Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-02-22 12:48:33 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
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 506/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dce 1.11.0  (landing page)
Kim Philipp Jablonski
Snapshot Date: 2024-02-21 14:10:10 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/dce
git_branch: devel
git_last_commit: 57c5fa4
git_last_commit_date: 2023-10-24 11:30:24 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for dce on palomino3


To the developers/maintainers of the dce package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: dce
Version: 1.11.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:dce.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings dce_1.11.0.tar.gz
StartedAt: 2024-02-22 02:06:02 -0500 (Thu, 22 Feb 2024)
EndedAt: 2024-02-22 02:12:05 -0500 (Thu, 22 Feb 2024)
EllapsedTime: 362.3 seconds
RetCode: 0
Status:   OK  
CheckDir: dce.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:dce.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings dce_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/dce.Rcheck'
* using R Under development (unstable) (2024-01-14 r85805 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'dce/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dce' version '1.11.0'
* 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
* 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 ... 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
  'F:/biocbuild/bbs-3.19-bioc/meat/dce.Rcheck/00check.log'
for details.



Installation output

dce.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL dce
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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 Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.4     ✔ readr     2.1.5
✔ forcats   1.0.0     ✔ stringr   1.5.1
✔ ggplot2   3.4.4     ✔ tibble    3.2.1
✔ lubridate 1.9.3     ✔ tidyr     1.3.1
✔ purrr     1.0.2     
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ lubridate::%--%()      masks igraph::%--%()
✖ 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::lag()           masks stats::lag()
✖ purrr::simplify()      masks igraph::simplify()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
> 
> 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 209 | SKIP 5 | PASS 40031 ]

══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• empty test (5): 'test-dce.R:185:1', 'test-deconfounding.R:51:1',
  'test-ideas.R:16:1', 'test-ideas.R:63:1', 'test-plotting.R:1:1'

[ FAIL 0 | WARN 209 | SKIP 5 | PASS 40031 ]
> 
> proc.time()
   user  system elapsed 
  99.98    7.01  122.71 

Example timings

dce.Rcheck/dce-Ex.timings

nameusersystemelapsed
as.data.frame.dce1.690.061.77
as_adjmat0.030.000.03
create_random_DAG0.020.000.01
dce-methods0.230.000.24
dce_nb3.350.053.40
estimate_latent_count1.300.051.35
g2dag0.210.030.28
get_pathway_info0.320.030.36
get_pathways4.260.124.40
get_prediction_counts000
graph2df0.060.000.07
graph_union0.100.020.11
pcor000
permutation_test0.010.020.03
plot.dce0.640.090.73
plot_network0.210.000.25
propagate_gene_edges0.110.000.35
resample_edge_weights000
simulate_data-methods0.030.000.03
topologically_ordering000
trueEffects0.000.000.02