Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-09-21 12:06:00 -0400 (Tue, 21 Sep 2021).

CHECK results for dce on riesling1

To the developers/maintainers of the dce package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dce.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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

Package 440/2029HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dce 1.1.0  (landing page)
Kim Philipp Jablonski
Snapshot Date: 2021-09-20 14:50:09 -0400 (Mon, 20 Sep 2021)
git_url: https://git.bioconductor.org/packages/dce
git_branch: master
git_last_commit: 56b47a6
git_last_commit_date: 2021-05-19 13:00:18 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: dce
Version: 1.1.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dce.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings dce_1.1.0.tar.gz
StartedAt: 2021-09-21 00:25:27 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 00:31:27 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 360.4 seconds
RetCode: 0
Status:   OK  
CheckDir: dce.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dce.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings dce_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/dce.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.1.0'
* 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
  'D:/biocbuild/bbs-3.14-bioc/meat/dce.Rcheck/00check.log'
for details.



Installation output

dce.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/dce_1.1.0.tar.gz && rm -rf dce.buildbin-libdir && mkdir dce.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dce.buildbin-libdir dce_1.1.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL dce_1.1.0.zip && rm dce_1.1.0.tar.gz dce_1.1.0.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  414k  100  414k    0     0  1583k      0 --:--:-- --:--:-- --:--:-- 1583k

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_1.1.0.zip
* DONE (dce)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'dce' successfully unpacked and MD5 sums checked

Tests output

dce.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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  3.1.4     v dplyr   1.0.7
v tidyr   1.1.3     v stringr 1.4.0
v readr   2.0.1     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")
== Skipped tests ===============================================================
* empty test (2)

[ FAIL 0 | WARN 200 | SKIP 2 | PASS 40028 ]
> 
> proc.time()
   user  system elapsed 
  45.75    0.73   46.64 

dce.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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  3.1.4     v dplyr   1.0.7
v tidyr   1.1.3     v stringr 1.4.0
v readr   2.0.1     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")
== Skipped tests ===============================================================
* empty test (2)

[ FAIL 0 | WARN 201 | SKIP 2 | PASS 40028 ]
> 
> proc.time()
   user  system elapsed 
  52.65    1.31   54.67 

Example timings

dce.Rcheck/examples_i386/dce-Ex.timings

nameusersystemelapsed
as.data.frame.dce1.170.001.17
as_adjmat0.030.000.03
create_random_DAG0.020.000.02
dce-methods0.190.010.20
dce_nb2.540.022.56
estimate_latent_count0.900.000.89
g2dag0.180.010.21
get_pathway_info0.270.000.26
get_pathways3.150.053.20
get_prediction_counts0.020.000.02
graph2df0.020.000.02
graph_union0.040.000.04
pcor000
permutation_test0.020.000.02
plot.dce0.470.020.49
plot_network0.140.000.14
propagate_gene_edges0.100.000.09
resample_edge_weights000
simulate_data-methods0.010.000.02
topologically_ordering000
trueEffects000

dce.Rcheck/examples_x64/dce-Ex.timings

nameusersystemelapsed
as.data.frame.dce1.140.021.15
as_adjmat0.030.000.03
create_random_DAG0.000.010.02
dce-methods0.170.030.20
dce_nb2.230.022.25
estimate_latent_count0.770.000.77
g2dag0.170.010.19
get_pathway_info0.230.000.24
get_pathways3.100.043.12
get_prediction_counts000
graph2df0.030.000.03
graph_union0.040.000.05
pcor000
permutation_test0.020.000.01
plot.dce0.470.000.47
plot_network0.150.000.16
propagate_gene_edges0.100.010.11
resample_edge_weights000
simulate_data-methods0.040.000.05
topologically_ordering000
trueEffects000