Jordi Martorell-Marugán
| Snapshot Date: 2025-08-07 13:45 -0400 (Thu, 07 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/pathMED |
| git_branch: devel |
| git_last_commit: 07a5010 |
| git_last_commit_date: 2025-07-29 04:19:11 -0400 (Tue, 29 Jul 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-08 12:06 -0400 (Fri, 08 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4815 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4550 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4592 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4534 |
| 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 1523/2315 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pathMED 1.1.4 (landing page) Jordi Martorell-Marugán
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.1 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: 1.1.4 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:pathMED.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings pathMED_1.1.4.tar.gz |
| StartedAt: 2025-08-08 01:15:01 -0400 (Fri, 08 Aug 2025) |
| EndedAt: 2025-08-08 01:21:34 -0400 (Fri, 08 Aug 2025) |
| EllapsedTime: 392.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pathMED.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:pathMED.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings pathMED_1.1.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/pathMED.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘pathMED/DESCRIPTION’ ... OK
* this is package ‘pathMED’ version ‘1.1.4’
* 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 26.909 0.497 27.408
mScores_imputeFromReference 26.344 0.337 26.681
mScores_createReference 24.128 0.237 24.366
predictExternal 15.744 0.155 15.905
ann2term 13.756 0.822 14.580
trainModel 11.875 0.161 12.037
* 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-3.22-bioc/R/bin/R CMD INSTALL pathMED ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘pathMED’ ... ** this is package ‘pathMED’ version ‘1.1.4’ ** 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 version 4.5.1 (2025-06-13) -- "Great Square Root"
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 2.3.1
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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Done
Calculating performance metrics...
Done
Training final model with all samples...
Done
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
Positive class not provided, selected: 'Healthy_sample'
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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Done
Calculating performance metrics...
Done
Training final model with all samples...
Done
RUNIT TEST PROTOCOL -- Fri Aug 8 01:20:28 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
67.299 3.425 70.751
pathMED.Rcheck/pathMED-Ex.timings
| name | user | system | elapsed | |
| ann2term | 13.756 | 0.822 | 14.580 | |
| buildRefObject | 0.114 | 0.012 | 0.126 | |
| dissectDB | 2.290 | 0.102 | 2.393 | |
| getScores | 3.165 | 0.146 | 3.312 | |
| mScores_createReference | 24.128 | 0.237 | 24.366 | |
| mScores_filterPaths | 26.909 | 0.497 | 27.408 | |
| mScores_imputeFromReference | 26.344 | 0.337 | 26.681 | |
| methodsML | 0.044 | 0.006 | 0.068 | |
| predictExternal | 15.744 | 0.155 | 15.905 | |
| trainModel | 11.875 | 0.161 | 12.037 | |