Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-08-16 11:05:11 -0400 (Tue, 16 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4378
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4161
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4169
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 dce on nebbiolo2


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? 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 471/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dce 1.5.1  (landing page)
Kim Philipp Jablonski
Snapshot Date: 2022-08-15 14:00:06 -0400 (Mon, 15 Aug 2022)
git_url: https://git.bioconductor.org/packages/dce
git_branch: master
git_last_commit: c6b8336
git_last_commit_date: 2022-05-10 09:15:34 -0400 (Tue, 10 May 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: dce
Version: 1.5.1
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:dce.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings dce_1.5.1.tar.gz
StartedAt: 2022-08-15 19:28:07 -0400 (Mon, 15 Aug 2022)
EndedAt: 2022-08-15 19:32:54 -0400 (Mon, 15 Aug 2022)
EllapsedTime: 286.9 seconds
RetCode: 0
Status:   OK  
CheckDir: dce.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:dce.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings dce_1.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/dce.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dce/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dce’ version ‘1.5.1’
* 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 for sufficient/correct file permissions ... 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
* 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
plot_network: no visible binding for global variable ‘.’
Undefined global functions or variables:
  .
* 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 3 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.16-bioc/meat/dce.Rcheck/00check.log’
for details.



Installation output

dce.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL dce
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* 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
*** copying figures
** 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
* DONE (dce)

Tests output

dce.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(igraph)

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

> library(tidyverse)
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
✔ ggplot2 3.3.6     ✔ purrr   0.3.4
✔ tibble  3.1.8     ✔ dplyr   1.0.9
✔ tidyr   1.2.0     ✔ stringr 1.4.0
✔ readr   2.1.2     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::as_data_frame() masks tibble::as_data_frame(), igraph::as_data_frame()
✖ purrr::compose()       masks igraph::compose()
✖ tidyr::crossing()      masks igraph::crossing()
✖ dplyr::filter()        masks stats::filter()
✖ dplyr::groups()        masks igraph::groups()
✖ dplyr::lag()           masks stats::lag()
✖ purrr::simplify()      masks igraph::simplify()
> 
> library(testthat)

Attaching package: 'testthat'

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

    matches

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

    is_null

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

    edition_get, local_edition

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

    matches

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

    compare

> 
> library(dce)

> 
> 
> test_check("dce")
[ FAIL 0 | WARN 200 | SKIP 5 | PASS 40031 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (5)

[ FAIL 0 | WARN 200 | SKIP 5 | PASS 40031 ]
> 
> proc.time()
   user  system elapsed 
 68.899   1.181  70.073 

Example timings

dce.Rcheck/dce-Ex.timings

nameusersystemelapsed
as.data.frame.dce2.3500.0492.399
as_adjmat0.0670.0000.067
create_random_DAG0.0180.0000.018
dce-methods0.2100.0080.219
dce_nb2.5650.0522.617
estimate_latent_count1.3270.0121.338
g2dag0.2640.0000.265
get_pathway_info0.3980.0120.410
get_pathways4.2840.1244.407
get_prediction_counts0.0020.0000.002
graph2df0.0330.0040.038
graph_union0.0660.0000.066
pcor0.0000.0020.002
permutation_test0.0220.0010.022
plot.dce0.5910.0320.623
plot_network0.2030.0200.223
propagate_gene_edges0.0810.0200.101
resample_edge_weights0.0020.0020.005
simulate_data-methods0.0430.0060.049
topologically_ordering0.0010.0000.000
trueEffects0.0050.0000.004