Jordi Martorell-Marugán
| Snapshot Date: 2025-11-13 13:40 -0500 (Thu, 13 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/pathMED |
| git_branch: devel |
| git_last_commit: 721d804 |
| git_last_commit_date: 2025-10-29 11:36:06 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-14 11:36 -0500 (Fri, 14 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4825 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4547 |
| 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 1536/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pathMED 1.3.0 (landing page) Jordi Martorell-Marugán
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
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. |
| Package: pathMED |
| Version: 1.3.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:pathMED.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings pathMED_1.3.0.tar.gz |
| StartedAt: 2025-11-14 02:28:19 -0500 (Fri, 14 Nov 2025) |
| EndedAt: 2025-11-14 02:34:55 -0500 (Fri, 14 Nov 2025) |
| EllapsedTime: 396.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pathMED.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:pathMED.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings pathMED_1.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/pathMED.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘pathMED/DESCRIPTION’ ... OK
* this is package ‘pathMED’ version ‘1.3.0’
* 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 ‘pathMED’ can be installed ... OK
* checking installed package size ... INFO
installed size is 5.9Mb
sub-directories of 1Mb or more:
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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
mScores_filterPaths 28.230 0.390 28.620
mScores_imputeFromReference 26.280 0.354 26.636
mScores_createReference 25.703 0.299 26.049
ann2term 12.962 1.208 14.172
predictExternal 13.488 0.194 13.684
trainModel 10.123 0.111 10.234
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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
pathMED.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL pathMED ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘pathMED’ ... ** this is package ‘pathMED’ version ‘1.3.0’ ** 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
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 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.
> BiocGenerics:::testPackage("pathMED")
Healthy samples supplied. Calculating M-Scores using healthy samples as reference for 30 samples
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ℹ GSVA version 2.5.6
ℹ Searching for genes/features with constant values
ℹ Calculating GSVA ranks
ℹ GSVA dense (classical) algorithm
ℹ Row-wise ECDF estimation with Gaussian kernels
ℹ Calculating row ECDFs
ℹ Calculating column ranks
ℹ GSVA dense (classical) algorithm
ℹ Calculating GSVA scores
✔ Calculations finished
Warning: stack imbalance in '<-', 25 then 26
ℹ GSVA version 2.5.6
ℹ Searching for genes/features with constant values
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 2.5.6
ℹ Searching for genes/features with constant values
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 2.5.6
ℹ Searching for genes/features with constant values
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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Warning: stack imbalance in '{', 21 then 22
ℹ GSVA version 2.5.6
ℹ Searching for genes/features with constant values
! 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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Done
Calculating performance metrics...
Done
Training final model with all samples...
Done
ℹ GSVA version 2.5.6
ℹ Searching for genes/features with constant values
! 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
Positive class not provided, selected: 'Healthy_sample'
ℹ GSVA version 2.5.6
ℹ Searching for genes/features with constant values
! 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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Done
Calculating performance metrics...
Done
Training final model with all samples...
Done
RUNIT TEST PROTOCOL -- Fri Nov 14 02:33:47 2025
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
pathMED RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3
Number of errors: 0
Number of failures: 0
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
63.838 2.830 66.662
pathMED.Rcheck/pathMED-Ex.timings
| name | user | system | elapsed | |
| ann2term | 12.962 | 1.208 | 14.172 | |
| buildRefObject | 0.112 | 0.014 | 0.126 | |
| dissectDB | 2.342 | 0.129 | 2.471 | |
| getScores | 3.038 | 0.161 | 3.203 | |
| mScores_createReference | 25.703 | 0.299 | 26.049 | |
| mScores_filterPaths | 28.23 | 0.39 | 28.62 | |
| mScores_imputeFromReference | 26.280 | 0.354 | 26.636 | |
| methodsML | 0.042 | 0.014 | 0.063 | |
| predictExternal | 13.488 | 0.194 | 13.684 | |
| trainModel | 10.123 | 0.111 | 10.234 | |