Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-03-14 11:40 -0400 (Fri, 14 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4781
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4537
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4567
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4519
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4451
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 451/2309HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CPSM 0.99.7  (landing page)
Harpreet Kaur
Snapshot Date: 2025-03-13 13:40 -0400 (Thu, 13 Mar 2025)
git_url: https://git.bioconductor.org/packages/CPSM
git_branch: devel
git_last_commit: f9ecfc0
git_last_commit_date: 2025-03-11 20:58:50 -0400 (Tue, 11 Mar 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for CPSM on nebbiolo1

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.

raw results


Summary

Package: CPSM
Version: 0.99.7
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CPSM.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CPSM_0.99.7.tar.gz
StartedAt: 2025-03-13 21:03:49 -0400 (Thu, 13 Mar 2025)
EndedAt: 2025-03-13 21:08:54 -0400 (Thu, 13 Mar 2025)
EllapsedTime: 304.4 seconds
RetCode: 0
Status:   OK  
CheckDir: CPSM.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CPSM.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CPSM_0.99.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CPSM.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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 ‘CPSM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CPSM’ version ‘0.99.7’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

CPSM.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL CPSM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘CPSM’ ...
** this is package ‘CPSM’ version ‘0.99.7’
** 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)

Tests output

CPSM.Rcheck/tests/testthat.Rout

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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.

> library(testthat)
> library(CPSM)
> 
> test_check("CPSM")
Massage :data set has no non-missing observations

Massage :contrasts can be applied only to factors with 2 or more levels

Using IDs as id variables
The sampleTCGA-TQ-A8XE-01is not present in the Test dataset.

[ FAIL 0 | WARN 68 | SKIP 0 | PASS 18 ]

[ FAIL 0 | WARN 68 | SKIP 0 | PASS 18 ]
> 
> proc.time()
   user  system elapsed 
 32.868   0.984  33.844 

Example timings

CPSM.Rcheck/CPSM-Ex.timings

nameusersystemelapsed
Example_TCGA_LGG_FPKM_data0.0470.0040.051
Key_Clin_feature_list0.0010.0000.001
Key_Clin_features_with_PI_list0.0010.0000.001
Key_PI_list0.0000.0010.001
Key_univariate_features_list0.0010.0020.002
Key_univariate_features_with_Clin_list0.0010.0010.002
Lasso_PI_scores_f1.4240.0961.520
MTLR_pred_model_f0.2310.0120.243
New_data0.0240.0000.024
Nomogram_generate_f2.8770.0092.888
Test_Clin0.0010.0000.001
Test_Norm_data0.0150.0000.016
Test_PI_data0.0000.0000.001
Test_Uni_sig_data0.0020.0000.002
Train_Clin0.0010.0010.001
Train_Data_Nomogram_input0.0020.0000.003
Train_Norm_data0.0980.0010.098
Train_PI_data0.0010.0020.003
Train_Uni_sig_data0.0110.0000.013
Univariate_sig_features_f0.0010.0010.002
data_process_f0.7070.6091.318
feature_list_for_Nomogram0.0010.0000.001
mean_median_surv_barplot_f0.6240.0720.697
mean_median_survival_time_data0.0000.0010.002
survCurves_data0.0000.0000.001
surv_curve_plots_f0.4590.0190.479
test_FPKM0.0120.0000.011
tr_test_f0.0030.0000.003
train_FPKM0.0580.0010.058
train_test_normalization_f0.0230.0010.025