| Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2025-04-02 19:35 -0400 (Wed, 02 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
| 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 376/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ClusterJudge 1.28.0 (landing page) Adrian Pasculescu
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the ClusterJudge package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ClusterJudge.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: ClusterJudge |
| Version: 1.28.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ClusterJudge.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ClusterJudge_1.28.0.tar.gz |
| StartedAt: 2025-04-01 05:09:01 -0000 (Tue, 01 Apr 2025) |
| EndedAt: 2025-04-01 05:11:49 -0000 (Tue, 01 Apr 2025) |
| EllapsedTime: 168.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ClusterJudge.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:ClusterJudge.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ClusterJudge_1.28.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ClusterJudge.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ClusterJudge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClusterJudge’ version ‘1.28.0’
* 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 ‘ClusterJudge’ 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 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ClusterJudge-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convert_Yeast_SGDId_2_systematic
> ### Title: converts the SGD Gene Id into the systematic name of the gene
> ### Aliases: convert_Yeast_SGDId_2_systematic
>
> ### ** Examples
>
>
> converted.genes <- convert_Yeast_SGDId_2_systematic(
+ SGD.Ids = c("S000007287", "S000007287", "S000007287"))
No encoding supplied: defaulting to UTF-8.
Error: lexical error: invalid char in json text.
<!DOCTYPE html PUBLIC "-//W3C//
(right here) ------^
Execution halted
* 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: 1 ERROR
See
‘/home/biocbuild/bbs-3.20-bioc/meat/ClusterJudge.Rcheck/00check.log’
for details.
ClusterJudge.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ClusterJudge ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.3/site-library’ * installing *source* package ‘ClusterJudge’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (ClusterJudge)
ClusterJudge.Rcheck/tests/testthat.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 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(ClusterJudge)
Loading required package: infotheo
Loading required package: lattice
Loading required package: latticeExtra
Loading required package: httr
Loading required package: jsonlite
>
> test_check("ClusterJudge")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
>
> proc.time()
user system elapsed
0.895 0.065 0.948
ClusterJudge.Rcheck/ClusterJudge-Ex.timings
| name | user | system | elapsed | |
| Yeast.GO.assocs | 0.049 | 0.000 | 0.050 | |
| attribute_mut_inf | 1.845 | 0.024 | 1.875 | |
| clusterJudge | 49.925 | 0.407 | 50.456 | |
| clusterJudge_z_score | 35.892 | 0.116 | 36.091 | |
| consolidate_entity_attribute | 50.006 | 0.188 | 50.308 | |