dce' 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 'dce' 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 ... NOTE
as.data.frame.dce: no visible binding for global variable '.'
graph2df: no visible binding for global variable '.'
plot_network: no visible global function definition for '%T>%'
plot_network: no visible binding for global variable '.'
Undefined global functions or variables:
  %T>% .
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... NOTE
  Note: found 6 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/dce.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/dce_1.2.0.tar.gz && rm -rf dce.buildbin-libdir && mkdir dce.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dce.buildbin-libdir dce_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL dce_1.2.0.zip && rm dce_1.2.0.tar.gz dce_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
 21  414k   21 91589    0     0   392k      0  0:00:01 --:--:--  0:00:01  392k
100  414k  100  414k    0     0   633k      0 --:--:-- --:--:-- --:--:--  633k

install for i386

* installing *source* package 'dce' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'dce'
    finding HTML links ... done
    as.data.frame.dce                       html  
    as_adjmat                               html  
    create_random_DAG                       html  
    dce-methods                             html  
    dce_nb                                  html  
    df_pathway_statistics                   html  
    estimate_latent_count                   html  
    g2dag                                   html  
    get_pathway_info                        html  
    get_pathways                            html  
    get_prediction_counts                   html  
    graph2df                                html  
    graph_union                             html  
    pcor                                    html  
    permutation_test                        html  
    plot.dce                                html  
    plot_network                            html  
    propagate_gene_edges                    html  
    resample_edge_weights                   html  
    rlm_dce                                 html  
    simulate_data-methods                   html  
    summary.rlm_dce                         html  
    topologically_ordering                  html  
    trueEffects                             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 'dce' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dce' as dce_1.2.0.zip
* DONE (dce)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'dce' 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(dce)

> library(igraph)

Attaching package: 'igraph'

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

    compare

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

    decompose, spectrum

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

    union

> library(tidyverse)
-- Attaching packages --------------------------------------- tidyverse 1.3.1 --
v ggplot2 3.3.5     v purrr   0.3.4
v tibble  3.1.6     v dplyr   1.0.8
v tidyr   1.2.0     v stringr 1.4.0
v readr   2.1.2     v forcats 0.5.1
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::as_data_frame() masks tibble::as_data_frame(), igraph::as_data_frame()
x purrr::compose()       masks igraph::compose()
x tidyr::crossing()      masks igraph::crossing()
x readr::edition_get()   masks testthat::edition_get()
x dplyr::filter()        masks stats::filter()
x dplyr::groups()        masks igraph::groups()
x purrr::is_null()       masks testthat::is_null()
x dplyr::lag()           masks stats::lag()
x readr::local_edition() masks testthat::local_edition()
x dplyr::matches()       masks tidyr::matches(), testthat::matches()
x purrr::simplify()      masks igraph::simplify()
> 
> 
> test_check("dce")
[ FAIL 0 | WARN 200 | SKIP 5 | PASS 40028 ]

== Skipped tests ===============================================================
* empty test (5)

[ FAIL 0 | WARN 200 | SKIP 5 | PASS 40028 ]
> 
> proc.time()
   user  system elapsed 
  68.50    1.89   70.37


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(dce)

> library(igraph)

Attaching package: 'igraph'

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

    compare

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

    decompose, spectrum

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

    union

> library(tidyverse)
-- Attaching packages --------------------------------------- tidyverse 1.3.1 --
v ggplot2 3.3.5     v purrr   0.3.4
v tibble  3.1.6     v dplyr   1.0.8
v tidyr   1.2.0     v stringr 1.4.0
v readr   2.1.2     v forcats 0.5.1
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::as_data_frame() masks tibble::as_data_frame(), igraph::as_data_frame()
x purrr::compose()       masks igraph::compose()
x tidyr::crossing()      masks igraph::crossing()
x readr::edition_get()   masks testthat::edition_get()
x dplyr::filter()        masks stats::filter()
x dplyr::groups()        masks igraph::groups()
x purrr::is_null()       masks testthat::is_null()
x dplyr::lag()           masks stats::lag()
x readr::local_edition() masks testthat::local_edition()
x dplyr::matches()       masks tidyr::matches(), testthat::matches()
x purrr::simplify()      masks igraph::simplify()
> 
> 
> test_check("dce")
[ FAIL 0 | WARN 201 | SKIP 5 | PASS 40028 ]

== Skipped tests ===============================================================
* empty test (5)

[ FAIL 0 | WARN 201 | SKIP 5 | PASS 40028 ]
> 
> proc.time()
   user  system elapsed 
  77.57    2.20   79.79

name	user	system	elapsed
as.data.frame.dce	1.78	0.09	2.01
as_adjmat	0.08	0.00	0.08
create_random_DAG	0.05	0.00	0.04
dce-methods	0.43	0.11	0.55
dce_nb	4.07	0.00	4.06
estimate_latent_count	1.73	0.05	1.79
g2dag	0.23	0.01	0.25
get_pathway_info	0.71	0.03	0.73
get_pathways	3.65	0.05	3.70
get_prediction_counts	0	0	0
graph2df	0.03	0.00	0.03
graph_union	0.08	0.00	0.08
pcor	0	0	0
permutation_test	0.03	0.00	0.03
plot.dce	1.33	0.05	1.37
plot_network	0.20	0.00	0.21
propagate_gene_edges	0.09	0.00	0.09
resample_edge_weights	0.02	0.00	0.02
simulate_data-methods	0.02	0.00	0.01
topologically_ordering	0	0	0
trueEffects	0.01	0.00	0.02

name	user	system	elapsed
as.data.frame.dce	1.65	0.02	1.68
as_adjmat	0.05	0.00	0.04
create_random_DAG	0.03	0.00	0.03
dce-methods	0.91	0.01	0.93
dce_nb	3.78	0.01	3.80
estimate_latent_count	1.03	0.00	1.03
g2dag	0.19	0.07	0.25
get_pathway_info	0.36	0.01	0.37
get_pathways	3.09	0.07	3.16
get_prediction_counts	0	0	0
graph2df	0.06	0.00	0.06
graph_union	0.14	0.00	0.14
pcor	0.02	0.00	0.02
permutation_test	0.03	0.00	0.03
plot.dce	1.54	0.01	1.56
plot_network	0.27	0.00	0.26
propagate_gene_edges	0.12	0.00	0.13
resample_edge_weights	0	0	0
simulate_data-methods	0.04	0.00	0.03
topologically_ordering	0	0	0
trueEffects	0.00	0.02	0.02

CHECK results for dce on tokay2

Summary

Command output

Installation output

Tests output

Example timings