| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-04 12:07 -0400 (Sat, 04 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4853 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
| 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 1542/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pathMED 1.1.5 (landing page) Jordi Martorell-Marugán
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the pathMED package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pathMED.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: pathMED |
| Version: 1.1.5 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:pathMED.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings pathMED_1.1.5.tar.gz |
| StartedAt: 2025-10-03 10:02:48 -0000 (Fri, 03 Oct 2025) |
| EndedAt: 2025-10-03 10:08:08 -0000 (Fri, 03 Oct 2025) |
| EllapsedTime: 320.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: pathMED.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:pathMED.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings pathMED_1.1.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/pathMED.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 ‘pathMED/DESCRIPTION’ ... OK
* this is package ‘pathMED’ version ‘1.1.5’
* 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 ‘pathMED’ can be installed ... OK
* checking installed package size ... INFO
installed size is 5.9Mb
sub-directories of 1Mb or more:
R 1.0Mb
data 4.8Mb
* 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 data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘pathMED-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predictExternal
> ### Title: Predict conditions in external datasets
> ### Aliases: predictExternal
>
> ### ** Examples
>
> data(refData)
>
> commonGenes <- intersect(rownames(refData$dataset1),
+ rownames(refData$dataset2))
> dataset1 <- refData$dataset1[commonGenes, ]
> dataset2 <- refData$dataset2[commonGenes, ]
>
> scoresExample <- getScores(dataset1, geneSets = "tmod", method = "Z-score")
ℹ GSVA version 2.3.1
! Some gene sets have size one. Consider setting minSize > 1
ℹ Using a SnowParam parallel back-end with 1 workers
ℹ Calculating Z-scores for 408 gene sets
ℹ Centering and scaling values
✔ Calculations finished
>
> set.seed(123)
> trainedModel <- trainModel(
+ inputData = scoresExample,
+ metadata = refData$metadata1,
+ var2predict = "group",
+ models = methodsML("svmLinear",
+ outcomeClass = "character"
+ ),
+ Koutter = 2,
+ Kinner = 2,
+ repeatsCV = 1
+ )
Training models...
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| | 0%Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
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Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
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Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
Warning in .local(x, ...) : Variable(s) `' constant. Cannot scale data.
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|=================================== | 50%Error in confusionMatrix.default(x, y, positive = positiveClass) :
positive argument must be character
Calls: trainModel ... lapply -> FUN -> <Anonymous> -> confusionMatrix.default
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
mScores_filterPaths 34.396 0.196 34.682
mScores_imputeFromReference 31.359 0.247 31.677
mScores_createReference 30.413 0.295 30.796
ann2term 17.030 0.627 17.699
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
ERROR in test_trainModel: Error in confusionMatrix.default(x, y, positive = positiveClass) :
positive argument must be character
Test files with failing tests
test_predictExternal.R
test_predictExternal
test_trainModel.R
test_trainModel
Error in BiocGenerics:::testPackage("pathMED") :
unit tests failed for package pathMED
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: 2 ERRORs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/pathMED.Rcheck/00check.log’
for details.
pathMED.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL pathMED ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘pathMED’ ... ** this is package ‘pathMED’ version ‘1.1.5’ ** using staged installation ** R ** data ** inst ** 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 (pathMED)
pathMED.Rcheck/tests/runTests.Rout.fail
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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.
> BiocGenerics:::testPackage("pathMED")
Healthy samples supplied. Calculating M-Scores using healthy samples as reference for 30 samples
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ℹ GSVA version 2.3.1
ℹ Using a SnowParam parallel back-end with 1 workers
ℹ Calculating GSVA ranks
ℹ GSVA dense (classical) algorithm
ℹ Row-wise ECDF estimation with Gaussian kernels
ℹ Calculating GSVA column ranks
ℹ Using a SnowParam parallel back-end with 1 workers
ℹ Calculating GSVA scores
✔ Calculations finished
ℹ GSVA version 2.3.1
ℹ Using a SnowParam parallel back-end with 1 workers
ℹ Calculating ssGSEA scores for 5 gene sets
ℹ Calculating ranks
ℹ Calculating rank weights
ℹ Normalizing ssGSEA scores
✔ Calculations finished
ℹ GSVA version 2.3.1
ℹ Using a SnowParam parallel back-end with 1 workers
ℹ Calculating PLAGE scores for 5 gene sets
ℹ Centering and scaling values
✔ Calculations finished
ℹ GSVA version 2.3.1
ℹ Using a SnowParam parallel back-end with 1 workers
ℹ Calculating Z-scores for 5 gene sets
ℹ Centering and scaling values
✔ Calculations finished
Filtering collinear pathways...
Loading required namespace: fgsea
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ℹ GSVA version 2.3.1
! Some gene sets have size one. Consider setting minSize > 1
ℹ Using a SnowParam parallel back-end with 1 workers
ℹ Calculating Z-scores for 408 gene sets
ℹ Centering and scaling values
✔ Calculations finished
Loading required namespace: randomForest
Loading required namespace: gam
Loading required namespace: xgboost
Loading required namespace: ada
Training models...
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|=================================== | 50%Timing stopped at: 9.885 0.08 9.992
Error in confusionMatrix.default(x, y, positive = positiveClass) :
positive argument must be character
In addition: There were 46 warnings (use warnings() to see them)
ℹ GSVA version 2.3.1
! Some gene sets have size one. Consider setting minSize > 1
ℹ Using a SnowParam parallel back-end with 1 workers
ℹ Calculating Z-scores for 427 gene sets
ℹ Centering and scaling values
✔ Calculations finished
Training models...
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|=================================== | 50%Timing stopped at: 8.281 0.084 8.391
Error in confusionMatrix.default(x, y, positive = positiveClass) :
positive argument must be character
RUNIT TEST PROTOCOL -- Fri Oct 3 10:08:05 2025
***********************************************
Number of test functions: 3
Number of errors: 2
Number of failures: 0
1 Test Suite :
pathMED RUnit Tests - 3 test functions, 2 errors, 0 failures
ERROR in test_predictExternal: Error in confusionMatrix.default(x, y, positive = positiveClass) :
positive argument must be character
ERROR in test_trainModel: Error in confusionMatrix.default(x, y, positive = positiveClass) :
positive argument must be character
Test files with failing tests
test_predictExternal.R
test_predictExternal
test_trainModel.R
test_trainModel
Error in BiocGenerics:::testPackage("pathMED") :
unit tests failed for package pathMED
Execution halted
pathMED.Rcheck/pathMED-Ex.timings
| name | user | system | elapsed | |
| ann2term | 17.030 | 0.627 | 17.699 | |
| buildRefObject | 0.094 | 0.016 | 0.110 | |
| dissectDB | 2.669 | 0.063 | 2.743 | |
| getScores | 3.881 | 0.056 | 3.943 | |
| mScores_createReference | 30.413 | 0.295 | 30.796 | |
| mScores_filterPaths | 34.396 | 0.196 | 34.682 | |
| mScores_imputeFromReference | 31.359 | 0.247 | 31.677 | |
| methodsML | 0.058 | 0.004 | 0.072 | |