Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 2165/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TOP 1.6.0  (landing page)
Harry Robertson
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/TOP
git_branch: RELEASE_3_20
git_last_commit: 0420c26
git_last_commit_date: 2024-10-29 11:20:53 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for TOP on merida1

To the developers/maintainers of the TOP package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TOP.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: TOP
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TOP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TOP_1.6.0.tar.gz
StartedAt: 2024-12-20 10:52:07 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 10:59:17 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 430.2 seconds
RetCode: 0
Status:   OK  
CheckDir: TOP.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TOP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TOP_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/TOP.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TOP/DESCRIPTION’ ... OK
* this is package ‘TOP’ version ‘1.6.0’
* 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 ‘TOP’ 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 ... NOTE
Surv_TOP_CI: no visible binding for global variable ‘offset’
TOP_coefPlot: no visible binding for global variable ‘lambda.min’
TOP_coefPlot: no visible binding for global variable ‘Features’
TOP_lambdaPlot: no visible binding for global variable ‘variable’
TOP_lambdaPlot: no visible binding for global variable ‘value’
TOP_lambdaPlot: no visible binding for global variable ‘Feature’
TOP_model: no visible binding for global variable ‘value’
TOP_model: no visible binding for global variable ‘SampleGroup’
TOP_model: no visible binding for global variable ‘n’
TOP_model: no visible binding for global variable ‘freq’
TOP_model: no visible binding for global variable ‘sd’
TOP_survival: no visible binding for global variable ‘coef’
TOP_survival: no visible binding for global variable ‘value’
TOP_survival: no visible binding for global variable ‘freq’
TOP_survival: no visible binding for global variable ‘sd’
TOP_survival: no visible binding for global variable ‘.’
TOP_survival: no visible binding for global variable ‘SampleGroup’
TOP_survival: no visible binding for global variable ‘n’
TOP_survivalPrediction: no visible binding for global variable ‘offset’
coefNetworkPlot: no visible binding for global variable ‘Features’
coefNetworkPlot: no visible binding for global variable ‘lambda.min’
coefNetworkPlot: no visible binding for global variable ‘score’
colCoxTests_combine: no visible binding for global variable ‘coef’
extractAUC: no visible binding for global variable ‘variable’
extractAUC: no visible binding for global variable ‘value’
simplenetworkPlot: no visible binding for global variable ‘Features’
simplenetworkPlot: no visible binding for global variable ‘lambda.min’
simplenetworkPlot: no visible binding for global variable ‘coef_abs’
simplenetworkPlot: no visible binding for global variable ‘from’
simplenetworkPlot: no visible binding for global variable ‘to’
simplenetworkPlot: no visible binding for global variable ‘name’
Undefined global functions or variables:
  . Feature Features SampleGroup coef coef_abs freq from lambda.min n
  name offset score sd to value variable
Consider adding
  importFrom("stats", "coef", "offset", "sd")
to your NAMESPACE file.
* 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 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/TOP.Rcheck/00check.log’
for details.


Installation output

TOP.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TOP
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘TOP’ ...
** using staged installation
** R
** data
** 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 (TOP)

Tests output


Example timings

TOP.Rcheck/TOP-Ex.timings

nameusersystemelapsed
ROC_Plot1.0440.0351.096
Surv_Frank_CI3.6080.0333.896
TOP_coefPlot1.0360.0661.144
TOP_lambdaPlot1.3990.0491.456
TOP_model0.2710.0090.282
TOP_survival2.6310.0192.661
TOP_survivalPrediction2.7290.0372.966
coefNetworkPlot1.5350.0661.969
filterFeatures0.0860.0070.101
logit-expit0.0500.0040.090
pairwise_col_diff0.0020.0020.008
performance_TOP0.4040.0190.460
predict_TOP0.2820.0060.308
simplenetworkPlot1.0670.0231.183