Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 784/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeDi 1.2.0  (landing page)
Annekathrin Nedwed
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/GeDi
git_branch: RELEASE_3_20
git_last_commit: abf007a
git_last_commit_date: 2024-10-29 11:30:20 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for GeDi on nebbiolo2

To the developers/maintainers of the GeDi package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeDi.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: GeDi
Version: 1.2.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GeDi_1.2.0.tar.gz
StartedAt: 2024-12-20 00:03:22 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 00:21:54 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 1112.8 seconds
RetCode: 0
Status:   OK  
CheckDir: GeDi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GeDi_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GeDi.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GeDi/DESCRIPTION’ ... OK
* this is package ‘GeDi’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘GeDi’ 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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
getAnnotation 82.038  6.099 176.806
getPPI        58.288  3.706  62.341
goDistance     4.374  0.831   5.205
getId          0.429  0.008   5.119
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

GeDi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL GeDi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘GeDi’ ...
** using staged installation
** R
** data
** 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 (GeDi)

Tests output

GeDi.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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(GeDi)

> 
> test_check("GeDi")
trying URL 'https://stringdb-downloads.org/download/protein.aliases.v12.0/9606.protein.aliases.v12.0.txt.gz'
Content type 'application/octet-stream' length 19777800 bytes (18.9 MB)
==================================================
downloaded 18.9 MB

trying URL 'https://stringdb-downloads.org/download/protein.info.v12.0/9606.protein.info.v12.0.txt.gz'
Content type 'application/octet-stream' length 1970090 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

trying URL 'https://stringdb-downloads.org/download/protein.links.v12.0/9606.protein.links.v12.0.txt.gz'
Content type 'application/octet-stream' length 83164437 bytes (79.3 MB)
==================================================
downloaded 79.3 MB


preparing gene to GO mapping data...
preparing gene to GO mapping data...
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 185 ]

[ FAIL 0 | WARN 9 | SKIP 0 | PASS 185 ]
> 
> proc.time()
   user  system elapsed 
107.918   7.996 209.519 

Example timings

GeDi.Rcheck/GeDi-Ex.timings

nameusersystemelapsed
GeDi0.0060.0000.006
buildClusterGraph0.1670.0220.189
buildGraph0.0050.0000.005
buildHistogramData0.0070.0000.008
calculateJaccard0.0070.0000.007
calculateKappa0.0130.0000.013
calculateSorensenDice0.0060.0000.006
checkInclusion0.0050.0000.005
clustering0.1230.0000.123
deprecated000
distanceDendro0.0980.0000.098
distanceHeatmap0.1090.0000.110
enrichmentWordcloud0.2350.0190.255
fuzzyClustering0.0040.0000.004
getAdjacencyMatrix0.0560.0000.057
getAnnotation 82.038 6.099176.806
getBipartiteGraph0.0060.0000.006
getClusterAdjacencyMatrix0.0440.0000.044
getGraphTitle0.0030.0000.003
getId0.4290.0085.119
getInteractionScore0.0550.0000.055
getJaccardMatrix0.8110.0020.813
getKappaMatrix1.2480.0001.249
getMeetMinMatrix1.8240.0321.856
getPPI58.288 3.70662.341
getSorensenDiceMatrix0.3660.0120.378
getStringDB0.3750.0353.421
getpMMMatrix0.6140.0430.656
goDistance4.3740.8315.205
gsHistogram0.0210.0010.022
kMeansClustering0.0150.0000.014
kNN_clustering0.0060.0010.008
louvainClustering0.0540.0050.060
markovClustering0.0660.0050.071
pMMlocal0.0300.0010.031
pamClustering0.0060.0000.006
prepareGenesetData0.0080.0000.008
scaleGO4.1060.4754.581
seedFinding0.0050.0010.005