Annekathrin Nedwed
| Snapshot Date: 2024-05-08 14:00:19 -0400 (Wed, 08 May 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) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-09 11:40:52 -0400 (Thu, 09 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4748 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| 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 794/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeDi 1.0.0 (landing page) Annekathrin Nedwed
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: GeDi |
| Version: 1.0.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings GeDi_1.0.0.tar.gz |
| StartedAt: 2024-05-09 07:37:02 -0000 (Thu, 09 May 2024) |
| EndedAt: 2024-05-09 07:54:40 -0000 (Thu, 09 May 2024) |
| EllapsedTime: 1057.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GeDi.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings GeDi_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GeDi.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 114.105 2.623 215.214
getPPI 75.662 1.489 77.922
goSimilarity 6.998 0.259 7.273
scaleGO 6.895 0.180 7.089
getId 0.159 0.004 5.986
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-downloadPPI.R:28:3'): PPI retrieval works ──────────────────────
Error in `download.file(urlStr, temp)`: download from 'https://stringdb-downloads.org/download/protein.links.v11.5/9606.protein.links.v11.5.txt.gz' failed
Backtrace:
▆
1. └─GeDi::getPPI(genes, stringdb, anno_df) at test-downloadPPI.R:28:3
2. └─string_db$get_interactions(string_ids)
3. └─STRINGdb (local) load()
4. └─STRINGdb::downloadAbsentFile(url, oD = input_directory)
5. └─utils::download.file(urlStr, temp)
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 181 ]
Error: Test failures
Execution halted
* 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: 1 ERROR
See
‘/home/biocbuild/bbs-3.19-bioc/meat/GeDi.Rcheck/00check.log’
for details.
GeDi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL GeDi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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)
GeDi.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 9.4 MB
preparing gene to GO mapping data...
preparing gene to GO mapping data...
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 181 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-downloadPPI.R:28:3'): PPI retrieval works ──────────────────────
Error in `download.file(urlStr, temp)`: download from 'https://stringdb-downloads.org/download/protein.links.v11.5/9606.protein.links.v11.5.txt.gz' failed
Backtrace:
▆
1. └─GeDi::getPPI(genes, stringdb, anno_df) at test-downloadPPI.R:28:3
2. └─string_db$get_interactions(string_ids)
3. └─STRINGdb (local) load()
4. └─STRINGdb::downloadAbsentFile(url, oD = input_directory)
5. └─utils::download.file(urlStr, temp)
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 181 ]
Error: Test failures
Execution halted
GeDi.Rcheck/GeDi-Ex.timings
| name | user | system | elapsed | |
| GeDi | 0.008 | 0.000 | 0.007 | |
| buildClusterGraph | 0.143 | 0.008 | 0.151 | |
| buildGraph | 0.008 | 0.000 | 0.009 | |
| buildHistogramData | 0.007 | 0.004 | 0.011 | |
| calculateJaccard | 0.01 | 0.00 | 0.01 | |
| calculateKappa | 0.022 | 0.000 | 0.022 | |
| calculateSorensenDice | 0.006 | 0.004 | 0.010 | |
| checkInclusion | 0.01 | 0.00 | 0.01 | |
| clustering | 0.172 | 0.012 | 0.184 | |
| distanceDendro | 0.169 | 0.000 | 0.170 | |
| distanceHeatmap | 0.171 | 0.004 | 0.175 | |
| enrichmentWordcloud | 0.339 | 0.004 | 0.345 | |
| fuzzyClustering | 0.006 | 0.000 | 0.006 | |
| getAdjacencyMatrix | 0.093 | 0.000 | 0.093 | |
| getAnnotation | 114.105 | 2.623 | 215.214 | |
| getBipartiteGraph | 0.012 | 0.000 | 0.012 | |
| getClusterAdjacencyMatrix | 0.039 | 0.000 | 0.038 | |
| getGenes | 0.011 | 0.000 | 0.011 | |
| getGraphTitle | 0.005 | 0.000 | 0.005 | |
| getId | 0.159 | 0.004 | 5.986 | |
| getInteractionScore | 0.038 | 0.000 | 0.038 | |
| getJaccardMatrix | 0.669 | 0.040 | 0.710 | |
| getKappaMatrix | 1.684 | 0.228 | 1.915 | |
| getMeetMinMatrix | 0.923 | 0.112 | 1.036 | |
| getPPI | 75.662 | 1.489 | 77.922 | |
| getSorensenDiceMatrix | 0.644 | 0.004 | 0.649 | |
| getStringDB | 0.121 | 0.004 | 3.847 | |
| getpMMMatrix | 0.923 | 0.036 | 0.961 | |
| goSimilarity | 6.998 | 0.259 | 7.273 | |
| gsHistogram | 0.027 | 0.004 | 0.030 | |
| kNN_clustering | 0.044 | 0.008 | 0.054 | |
| pMMlocal | 0.036 | 0.000 | 0.036 | |
| scaleGO | 6.895 | 0.180 | 7.089 | |
| seedFinding | 0.007 | 0.000 | 0.007 | |