| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-17 11:44 -0400 (Thu, 17 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" | 4667 |
| 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: 2025-04-16 23:07:26 -0400 (Wed, 16 Apr 2025) |
| EndedAt: 2025-04-16 23:12:38 -0400 (Wed, 16 Apr 2025) |
| EllapsedTime: 312.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: pathMED.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################
* 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: 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 ‘1.0.0’
* 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_filterPaths 29.256 0.871 30.295
mScores_imputeFromReference 28.770 0.788 29.718
mScores_createReference 27.454 1.118 28.859
predictExternal 17.195 0.254 17.568
ann2term 14.777 0.843 15.689
trainModel 12.471 0.312 13.141
* 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-x86_64/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: 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
|
| | 0%
|
|== | 3%
|
|===== | 7%
|
|======= | 10%
|
|========= | 13%
|
|============ | 17%
|
|============== | 20%
|
|================ | 23%
|
|=================== | 27%
|
|===================== | 30%
|
|======================= | 33%
|
|========================== | 37%
|
|============================ | 40%
|
|============================== | 43%
|
|================================= | 47%
|
|=================================== | 50%
|
|===================================== | 53%
|
|======================================== | 57%
|
|========================================== | 60%
|
|============================================ | 63%
|
|=============================================== | 67%
|
|================================================= | 70%
|
|=================================================== | 73%
|
|====================================================== | 77%
|
|======================================================== | 80%
|
|========================================================== | 83%
|
|============================================================= | 87%
|
|=============================================================== | 90%
|
|================================================================= | 93%
|
|==================================================================== | 97%
|
|======================================================================| 100%
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: 19.01 0.949 20.14
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...
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
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...
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
Done
Calculating performance metrics...
Done
Training final model with all samples...
Done
RUNIT TEST PROTOCOL -- Wed Apr 16 23:12:29 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 | 14.777 | 0.843 | 15.689 | |
| buildRefObject | 0.079 | 0.007 | 0.086 | |
| dissectDB | 3.971 | 0.109 | 4.103 | |
| getScores | 3.617 | 0.032 | 3.670 | |
| mScores_createReference | 27.454 | 1.118 | 28.859 | |
| mScores_filterPaths | 29.256 | 0.871 | 30.295 | |
| mScores_imputeFromReference | 28.770 | 0.788 | 29.718 | |
| methodsML | 0.040 | 0.014 | 0.068 | |
| predictExternal | 17.195 | 0.254 | 17.568 | |
| trainModel | 12.471 | 0.312 | 13.141 | |