Jordi Martorell-Marugán
| Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/pathMED |
| git_branch: devel |
| git_last_commit: 5a1b067 |
| git_last_commit_date: 2025-10-06 07:44:30 -0400 (Mon, 06 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-24 12:05 -0400 (Fri, 24 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" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 1555/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pathMED 1.1.6 (landing page) Jordi Martorell-Marugán
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 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 | NA | ||||||||||
|
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: 1.1.6 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pathMED.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pathMED_1.1.6.tar.gz |
| StartedAt: 2025-10-23 23:08:10 -0400 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 23:13:35 -0400 (Thu, 23 Oct 2025) |
| EllapsedTime: 324.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: pathMED.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pathMED.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pathMED_1.1.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/pathMED.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pathMED/DESCRIPTION’ ... OK
* this is package ‘pathMED’ version ‘1.1.6’
* 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 5.8Mb
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 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 33.034 0.840 34.042
mScores_imputeFromReference 31.284 0.894 32.401
mScores_createReference 30.491 1.061 31.901
predictExternal 17.172 0.317 17.661
ann2term 15.337 0.828 16.272
trainModel 13.397 0.335 14.034
* 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:
pathMED RUnit Tests - 3 test functions, 0 errors, 1 failure
FAILURE in test_getScores: Error in checkEquals(round(scoresExample[1, 1], 5), 43.8289) :
Mean relative difference: 0.1730913
Test files with failing tests
test_getScores.R
test_getScores
Error in BiocGenerics:::testPackage("pathMED") :
unit tests failed for package pathMED
In addition: There were 50 or more warnings (use warnings() to see the first 50)
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
‘/Users/biocbuild/bbs-3.22-bioc/meat/pathMED.Rcheck/00check.log’
for details.
pathMED.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pathMED ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘pathMED’ ... ** this is package ‘pathMED’ version ‘1.1.6’ ** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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 2.3.4
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 2.3.4
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 2.3.4
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 2.3.4
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
Timing stopped at: 18.4 0.882 19.4
Error in checkEquals(round(scoresExample[1, 1], 5), 43.8289) :
Mean relative difference: 0.1730913
In addition: Warning messages:
1: In checkGenes(upSet, rownames(rankData)) : 1 genes missing: IL8
2: In checkGenes(upSet, rownames(rankData)) :
21 genes missing: ITGA9, PTK2, TNC, PDGFRB, EGFR, ITGA5, LAMB1, COL3A1, LAMB2, KDR, ITGB3, COL5A2, COL5A1, COL4A2, COL4A1, FN1, ITGAV, MET, COL6A1, COL6A3, COL6A2
3: In checkGenes(upSet, rownames(rankData)) :
8 genes missing: TNC, FN1, FBN1, COL4A5, COL4A2, COL4A1, LAMB1, LAMB2
4: In checkGenes(upSet, rownames(rankData)) :
22 genes missing: CDH11, PDGFRB, VCAN, BGN, AEBP1, COL3A1, LUM, THBS2, NID2, NID1, PCOLCE, SPP1, LAMA4, FBN1, COL5A2, COL5A1, COL4A2, COL4A1, MXRA8, COL6A1, COL6A3, COL6A2
5: In checkGenes(upSet, rownames(rankData)) :
35 genes missing: TNFSF13, VCAN, TFF3, AEBP1, OLFM4, COL3A1, LOX, TNFAIP2, HTRA1, LILRB2, PLA2G7, CHIT1, THBS2, NID2, NID1, CRISP3, CST3, CTSH, LAMA4, ENTPD1, FBN1, COL5A2, POSTN, COL5A1, COL4A2, GRN, ACHE, LRG1, CXCL1, SMPDL3A, ORM1, FGL2, ANGPTL2, TGFBI, COL6A2
ℹ GSVA version 2.3.4
! 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 2.3.4
! 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 2.3.4
! 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 -- Thu Oct 23 23:13:26 2025
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 1
1 Test Suite :
pathMED RUnit Tests - 3 test functions, 0 errors, 1 failure
FAILURE in test_getScores: Error in checkEquals(round(scoresExample[1, 1], 5), 43.8289) :
Mean relative difference: 0.1730913
Test files with failing tests
test_getScores.R
test_getScores
Error in BiocGenerics:::testPackage("pathMED") :
unit tests failed for package pathMED
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted
pathMED.Rcheck/pathMED-Ex.timings
| name | user | system | elapsed | |
| ann2term | 15.337 | 0.828 | 16.272 | |
| buildRefObject | 0.069 | 0.005 | 0.075 | |
| dissectDB | 2.666 | 0.119 | 2.796 | |
| getScores | 3.185 | 0.026 | 3.227 | |
| mScores_createReference | 30.491 | 1.061 | 31.901 | |
| mScores_filterPaths | 33.034 | 0.840 | 34.042 | |
| mScores_imputeFromReference | 31.284 | 0.894 | 32.401 | |
| methodsML | 0.060 | 0.016 | 0.094 | |
| predictExternal | 17.172 | 0.317 | 17.661 | |
| trainModel | 13.397 | 0.335 | 14.034 | |