| Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-04-22 13:18 -0400 (Tue, 22 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 1538/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pathMED 1.0.0 (landing page) Jordi Martorell-Marugán
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino7 | 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 | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | 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: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2025-04-21 20:49:46 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 20:51:41 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 115.3 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_1.0.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/pathMED.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pathMED/DESCRIPTION’ ... OK
* this is package ‘pathMED’ version ‘1.0.0’
* 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 5.8Mb
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_imputeFromReference 11.642 1.323 13.017
mScores_filterPaths 11.320 1.440 12.784
mScores_createReference 10.553 1.145 11.766
predictExternal 6.055 0.096 6.172
ann2term 5.388 0.209 5.621
* 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-3.21-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-arm64/Resources/library’ * installing *source* package ‘pathMED’ ... ** this is package ‘pathMED’ version ‘1.0.0’ ** 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.fail
R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 2.2.0
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 2.2.0
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 2.2.0
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 2.2.0
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: 7.693 0.243 7.938
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 2.2.0
! 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 2.2.0
! 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 2.2.0
! 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 -- Mon Apr 21 20:51:38 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 | 5.388 | 0.209 | 5.621 | |
| buildRefObject | 0.050 | 0.003 | 0.053 | |
| dissectDB | 1.360 | 0.029 | 1.390 | |
| getScores | 1.393 | 0.006 | 1.400 | |
| mScores_createReference | 10.553 | 1.145 | 11.766 | |
| mScores_filterPaths | 11.320 | 1.440 | 12.784 | |
| mScores_imputeFromReference | 11.642 | 1.323 | 13.017 | |
| methodsML | 0.014 | 0.004 | 0.019 | |
| predictExternal | 6.055 | 0.096 | 6.172 | |
| trainModel | 4.313 | 0.059 | 4.373 | |