Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-03-17 11:37 -0400 (Mon, 17 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 452/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CPSM 0.99.7  (landing page)
Harpreet Kaur
Snapshot Date: 2025-03-16 13:40 -0400 (Sun, 16 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)
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 palomino7

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: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CPSM.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings CPSM_0.99.7.tar.gz
StartedAt: 2025-03-17 00:04:21 -0400 (Mon, 17 Mar 2025)
EndedAt: 2025-03-17 00:10:07 -0400 (Mon, 17 Mar 2025)
EllapsedTime: 346.4 seconds
RetCode: 0
Status:   OK  
CheckDir: CPSM.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CPSM.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings CPSM_0.99.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/CPSM.Rcheck'
* using R Under development (unstable) (2025-03-01 r87860 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 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
* 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


Installation output

CPSM.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL CPSM
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
  39.87    1.25   41.07 

Example timings

CPSM.Rcheck/CPSM-Ex.timings

nameusersystemelapsed
Example_TCGA_LGG_FPKM_data0.030.000.03
Key_Clin_feature_list000
Key_Clin_features_with_PI_list0.020.000.02
Key_PI_list000
Key_univariate_features_list000
Key_univariate_features_with_Clin_list000
Lasso_PI_scores_f1.930.041.97
MTLR_pred_model_f0.360.050.41
New_data0.030.000.03
Nomogram_generate_f3.580.053.64
Test_Clin0.010.000.02
Test_Norm_data0.020.030.04
Test_PI_data0.010.000.02
Test_Uni_sig_data0.000.010.02
Train_Clin000
Train_Data_Nomogram_input0.000.020.01
Train_Norm_data0.140.010.16
Train_PI_data000
Train_Uni_sig_data0.020.000.02
Univariate_sig_features_f000
data_process_f1.360.361.72
feature_list_for_Nomogram000
mean_median_surv_barplot_f0.750.080.83
mean_median_survival_time_data000
survCurves_data000
surv_curve_plots_f0.690.010.70
test_FPKM0.020.000.02
tr_test_f000
train_FPKM0.040.020.06
train_test_normalization_f0.050.000.04