Harpreet Kaur
| Snapshot Date: 2025-09-24 13:45 -0400 (Wed, 24 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/CPSM |
| git_branch: devel |
| git_last_commit: 2fd0047 |
| git_last_commit_date: 2025-09-22 17:11:10 -0400 (Mon, 22 Sep 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-25 12:06 -0400 (Thu, 25 Sep 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" | 4831 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4618 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4562 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4560 |
| 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 458/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CPSM 1.1.4 (landing page) Harpreet Kaur
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the CPSM package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CPSM.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: CPSM |
| Version: 1.1.4 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CPSM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CPSM_1.1.4.tar.gz |
| StartedAt: 2025-09-24 18:52:04 -0400 (Wed, 24 Sep 2025) |
| EndedAt: 2025-09-24 18:54:23 -0400 (Wed, 24 Sep 2025) |
| EllapsedTime: 138.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CPSM.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CPSM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CPSM_1.1.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/CPSM.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CPSM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CPSM’ 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 ‘CPSM’ can be installed ... OK
* checking installed package size ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MTLR_pred_model_f 5.902 0.211 6.273
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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: OK
CPSM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CPSM ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘CPSM’ ... ** this is package ‘CPSM’ 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 (CPSM)
CPSM.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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.
> library(testthat)
> library(CPSM)
>
> test_check("CPSM")
ZPH test failed for AADACL2: subscript out of bounds
ZPH test failed for ABCF2.H2BE1: subscript out of bounds
ZPH test failed for ABHD14A.ACY1: subscript out of bounds
ZPH test failed for ABHD16B: subscript out of bounds
ZPH test failed for AC000120.3: subscript out of bounds
ZPH test failed for AC002094.3: subscript out of bounds
ZPH test failed for AC002310.4: subscript out of bounds
ZPH test failed for AC002985.1: subscript out of bounds
ZPH test failed for AC002996.1: subscript out of bounds
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ZPH test failed for AC003688.1: subscript out of bounds
ZPH test failed for AC004080.3: subscript out of bounds
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ZPH test failed for AC004832.3: subscript out of bounds
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ZPH test failed for AC007998.2: subscript out of bounds
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ZPH test failed for AC008403.1: subscript out of bounds
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ZPH test failed for AC011479.1: subscript out of bounds
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ZPH test failed for AC011530.1: subscript out of bounds
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ZPH test failed for AC012531.3: subscript out of bounds
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ZPH test failed for AC018362.3: subscript out of bounds
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ZPH test failed for AC084337.2: subscript out of bounds
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ZPH test failed for AC087721.2: subscript out of bounds
ZPH test failed for AC090227.2: subscript out of bounds
ZPH test failed for AC090527.2: subscript out of bounds
ZPH test failed for AC091551.1: subscript out of bounds
ZPH test failed for AC092017.2: subscript out of bounds
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ZPH test failed for AC092111.3: subscript out of bounds
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ZPH test failed for AC092329.3: subscript out of bounds
ZPH test failed for AC092442.1: subscript out of bounds
ZPH test failed for AC093246.1: subscript out of bounds
ZPH test failed for AC093423.3: subscript out of bounds
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ZPH test failed for AC093525.2: subscript out of bounds
ZPH test failed for AC093668.1: subscript out of bounds
ZPH test failed for AC093884.1: subscript out of bounds
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ZPH test failed for AC097104.1: subscript out of bounds
ZPH test failed for AC097634.4: subscript out of bounds
ZPH test failed for AC097637.1: subscript out of bounds
ZPH test failed for AC098582.1: subscript out of bounds
ZPH test failed for AC099569.1: subscript out of bounds
ZPH test failed for AC099811.2: subscript out of bounds
ZPH test failed for AC099850.2: subscript out of bounds
ZPH test failed for AC104109.3: subscript out of bounds
ZPH test failed for AC104389.6: subscript out of bounds
ZPH test failed for AC104581.2: subscript out of bounds
ZPH test failed for AC105001.2: subscript out of bounds
ZPH test failed for AC106873.8: subscript out of bounds
ZPH test failed for AC106886.5: subscript out of bounds
ZPH test failed for AC107959.5: subscript out of bounds
ZPH test failed for AC110275.1: subscript out of bounds
ZPH test failed for AC112504.2: subscript out of bounds
ZPH test failed for AC113189.12: subscript out of bounds
ZPH test failed for AC113348.1: subscript out of bounds
ZPH test failed for AC114402.2: subscript out of bounds
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ZPH test failed for AC116366.2: subscript out of bounds
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ZPH test failed for AC118470.1: subscript out of bounds
ZPH test failed for AC119676.1: subscript out of bounds
ZPH test failed for AC119733.1: subscript out of bounds
ZPH test failed for AC120057.2: subscript out of bounds
ZPH test failed for AC120114.4: subscript out of bounds
ZPH test failed for AC124312.1: subscript out of bounds
ZPH test failed for AC126283.2: subscript out of bounds
ZPH test failed for AC127029.3: subscript out of bounds
ZPH test failed for AC135050.2: subscript out of bounds
ZPH test failed for AC135068.4: subscript out of bounds
ZPH test failed for AC135178.3: subscript out of bounds
ZPH test failed for AC138696.1: subscript out of bounds
ZPH test failed for AC138811.2: subscript out of bounds
ZPH test failed for AC139530.2: subscript out of bounds
ZPH test failed for AC142391.1: subscript out of bounds
ZPH test failed for AC231656.1: subscript out of bounds
ZPH test failed for AC231657.3: subscript out of bounds
ZPH test failed for AC242628.1: subscript out of bounds
ZPH test failed for AC242842.3: subscript out of bounds
ZPH test failed for AC243547.3: subscript out of bounds
ZPH test failed for AC243967.1: subscript out of bounds
ZPH test failed for AC244517.10: subscript out of bounds
ZPH test failed for AC245033.1: subscript out of bounds
ZPH test failed for AC245748.1: subscript out of bounds
ZPH test failed for ACTB: subscript out of bounds
ZPH test failed for ACTBL2: subscript out of bounds
ZPH test failed for AD000671.1: subscript out of bounds
ZPH test failed for AD000671.2: subscript out of bounds
ZPH test failed for ADAM10: subscript out of bounds
ZPH test failed for ADAM21: subscript out of bounds
ZPH test failed for ADAM29: subscript out of bounds
ZPH test failed for ADGRF2: subscript out of bounds
ZPH test failed for ADIRF: subscript out of bounds
ZPH test failed for AF241726.1: subscript out of bounds
ZPH test failed for AL020996.2: subscript out of bounds
ZPH test failed for AL021546.1: subscript out of bounds
ZPH test failed for AL022312.1: subscript out of bounds
ZPH test failed for AL022318.4: subscript out of bounds
ZPH test failed for AL024498.2: subscript out of bounds
ZPH test failed for AL031178.1: subscript out of bounds
ZPH test failed for AL031178.2: subscript out of bounds
ZPH test failed for AL031681.2: subscript out of bounds
ZPH test failed for AL034430.1: subscript out of bounds
ZPH test failed for AL034430.2: subscript out of bounds
ZPH test failed for AL035078.4: subscript out of bounds
ZPH test failed for AL035425.2: subscript out of bounds
ZPH test failed for AL035460.1: subscript out of bounds
ZPH test failed for AL035461.3: subscript out of bounds
ZPH test failed for AL035699.1: subscript out of bounds
ZPH test failed for AL049569.3: subscript out of bounds
ZPH test failed for AL049650.1: subscript out of bounds
ZPH test failed for AL096711.2: subscript out of bounds
ZPH test failed for AL096814.1: subscript out of bounds
ZPH test failed for AL109811.3: subscript out of bounds
ZPH test failed for AL109827.1: subscript out of bounds
ZPH test failed for AL117348.2: subscript out of bounds
ZPH test failed for AL121845.2: subscript out of bounds
ZPH test failed for AL121900.1: subscript out of bounds
ZPH test failed for AL132671.2: subscript out of bounds
ZPH test failed for AL132780.3: subscript out of bounds
ZPH test failed for AL133352.1: subscript out of bounds
ZPH test failed for AL133410.3: subscript out of bounds
ZPH test failed for AL136295.1: subscript out of bounds
ZPH test failed for AL136295.3: subscript out of bounds
ZPH test failed for AL136295.4: subscript out of bounds
ZPH test failed for AL139300.1: subscript out of bounds
ZPH test failed for AL157392.5: subscript out of bounds
ZPH test failed for AL158151.3: subscript out of bounds
ZPH test failed for AL162231.3: subscript out of bounds
ZPH test failed for AL162377.3: subscript out of bounds
ZPH test failed for AL162417.1: subscript out of bounds
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ZPH test failed for AL353579.1: subscript out of bounds
ZPH test failed for AL355102.2: subscript out of bounds
ZPH test failed for AL355315.1: subscript out of bounds
ZPH test failed for AL355916.3: subscript out of bounds
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ZPH test failed for AL365273.2: subscript out of bounds
ZPH test failed for AL391987.1: subscript out of bounds
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ZPH test failed for AL451106.1: subscript out of bounds
ZPH test failed for AL451136.1: subscript out of bounds
ZPH test failed for AL512428.1: subscript out of bounds
ZPH test failed for AL512785.2: subscript out of bounds
ZPH test failed for AL513165.2: subscript out of bounds
ZPH test failed for AL583836.1: subscript out of bounds
ZPH test failed for AL589666.1: subscript out of bounds
ZPH test failed for AL590764.2: subscript out of bounds
ZPH test failed for AL627230.3: subscript out of bounds
ZPH test failed for AL645922.1: subscript out of bounds
ZPH test failed for AL662899.1: subscript out of bounds
ZPH test failed for AL662899.2: subscript out of bounds
ZPH test failed for AL672142.1: subscript out of bounds
ZPH test failed for AL691442.1: subscript out of bounds
ZPH test failed for AL713999.2: subscript out of bounds
ZPH test failed for AL807752.6: subscript out of bounds
ZPH test failed for AL807752.7: subscript out of bounds
ZPH test failed for AL929554.1: subscript out of bounds
ZPH test failed for ALKBH1: subscript out of bounds
ZPH test failed for ANKRD31: subscript out of bounds
ZPH test failed for ANKRD50: subscript out of bounds
ZPH test failed for AP000295.1: subscript out of bounds
ZPH test failed for AP000350.4: subscript out of bounds
ZPH test failed for AP000721.1: subscript out of bounds
ZPH test failed for AP001273.2: subscript out of bounds
ZPH test failed for AP001458.2: subscript out of bounds
ZPH test failed for AP001781.2: subscript out of bounds
ZPH test failed for AP002748.5: subscript out of bounds
ZPH test failed for AP002884.2: subscript out of bounds
ZPH test failed for AP003419.1: subscript out of bounds
ZPH test failed for APPL1: subscript out of bounds
ZPH test failed for ARID1B: subscript out of bounds
ZPH test failed for ARPIN.AP3S2: subscript out of bounds
ZPH test failed for AS3MT: subscript out of bounds
ZPH test failed for ATP2A2: subscript out of bounds
ZPH test failed for ATP6V1G2.DDX39B: subscript out of bounds
ZPH test failed for BAALC: subscript out of bounds
Massage :data set has no non-missing observations
Massage :contrasts can be applied only to factors with 2 or more levels
selected_sample 'TCGA-TQ-A7RQ-01' is present in the Test_results data.
selected_sample 'TCGA-TQ-A7RQ-01' is present in the Test_results data.
Using IDs as id variables
Training _with ntree = 10
Training _with ntree = 20
Training _with ntree = 50
Training _with ntree = 100
Training _with ntree = 250
Training _with ntree = 500
Training _with ntree = 750
Training _with ntree = 1000
The sampleTCGA-TQ-A8XE-01is not present in the Test dataset.
The sampleTCGA-TQ-A8XE-01is not present in the Test dataset.
[ FAIL 0 | WARN 75 | SKIP 0 | PASS 24 ]
[ FAIL 0 | WARN 75 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
21.314 1.125 22.807
CPSM.Rcheck/CPSM-Ex.timings
| name | user | system | elapsed | |
| Example_TCGA_LGG_FPKM_data | 0.012 | 0.001 | 0.013 | |
| Key_Clin_feature_list | 0.000 | 0.000 | 0.001 | |
| Key_Clin_features_with_PI_list | 0.000 | 0.001 | 0.001 | |
| Key_PI_list | 0.000 | 0.000 | 0.001 | |
| Key_univariate_features_list | 0.001 | 0.001 | 0.002 | |
| Key_univariate_features_with_Clin_list | 0.000 | 0.000 | 0.001 | |
| Lasso_PI_scores_f | 0.323 | 0.016 | 0.339 | |
| MTLR_pred_model_f | 5.902 | 0.211 | 6.273 | |
| New_data | 0.010 | 0.001 | 0.011 | |
| Nomogram_generate_f | 0.921 | 0.053 | 1.141 | |
| Test_Clin | 0.000 | 0.000 | 0.001 | |
| Test_Norm_data | 0.007 | 0.001 | 0.009 | |
| Test_PI_data | 0.001 | 0.000 | 0.001 | |
| Test_Uni_sig_data | 0.001 | 0.000 | 0.002 | |
| Train_Clin | 0.001 | 0.001 | 0.001 | |
| Train_Data_Nomogram_input | 0.001 | 0.001 | 0.005 | |
| Train_Norm_data | 0.042 | 0.002 | 0.058 | |
| Train_PI_data | 0.001 | 0.000 | 0.002 | |
| Train_Uni_sig_data | 0.006 | 0.002 | 0.008 | |
| Univariate_sig_features_f | 0.000 | 0.000 | 0.001 | |
| data_process_f | 0.360 | 0.377 | 0.793 | |
| feature_list_for_Nomogram | 0.001 | 0.000 | 0.000 | |
| km_overlay_plot_f | 0.003 | 0.001 | 0.004 | |
| mean_median_surv_barplot_f | 0.646 | 0.016 | 0.753 | |
| mean_median_survival_time_data | 0.000 | 0.001 | 0.001 | |
| predict_survival_risk_group_f | 0.588 | 0.336 | 0.970 | |
| survCurves_data | 0.001 | 0.001 | 0.001 | |
| surv_curve_plots_f | 0.247 | 0.079 | 0.330 | |
| test_FPKM | 0.005 | 0.001 | 0.008 | |
| tr_test_f | 0.001 | 0.001 | 0.002 | |
| train_FPKM | 0.028 | 0.002 | 0.035 | |
| train_test_normalization_f | 0.009 | 0.004 | 0.016 | |