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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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 794/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeDi 1.0.0  (landing page)
Annekathrin Nedwed
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/GeDi
git_branch: RELEASE_3_19
git_last_commit: 1ad6866
git_last_commit_date: 2024-04-30 11:56:08 -0400 (Tue, 30 Apr 2024)
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 GeDi on nebbiolo1

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: 1.0.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GeDi_1.0.0.tar.gz
StartedAt: 2024-06-12 23:20:17 -0400 (Wed, 12 Jun 2024)
EndedAt: 2024-06-12 23:34:22 -0400 (Wed, 12 Jun 2024)
EllapsedTime: 844.8 seconds
RetCode: 0
Status:   OK  
CheckDir: GeDi.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GeDi_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GeDi.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘GeDi/DESCRIPTION’ ... OK
* this is package ‘GeDi’ version ‘1.0.0’
* 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 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 88.603  8.403 174.621
getPPI        66.286  4.055  71.116
goSimilarity   5.340  0.660   6.000
scaleGO        4.685  0.620   5.305
getId          0.492  0.053   5.260
* 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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL GeDi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup"
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.v11.5/9606.protein.aliases.v11.5.txt.gz'
Content type 'application/octet-stream' length 21726816 bytes (20.7 MB)
==================================================
downloaded 20.7 MB

trying URL 'https://stringdb-downloads.org/download/protein.info.v11.5/9606.protein.info.v11.5.txt.gz'
Content type 'application/octet-stream' length 1901833 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://stringdb-downloads.org/download/protein.links.v11.5/9606.protein.links.v11.5.txt.gz'
Content type 'application/octet-stream' length 72718210 bytes (69.3 MB)
==================================================
downloaded 69.3 MB


preparing gene to GO mapping data...
preparing gene to GO mapping data...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 182 ]
> 
> proc.time()
   user  system elapsed 
129.320   8.274 222.027 

Example timings

GeDi.Rcheck/GeDi-Ex.timings

nameusersystemelapsed
GeDi0.0070.0000.007
buildClusterGraph0.1320.0200.152
buildGraph0.0060.0010.006
buildHistogramData0.0080.0000.009
calculateJaccard0.0040.0030.007
calculateKappa0.0190.0010.018
calculateSorensenDice0.0080.0000.008
checkInclusion0.0070.0000.007
clustering0.1020.0000.102
distanceDendro0.1250.0040.129
distanceHeatmap0.2110.0000.210
enrichmentWordcloud0.2240.0400.264
fuzzyClustering0.0030.0020.005
getAdjacencyMatrix0.0630.0050.068
getAnnotation 88.603 8.403174.621
getBipartiteGraph0.0060.0030.008
getClusterAdjacencyMatrix0.0280.0120.039
getGenes0.0060.0040.010
getGraphTitle0.0010.0040.004
getId0.4920.0535.260
getInteractionScore0.0390.0080.047
getJaccardMatrix0.4960.0760.572
getKappaMatrix1.8560.4802.337
getMeetMinMatrix0.6690.0640.733
getPPI66.286 4.05571.116
getSorensenDiceMatrix0.4130.0200.433
getStringDB0.4160.0413.001
getpMMMatrix0.7060.0680.774
goSimilarity5.340.666.00
gsHistogram0.0220.0060.028
kNN_clustering0.0350.0090.044
pMMlocal0.0270.0040.032
scaleGO4.6850.6205.305
seedFinding0.0060.0000.007